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Nogueira VG, Reis EA, Godman B, Martin AP, Godói IPD. Acceptability and willingness to pay for a hypothetical HIV vaccine in Brazil and the implications: a cross-sectional study. Expert Rev Pharmacoecon Outcomes Res 2024:1-10. [PMID: 39049463 DOI: 10.1080/14737167.2024.2384543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
INTRODUCTION The Human Immunodeficiency Virus (HIV) is one of the greatest public health challenges still facing communities worldwide, and until this moment, no vaccine is available for its prevention. In Brazil, the Rio de Janeiro State has stood out regarding the prevalence of this disease. As a result, an important state to consider the Willingness to Pay (WTP) for a hypothetical HIV vaccine to help with future pricing. METHODS A cross-sectional study was conducted to assess the acceptability and WTP of individuals from Rio de Janeiro State for a hypothetical HIV vaccine with a 70% efficacy. RESULTS 600 individuals were interviewed and the acceptability for this hypothetical vaccine was 77.2%. In addition, 452 participants were eligible for the WTP analysis and would accept a WTP US$79.37 (400 BRL) for this vaccine, a higher value than that found in another study (200 BRL) conducted in the Northern region of Brazil under the same methodological conditions. CONCLUSION Economic studies such as WTP can contribute to discussions regarding the prices and specifications for future vaccines, particularly for a HIV vaccine in countries such as Brazil with over 5,000 municipalities spread across regions with diverse characteristics and challenges in terms of socioeconomic, epidemiological and cultural differences.
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Affiliation(s)
| | - Edna Afonso Reis
- Department of Statistics, Exact Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Brian Godman
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- School of Pharmacy, Department of Public Health and Pharmacy Management, Sefako Health Sciences University, Pretoria, South Africa
| | - Antony Paul Martin
- Faculty of Health & Life Sciences, UK
- QC Medica, York, North Yorkshire, UK
| | - Isabella Piassi Dias Godói
- Institute of Pharmaceutical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Health Technology Assessment Center - Management, Economics, Health Education and Pharmaceutical Services (GEESFAR/NATS/UFRJ) of the Federal University of Rio de Janeiro; Brazil
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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Mukhatayeva A, Mustafa A, Dzissyuk N, Issanov A, Mukhatayev Z, Bayserkin B, Vermund SH, Ali S. Antiretroviral therapy resistance mutations among HIV infected people in Kazakhstan. Sci Rep 2022; 12:17195. [PMID: 36229577 PMCID: PMC9562405 DOI: 10.1038/s41598-022-22163-7] [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: 02/11/2022] [Accepted: 10/10/2022] [Indexed: 01/05/2023] Open
Abstract
In Kazakhstan, the number of people living with HIV (PLHIV) has increased steadily by 39% since 2010. Development of antiretroviral therapy (ART) resistance mutations (ARTRM) is a major hurdle in achieving effective treatment and prevention against HIV. Using HIV pol sequences from 602 PLHIV from Kazakhstan, we analyzed ARTRMs for their association with factors that may promote development of ARTRMs. 56% PLHIV were infected with HIV subtype A6 and 42% with CRF02_AG. The ARTRM Q174K was associated with increased viral load and decreased CD4+ cell count, while infection with CRF02_AG was associated with a lower likelihood of Q174K. Interestingly, CRF02_AG was positively associated with the ARTRM L10V that, in turn, was observed frequently with darunavir administration. Infection with CRF02_AG was positively associated with the ARTRM S162A that, in turn, was frequently observed with the administration of nevirapine, also associated with lower CD4 counts. Zidovudine or Nevirapine receipt was associated with the development of the ARTRM E138A, that, in turn, was associated with lower CD4 counts. Determination of a patient's HIV variant can help guide ART choice in Kazakhstan. For example, PLHIV infected with CRF02_AG will benefit less from darunavir and nevirapine, and emtricitabine should replace zidovudine.
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Affiliation(s)
- Ainur Mukhatayeva
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Aidana Mustafa
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Natalya Dzissyuk
- Kazakh Scientific Center of Dermatology and Infectious Diseases, Almaty, Kazakhstan
| | - Alpamys Issanov
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Zhussipbek Mukhatayev
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Bauyrzhan Bayserkin
- Kazakh Scientific Center of Dermatology and Infectious Diseases, Almaty, Kazakhstan
| | | | - Syed Ali
- Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Astana, Kazakhstan.
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Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting. Viruses 2022; 14:v14102208. [PMID: 36298763 PMCID: PMC9608942 DOI: 10.3390/v14102208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/15/2022] Open
Abstract
The HIV genotypic resistance test (GRT) is a standard of care for the clinical management of HIV/AIDS patients. In recent decades, population or Sanger sequencing has been the foundation for drug resistance monitoring in clinical settings. However, the advent of high-throughput or next-generation sequencing has caused a paradigm shift towards the detection and characterization of low-abundance covert mutations that would otherwise be missed by population sequencing. This is clinically significant, as these mutations can potentially compromise the efficacy of antiretroviral therapy, causing poor virologic suppression. Therefore, it is important to develop a more sensitive method so as to reliably detect clinically actionable drug-resistant mutations (DRMs). Here, we evaluated the diagnostic performance of a laboratory-developed, high-throughput, sequencing-based GRT using 103 archived clinical samples that were previously tested for drug resistance using population sequencing. As expected, high-throughput sequencing found all the DRMs that were detectable by population sequencing. Significantly, 78 additional DRMs were identified only by high-throughput sequencing, which is statistically significant based on McNemar's test. Overall, our results complement previous studies, supporting the notion that the two methods are well correlated, and the high-throughput sequencing method appears to be an excellent alternative for drug resistance testing in a clinical setting.
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Maruapula D, Seatla KK, Morerinyane O, Molebatsi K, Giandhari J, de Oliveira T, Musonda RM, Leteane M, Mpoloka SW, Rowley CF, Moyo S, Gaseitsiwe S. Low-frequency HIV-1 drug resistance mutations in antiretroviral naïve individuals in Botswana. Medicine (Baltimore) 2022; 101:e29577. [PMID: 35838991 PMCID: PMC11132386 DOI: 10.1097/md.0000000000029577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Individuals living with human immunodeficiency virus (HIV) who experience virological failure (VF) after combination antiretroviral therapy (cART) initiation may have had low-frequency drug resistance mutations (DRMs) at cART initiation. There are no data on low-frequency DRMs among cART-naïve HIV-positive individuals in Botswana. METHODS We evaluated the prevalence of low-frequency DRMs among cART-naïve individuals previously sequenced using Sanger sequencing. The generated pol amplicons were sequenced by next-generation sequencing. RESULTS We observed low-frequency DRMs (detected at <20% in 33/103 (32%) of the successfully sequenced individuals, of whom four also had mutations detected at >20%. K65R was the most common low-frequency DRM detected in 8 individuals. Eighty-two of the 103 individuals had follow-up viral load data while on cART. Twenty-seven of the 82 individuals harbored low-frequency DRMs. Only 12 of 82 individuals experienced VF. The following low-frequency DRMs were observed in four individuals experiencing VF: K65R, K103N, V108I, and Y188C. No statistically significant difference was observed in the prevalence of low-frequency DRMs between individuals experiencing VF (4/12) and those not experiencing VF (23/70) (P = .97). However, individuals with non-nucleoside reverse transcriptase inhibitors-associated low-frequency DRMs were 2.68 times more likely to experience VF (odds ratio, 2.68; 95% confidential interval, 0.4-13.9) compared with those without (P = .22). CONCLUSION Next-generation sequencing was able to detect low-frequency DRMs in this cohort in Botswana, but these DRMs did not contribute significantly to VF.
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Affiliation(s)
- Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Kaelo K. Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professions, University of Botswana, Gaborone, Botswana
| | | | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Statistics, University of Botswana, Gaborone, Botswana
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rosemary M. Musonda
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Melvin Leteane
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Christopher F. Rowley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - 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
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Joussef-Piña S, Nankya I, Nalukwago S, Baseke J, Rwambuya S, Winner D, Kyeyune F, Chervenak K, Thiel B, Asaad R, Dobrowolski C, Luttge B, Lawley B, Kityo CM, Boom WH, Karn J, Quiñones-Mateu ME. Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda. Retrovirology 2022; 19:1. [PMID: 35033105 PMCID: PMC8760765 DOI: 10.1186/s12977-022-00587-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our understanding of the peripheral human immunodeficiency virus type 1 (HIV-1) reservoir is strongly biased towards subtype B HIV-1 strains, with only limited information available from patients infected with non-B HIV-1 subtypes, which are the predominant viruses seen in low- and middle-income countries (LMIC) in Africa and Asia. RESULTS In this study, blood samples were obtained from well-suppressed ART-experienced HIV-1 patients monitored in Uganda (n = 62) or the U.S. (n = 50), with plasma HIV-1 loads < 50 copies/ml and CD4+ T-cell counts > 300 cells/ml. The peripheral HIV-1 reservoir, i.e., cell-associated HIV-1 RNA and proviral DNA, was characterized using our novel deep sequencing-based EDITS assay. Ugandan patients were slightly younger (median age 43 vs 49 years) and had slightly lower CD4+ counts (508 vs 772 cells/ml) than U.S. individuals. All Ugandan patients were infected with non-B HIV-1 subtypes (31% A1, 64% D, or 5% C), while all U.S. individuals were infected with subtype B viruses. Unexpectedly, we observed a significantly larger peripheral inducible HIV-1 reservoir in U.S. patients compared to Ugandan individuals (48 vs. 11 cell equivalents/million cells, p < 0.0001). This divergence in reservoir size was verified measuring proviral DNA (206 vs. 88 cell equivalents/million cells, p < 0.0001). However, the peripheral HIV-1 reservoir was more diverse in Ugandan than in U.S. individuals (8.6 vs. 4.7 p-distance, p < 0.0001). CONCLUSIONS The smaller, but more diverse, peripheral HIV-1 reservoir in Ugandan patients might be associated with viral (e.g., non-B subtype with higher cytopathicity) and/or host (e.g., higher incidence of co-infections or co-morbidities leading to less clonal expansion) factors. This highlights the need to understand reservoir dynamics in diverse populations as part of ongoing efforts to find a functional cure for HIV-1 infection in LMICs.
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Affiliation(s)
- Samira Joussef-Piña
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sophie Nalukwago
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Joy Baseke
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sandra Rwambuya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Dane Winner
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Keith Chervenak
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bonnie Thiel
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Asaad
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Curtis Dobrowolski
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin Luttge
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand
| | - Cissy M Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - W Henry Boom
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand.
- Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand.
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Sarinoglu RC, Sili U, Hasdemir U, Aksu B, Soyletir G, Korten V. Diversity of HIV-1 subtypes and transmitted drug-resistance mutations among minority HIV-1 variants in a Turkish cohort. Curr HIV Res 2021; 20:54-62. [PMID: 34802406 DOI: 10.2174/1570162x19666211119111740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/02/2021] [Accepted: 08/13/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The World Health Organization (WHO) recommends the surveillance of transmitted drug resistance mutations (TDRMs) to ensure the effectiveness and sustainability of HIV treatment programs. OBJECTIVE Our aim was to determine the TDRMs and evaluate the distribution of HIV-1 subtypes using and compared next-generation sequencing (NGS) and Sanger-based sequencing (SBS) in a cohort of 44 antiretroviral treatment-naïve patients. METHODS All samples that were referred to the microbiology laboratory for HIV drug resistance analysis between December 2016 and February 2018 were included in the study. After exclusions, 44 treatment-naive adult patients with a viral load of >1000 copies/mL were analyzed. DNA sequencing for reverse transcriptase and protease regions was performed using both DeepChek ABL single round kit and Sanger-based ViroSeq HIV-1 Genotyping System. The mutations and HIV-1 subtypes were analyzed using the Stanford HIVdb version 8.6.1 Genotypic Resistance software, and TDRMs were assessed using the WHO surveillance drug-resistance mutation database. HIV-1 subtypes were confirmed by constructing a maximum-likelihood phylogenetic tree using Los Alamos IQ-Tree software. RESULTS NGS identified nucleos(t)ide reverse transcriptase inhibitor (NRTI)-TDRMs in 9.1% of the patients, non-nucleos(t)ide reverse transcriptase inhibitor (NNRTI)-TDRMs in 6.8% of the patients, and protease inhibitor (PI)-TDRMs in 18.2% of the patients at a detection threshold of ≥1%. Using SBS, 2.3% and 6.8% of the patients were found to have NRTI- and NNRTI-TDRMs, respectively, but no major PI mutations were detected. M41L, L74I, K65R, M184V, and M184I related to NRTI, K103N to NNRTI, and N83D, M46I, I84V, V82A, L24I, L90M, I54V to the PI sites were identified using NGS. Most mutations were found in low-abundance (frequency range: 1.0% - 4.7%) HIV-1 variants, except M41L and K103N. The subtypes of the isolates were found as follows; 61.4% subtype B, 18.2% subtype B/CRF02_AG recombinant, 13.6% subtype A, 4.5% CRF43_02G, and 2.3% CRF02_AG. All TDRMs, except K65R, were detected in HIV-1 subtype B isolates. CONCLUSION The high diversity of protease site TDRMs in the minority HIV-1 variants and prevalence of CRFs were remarkable in this study. All minority HIV-1 variants were missed by conventional sequencing. TDRM prevalence among minority variants appears to be decreasing over time at our center.
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Affiliation(s)
- Rabia Can Sarinoglu
- Marmara University School of Medicine, Pendik Training and Research Hospital, Department of Medical Microbiology, Istanbul. Turkey
| | - Uluhan Sili
- Marmara University School of Medicine, Pendik Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul. Turkey
| | - Ufuk Hasdemir
- Marmara University School of Medicine, Pendik Training and Research Hospital, Department of Medical Microbiology, Istanbul. Turkey
| | - Burak Aksu
- Marmara University School of Medicine, Pendik Training and Research Hospital, Department of Medical Microbiology, Istanbul. Turkey
| | - Guner Soyletir
- Marmara University School of Medicine, Pendik Training and Research Hospital, Department of Medical Microbiology, Istanbul. Turkey
| | - Volkan Korten
- Marmara University School of Medicine, Pendik Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul. Turkey
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Montejano R, Dominguez-Dominguez L, de Miguel R, Rial-Crestelo D, Esteban-Cantos A, Aranguren-Rivas P, García-Álvarez M, Alejos B, Bisbal O, Santacreu-Guerrero M, Hernando A, Bermejo-Plaza L, Cadiñanos J, Mayoral M, Castro JM, Moreno V, Martin-Carbonero L, Rodés B, Delgado R, Rubio R, Pulido F, Arribas JR. Detection of archived lamivudine-associated resistance mutations in virologically suppressed, lamivudine-experienced HIV-infected adults by different genotyping techniques (GEN-PRO study). J Antimicrob Chemother 2021; 76:3263-3271. [PMID: 34459889 DOI: 10.1093/jac/dkab323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/04/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Previously selected lamivudine resistance-associated mutations (RAMs) may remain archived within the proviral HIV-DNA. OBJECTIVES To evaluate the ability of proviral DNA genotyping to detect lamivudine RAMs in HIV-1 virologically suppressed participants; the correlation between Sanger and next generation sequencing (NGS); and predictive factors for detection of lamivudine RAMs in proviral DNA. METHODS Cross-sectional study of participants on stable antiretroviral therapy and suppressed for ≥1 year. Analysis of proviral DNA was performed by Sanger sequencing in whole blood and by NGS in PBMCs. RESULTS We analysed samples from 102 subjects (52 with and 50 without lamivudine RAMs in historical plasma RNA-genotypes). Among participants with previous lamivudine resistance, Sanger sequencing detected RAMs in 26.9%. Detection rates significantly increased using NGS: 47.9%, 64.6%, 75% and 87.5% with the 20%, 10%, 5% and 1% thresholds, respectively. As for participants without historical lamivudine resistance, Sanger detected the RAMs in 1/49 (2%), and NGS (5% threshold) in 8/45 (17.8%). Multivariate models fitted to the whole population revealed that having a history of lamivudine resistance was a risk factor for detection of lamivudine RAMs by NGS. Among participants with historical lamivudine resistance, multivariate analysis showed that a longer time since HIV diagnosis was associated with persistence of archived mutations by NGS at thresholds of >10% [OR 1.10 (95% CI: 1.00-1.24)] and >5% [OR 1.16 (95% CI: 1.02-1.32)]. CONCLUSIONS Proviral DNA Sanger sequencing does not detect the majority of historical lamivudine RAMs. NGS increases the sensitivity of detection at lower thresholds, although the relevance of these minority populations with lamivudine RAMs needs further evaluation.
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Affiliation(s)
- Rocio Montejano
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Lourdes Dominguez-Dominguez
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Rosa de Miguel
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - David Rial-Crestelo
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Andrés Esteban-Cantos
- Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Paula Aranguren-Rivas
- Microbiology Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Mónica García-Álvarez
- Microbiology Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Belén Alejos
- Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - Otilia Bisbal
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Mireia Santacreu-Guerrero
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Asunción Hernando
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Laura Bermejo-Plaza
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Julen Cadiñanos
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Mario Mayoral
- HIV Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261 28046, Madrid, Spain
| | - Juan Miguel Castro
- HIV Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261 28046, Madrid, Spain
| | - Victoria Moreno
- HIV Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261 28046, Madrid, Spain
| | - Luz Martin-Carbonero
- HIV Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261 28046, Madrid, Spain
| | - Berta Rodés
- Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Rafael Delgado
- Microbiology Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Rafael Rubio
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - Federico Pulido
- HIV Unit, Internal Medicine Department, Hospital Universitario 12 de Octubre-Imas12, Av. de Córdoba, s/n, 28041 Madrid, Spain
| | - José Ramón Arribas
- Infectious Diseases Unit, Internal Medicine Department, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046 Madrid, Spain
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Brice J, Sylla M, Desire N, Sayon S, Telly F, Bocar-Fofana D, Murphy R, Peytavin G, Diallo S, Nastouli E, Calvez V, Marcelin AG, Maiga AI, Lambert-Niclot S. Characterization of drug resistance and the defective HIV reservoir in virally suppressed vertically infected children in Mali. J Antimicrob Chemother 2021; 75:1272-1279. [PMID: 32073629 DOI: 10.1093/jac/dkaa002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/20/2019] [Accepted: 12/26/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In the perspective of ART-free HIV remission, vertically infected children treated with suppressive ART from early infancy represent an optimal population model to better understand the genetic complexity of the reservoir. OBJECTIVES To evaluate the proportion of defective viral population and the genotypic resistance patterns in cell-associated HIV DNA. METHODS In a cohort including 93 ART-treated vertically HIV-infected (VHIV) children in Mali with plasma HIV-1 RNA ≤50 copies/mL for at least 6 months, we studied total HIV DNA, percentage of defective genomes and resistance by reverse transcriptase and protease bulk sequencing from whole blood in dried blood spots. RESULTS Children had a median age of 9.9 years at the time of inclusion (IQR = 7.6-13.4) and 3.3 years (IQR = 2-7) at ART initiation; median ART duration was 5.5 years (IQR = 3.7-7.3). The median level of total HIV DNA was 470 copies/106 cells with one patient presenting undetectable HIV DNA (<66 copies/106 cells). We observed the presence of at least one stop codon in viruses from 34 patients (37%). The presence of stop codons was not correlated with the level of HIV DNA or duration of ART. We showed a high prevalence of HIV-1 resistance in DNA with 26% of children harbouring virus resistant to at least one NRTI and 40% to at least one NNRTI. CONCLUSIONS While these VHIV children were successfully treated for a long time, they showed high prevalence of resistance in HIV DNA and a moderate defective HIV reservoir.
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Affiliation(s)
- Josephine Brice
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Department of Virology, F-75013 Paris, France
| | - Mariam Sylla
- Department of Pediatrics, University Hospital Gabriel Toure, Bamako, Mali
| | - Nathalie Desire
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Department of Virology, F-75013 Paris, France
| | - Sophie Sayon
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Department of Virology, F-75013 Paris, France
| | - Fatoumata Telly
- Unité d'Epidémiologie Moléculaire de la Résistance du VIH aux ARV, SEREFO, FMOS, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Djeneba Bocar-Fofana
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Saint Antoine Hospital, Department of Virology, F-75012 Paris, France
| | - Robert Murphy
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, 645 N. Michigan Avenue, Suite 900, Chicago, IL 60611, USA
| | - Gilles Peytavin
- AP-HP, Department of Pharmacology, Bichat-Claude Bernard Hospital, F-75018 Paris, France
| | - Souleymane Diallo
- Unité d'Epidémiologie Moléculaire de la Résistance du VIH aux ARV, SEREFO, FMOS, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Eleni Nastouli
- Department of Population, Policy and Practice, University College London GOS Institute of Child Health, London, UK
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Department of Virology, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Pitié Salpêtrière Hospital, Department of Virology, F-75013 Paris, France
| | - Almoustapha Issiaka Maiga
- Unité d'Epidémiologie Moléculaire de la Résistance du VIH aux ARV, SEREFO, FMOS, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.,Clinical and Microbiology Laboratory, University Hospital Gabriel Toure, Bamako, Mali
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Saint Antoine Hospital, Department of Virology, F-75012 Paris, France
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10
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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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11
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Chen CW, Saubi N, Joseph-Munné J. Design Concepts of Virus-Like Particle-Based HIV-1 Vaccines. Front Immunol 2020; 11:573157. [PMID: 33117367 PMCID: PMC7561392 DOI: 10.3389/fimmu.2020.573157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
Prophylactic vaccines remain the best approach for controlling the human immunodeficiency virus-1 (HIV-1) transmission. Despite the limited efficacy of the RV144 trial in Thailand, there is still no vaccine candidate that has been proven successful. Consequently, great efforts have been made to improve HIV-1 antigens design and discover delivery platforms for optimal immune elicitation. Owing to immunogenic, structural, and functional diversity, virus-like particles (VLPs) could act as efficient vaccine carriers to display HIV-1 immunogens and provide a variety of HIV-1 vaccine development strategies as well as prime-boost regimes. Here, we describe VLP-based HIV-1 vaccine candidates that have been enrolled in HIV-1 clinical trials and summarize current advances and challenges according to preclinical results obtained from five distinct strategies. This mini-review provides multiple perspectives to help in developing new generations of VLP-based HIV-1 vaccine candidates with better capacity to elicit specific anti-HIV immune responses.
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Affiliation(s)
- Chun-Wei Chen
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Narcís Saubi
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,EAVI2020 European AIDS Vaccine Initiative H2020 Research Programme, London, United Kingdom
| | - Joan Joseph-Munné
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,EAVI2020 European AIDS Vaccine Initiative H2020 Research Programme, London, United Kingdom.,Microbiology Department, Hospital Universitari de la Vall d'Hebron, Barcelona, Spain
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12
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Tenth Scientific Biennial Meeting of the Australasian Virology Society-AVS10 2019. Viruses 2020; 12:v12060621. [PMID: 32517260 PMCID: PMC7354434 DOI: 10.3390/v12060621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 11/17/2022] Open
Abstract
The Australasian Virology Society (AVS) aims to promote, support and advocate for the discipline of virology in the Australasian region. The society was incorporated in 2011 after 10 years operating as the Australian Virology Group (AVG) founded in 2001, coinciding with the inaugural biennial scientific meeting. AVS conferences aim to provide a forum for the dissemination of all aspects of virology, foster collaboration, and encourage participation by students and post-doctoral researchers. The tenth Australasian Virology Society (AVS10) scientific meeting was held on 2–5 December 2019 in Queenstown, New Zealand. This report highlights the latest research presented at the meeting, which included cutting-edge virology presented by our international plenary speakers Ana Fernandez-Sesma and Benjamin tenOever, and keynote Richard Kuhn. AVS10 honoured female pioneers in Australian virology, Lorena Brown and Barbara Coulson. We report outcomes from the AVS10 career development session on “Successfully transitioning from post-doc to lab head”, winners of best presentation awards, and the AVS gender equity policy, initiated in 2013. Plans for the 2021 meeting are underway which will celebrate the 20th anniversary of AVS where it all began, in Fraser Island, Queensland, Australia.
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13
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Kagan RM, Dunn KJ, Snell GP, Nettles RE, Kaufman HW. Trends in HIV-1 Drug Resistance Mutations from a U.S. Reference Laboratory from 2006 to 2017. AIDS Res Hum Retroviruses 2019; 35:698-709. [PMID: 31169022 DOI: 10.1089/aid.2019.0063] [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: 12/24/2022] Open
Abstract
Trends in resistance to antiretroviral drugs for HIV-1 may inform clinical support and drug development. We evaluated drug resistance mutation (DRM) trends for nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI), protease inhibitor (PI), and integrase strand transfer inhibitor (INSTI) in a large U.S. reference laboratory database. DRMs with a Stanford HIV Drug Resistance Database mutation score ≥10 from deidentified subtype B NRTI/NNRTI/PI specimens (2006-2017; >10,000/year) and INSTI specimens (2010-2017; >1,000/year) were evaluated. Sequences with NRTI, NNRTI, or PI single- or multiclass DRMs declined from 48.9% to 39.3%. High-level dual- and triple-class resistance declined from 43.3% (2006) to 17.1% (2017), while sequences with only single-class DRMs increased from 40.0% to 52.9%. The prevalence of DRMs associated with earlier treatment regimens declined, while prevalence of some DRMs associated with newer regimens increased. M184V/I decreased from 48.3% to 29.4%. K103N/S/T declined from 42.5% in 2012 to 36.4% in 2017. Rilpivirine and etravirine DRMs E138A/Q/R and E138K increased from 4.9% and 0.4% to 9.7% and 1.7%, respectively. Sequences with ≥1 darunavir DRM declined from 18.1% to 4.8% by 2017. INSTI DRM Q148H/K/R declined from 39.3% (2010) to 13.8% (2017). Prevalence of elvitegravir-associated DRMs T66A/I/K, E92Q, S147G, and the dolutegravir-associated DRM R263K increased. For a subset of patients with serial testing, 50% (2,646/5,290) of those who initially had no reportable DRM subsequently developed ≥1 DRM for NRTI/NNRTI/PI and 49.7% (159/320) for INSTI. These trends may inform the need for baseline genotypic resistance testing. The detection of treatment-emergent DRMs in serially tested patients confirms the value of genotypic testing following virologic failure.
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Affiliation(s)
- Ron M. Kagan
- Quest Diagnostics Infectious Disease, San Juan Capistrano, California
| | - Keith J. Dunn
- Janssen Scientific Affairs, LLC, Titusville, New Jersey
| | - Gregg P. Snell
- Quest Diagnostics Medical Informatics, Needham, Massachusetts
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14
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Sili U, Aksu B, Tekin A, Hasdemir U, Soyletir G, Korten V. Assessment of Transmitted HIV-1 Drug Resistance Mutations Using Ultra- Deep Pyrosequencing in a Turkish Cohort. Curr HIV Res 2019; 16:216-221. [PMID: 30198436 DOI: 10.2174/1570162x16666180910130112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/11/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Antiretroviral treatment (ART) reduces morbidity and mortality caused by human immunodeficiency virus (HIV) infection; however, the emergence of drug-resistant strains poses an important obstacle to treatment success. Using conventional sequencing methods to determine antiretroviral resistance, mutations present in ≥20% of quasispecies can be identified, but drug-resistant minority variants can lead to virologic failure. OBJECTIVE We aimed to assess transmitted drug resistance mutations (TDRMs) within minority variants using ultra-deep pyrosequencing (UDPS). METHOD Treatment-naive adult patients were included in this observational study. Surveillance TDRMs were classified as ≥20% or at minority variant level (≥2% - <20%). Genotypic sensitivity score calculated by using all pre-treatment drug resistance mutations (PDRMs) was also evaluated. RESULTS Thirty-six patients were analyzed. Any TDRM at ≥20% level was detected in 8.3% of the patients (n=3). This prevalence increased to 30.6% (n=11) with the inclusion of minority variants. All non-nucleoside reverse transcriptase inhibitor and protease inhibitor-related TDRMs were within minority variants. The genotypic sensitivity score of rilpivirine-based regimens was considerably diminished when minority variants were included in the PDRM analysis. CONCLUSION UDPS was used for the first time to assess TDRM in a Turkish HIV cohort and uncovered several mutations hidden within minority variants. UDPS may be preferred to detect PDRMs for avoiding virologic failure with rilpivirine-based ART regimens.
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Affiliation(s)
- Uluhan Sili
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Burak Aksu
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Aysun Tekin
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Ufuk Hasdemir
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Guner Soyletir
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Volkan Korten
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
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15
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Liu CC, Ji H. PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing. Curr HIV Res 2019; 16:98-105. [PMID: 29943704 DOI: 10.2174/1570162x16666180626152252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/05/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream. Here we reviewed existing PCR protocols leading to HIV-1 full genome sequencing. In addition to the discussion on basic considerations on relevant PCR design, the advantages as well as the pitfalls of the published protocols were reviewed.
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Affiliation(s)
- Chao Chun Liu
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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16
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Li J, Xu Y, Liu J, Yang B, Yang C, Zhang M, Dong X. Drug resistance evolution in patients with human immunodeficiency virus-1 under long-term antiretroviral treatment-failure in Yunnan Province, China. Virol J 2019; 16:5. [PMID: 30621727 PMCID: PMC6325746 DOI: 10.1186/s12985-018-1112-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/26/2018] [Indexed: 12/31/2022] Open
Abstract
Background Understanding the prevalence and evolution of HIV-1 drug resistance (DR) and associated mutation patterns is critical to implementing free antiretroviral therapy in Yunnan, the first antiretroviral treatment location in China. Here We provide a basis for understanding the occurrence and development of HIV-1 resistance in Yunnan and a theoretical foundational for strategy to delay HIV-1 drug resistance and achieve successful individualized treatment. Methods Plasma samples from different cities/prefectures were collected at Yunnan Provincial Hospital of Infectious Disease from January 2010 to September 2016, and those from drug-resistant individuals were genotyped using in-house assays, 88 patients were selected for the study who had been on treatment for ≥6 months (and for whom drug resistance was then measured), and each patient had at least 3 genotype resistance tests and who were enrolled to analyze mutation and evolution of HIV resistance. Results 264 Pol sequences of 88 patients were obtained. Drug resistance levels to eight drugs increased to varying degrees with prolonged treatment. Resistance to efavirenz (EFV) and etravirine (ETR) showed the highest change, comparisons of resistant changes to second and first and to third and second agents showed altered level of drug resistance were 25 and 20 cases, 28 and 18 cases, respectively. The smallest change was Lopinavir/Ritonavir (LPV/r) present 2 and 3 cases; Resistance to lamivudine (3TC) and lopinavir/ritonavir (LPV/r) was high among patients detected thrice, whereas other drugs were distributed in all resistance levels. M184 V/I (26.14%), T69S (11.36%), and T215Y/I (10.23%) mutations were the most common in nucleoside reverse transcriptase inhibitors (NRTIs), and K103 N/R/S (21.59%), V179D/E (20.45%) in Non-NRTIs (NNRTIs). Furthermore, L10 V/F/I (6.82%), A71V (4.55%), and I54V (4.55%) mutations were common in protease inhibitors (PIs). Conclusions We found dynamic genotypic changes in HIV-1 drug-resistance in Yunnan, with prolonged treatment, and drug resistance was inevitable. However, resistance to different drugs occurred at varying times, and mutation site emergence was the main cause. These findings enhance our understanding of evolution and regulation, and are valuable for developing HIV-1 DR prevention strategies in Yunnan.
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Affiliation(s)
- Jianjian Li
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming Medical University affiliated Infectious diseases hospital, 28 Shian Road, Taiping District, Kunming, 650301, China
| | - Yawen Xu
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming Medical University affiliated Infectious diseases hospital, 28 Shian Road, Taiping District, Kunming, 650301, China
| | - Jiafa Liu
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming Medical University affiliated Infectious diseases hospital, 28 Shian Road, Taiping District, Kunming, 650301, China
| | - Bihui Yang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming Medical University affiliated Infectious diseases hospital, 28 Shian Road, Taiping District, Kunming, 650301, China
| | - Cuixian Yang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming Medical University affiliated Infectious diseases hospital, 28 Shian Road, Taiping District, Kunming, 650301, China
| | - Mi Zhang
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming Medical University affiliated Infectious diseases hospital, 28 Shian Road, Taiping District, Kunming, 650301, China.
| | - Xingqi Dong
- Yunnan Provincial Hospital of Infectious Disease, AIDS Care Center (YNACC), Kunming Medical University affiliated Infectious diseases hospital, 28 Shian Road, Taiping District, Kunming, 650301, China.
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17
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Silver N, Paynter M, McAllister G, Atchley M, Sayir C, Short J, Winner D, Alouani DJ, Sharkey FH, Bergefall K, Templeton K, Carrington D, Quiñones-Mateu ME. Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Res Ther 2018; 15:18. [PMID: 30409215 PMCID: PMC6223033 DOI: 10.1186/s12981-018-0206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals. METHODS We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals. RESULTS Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4+ T cell counts in the NHS Lothian patients. CONCLUSIONS This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
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18
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Gibson RM, Nickel G, Crawford M, Kyeyune F, Venner C, Nankya I, Nabulime E, Ndashimye E, Poon AFY, Salata RA, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ. Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries. Infect Dis Poverty 2017; 6:163. [PMID: 29202874 PMCID: PMC5716384 DOI: 10.1186/s40249-017-0377-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
Background Thymidine analogs, namely AZT (Zidovudine or Retrovir™) and d4T (Stavudine or Zerit™) are antiretroviral drugs still employed in over 75% of first line combination antiretroviral therapy (cART) in Kampala, Uganda despite aversion to prescribing these drugs for cART in high income countries due in part to adverse events. For this study, we explored how the continued use of these thymidine analogs in cART could impact emergence of drug resistance and impact on future treatment success in Uganda, a low-income country. Methods We examined the drug resistance genotypes by Sanger sequencing of 262 HIV-infected patients failing a first line combined antiretroviral treatment containing either AZT or d4T, which represents approximately 5% of the patients at the Joint Clinical Research Center receiving a AZT or d4T containing treatment. Next generation sequencing (DEEPGEN™HIV) and multiplex oligonucleotide ligation assays (AfriPOLA) were then performed on a subset of patient samples to detect low frequency drug resistant mutations. CD4 cell counts, viral RNA loads, and treatment changes were analyzed in a cohort of treatment success and failures. Results Over 80% of patients failing first line AZT/d4T-containing cART had predicted drug resistance to 3TC (Lamivudine) and non-nucleoside RT inhibitors (NNRTIs) in the treatment regimen but only 45% had resistance AZT/d4T associated resistance mutations (TAMs). TAMs were however detected at low frequency within the patients HIV quasispecies (1–20%) in 21 of 34 individuals who were failing first-line AZT-containing cART and lacked TAMs by Sanger. Due to lack of TAMs by Sanger, AZT was typically maintained in second-line therapies and these patients had a low frequency of subsequent virologic success. Conclusions Our findings suggest that continued use of AZT and d4T in first-line treatment in low-to-middle income countries may lead to misdiagnosis of HIV-1 drug resistance and possibly enhance a succession of second- and third-line treatment failures. Electronic supplementary material The online version of this article (doi: 10.1186/s40249-017-0377-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard M Gibson
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Michael Crawford
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Colin Venner
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada
| | - Immaculate Nankya
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.,Department of Pathology and Laboratory Medicine, University of Western Ontario, Kampala, Uganda
| | - Eva Nabulime
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Emmanuel Ndashimye
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, University of Western Ontario, Kampala, Uganda
| | - Robert A Salata
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Cissy Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Peter Mugyenyi
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Eric J Arts
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada. .,TREAT, Joint Clinical Research Centre, Kampala, Uganda.
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Pessôa R, Sanabani SS. High prevalence of HIV-1 transmitted drug-resistance mutations from proviral DNA massively parallel sequencing data of therapy-naïve chronically infected Brazilian blood donors. PLoS One 2017; 12:e0185559. [PMID: 28953964 PMCID: PMC5617215 DOI: 10.1371/journal.pone.0185559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/14/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND An improved understanding of the prevalence of low-abundance transmitted drug-resistance mutations (TDRM) in therapy-naïve HIV-1-infected patients may help determine which patients are the best candidates for therapy. In this study, we aimed to obtain a comprehensive picture of the evolving HIV-1 TDRM across the massive parallel sequences (MPS) of the viral entire proviral genome in a well-characterized Brazilian blood donor naïve to antiretroviral drugs. MATERIALS AND METHODS The MPS data from 128 samples used in the analysis were sourced from Brazilian blood donors and were previously classified by less-sensitive (LS) or "detuned" enzyme immunoassay as non-recent or longstanding HIV-1 infections. The Stanford HIV Resistance Database (HIVDBv 6.2) and IAS-USA mutation lists were used to interpret the pattern of drug resistance. The minority variants with TDRM were identified using a threshold of ≥ 1.0% and ≤ 20% of the reads sequenced. The rate of TDRM in the MPS data of the proviral genome were compared with the corresponding published consensus sequences of their plasma viruses. RESULTS No TDRM were detected in the integrase or envelope regions. The overall prevalence of TDRM in the protease (PR) and reverse transcriptase (RT) regions of the HIV-1 pol gene was 44.5% (57/128), including any mutations to the nucleoside analogue reverse transcriptase inhibitors (NRTI) and non-nucleoside analogue reverse transcriptase inhibitors (NNRTI). Of the 57 subjects, 43 (75.4%) harbored a minority variant containing at least one clinically relevant TDRM. Among the 43 subjects, 33 (76.7%) had detectable minority resistant variants to NRTIs, 6 (13.9%) to NNRTIs, and 16 (37.2%) to PR inhibitors. The comparison of viral sequences in both sources, plasma and cells, would have detected 48 DNA provirus disclosed TDRM by MPS previously missed by plasma bulk analysis. CONCLUSION Our findings revealed a high prevalence of TDRM found in this group, as the use of MPS drastically increased the detection of these mutations. Sequencing proviral DNA provided additional information about TDRM, which may impact treatment decisions. The overall results emphasize the importance of continuous monitoring.
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Affiliation(s)
- Rodrigo Pessôa
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Sabri S. Sanabani
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil
- Clinical Laboratory, Department of Pathology, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo, Brazil
- * E-mail:
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20
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Ensemble Classifiers for Predicting HIV-1 Resistance from Three Rule-Based Genotypic Resistance Interpretation Systems. J Med Syst 2017; 41:155. [PMID: 28856560 DOI: 10.1007/s10916-017-0802-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/22/2017] [Indexed: 10/19/2022]
Abstract
Resistance to antiretrovirals (ARVs) is a major problem faced by HIV-infected individuals. Different rule-based algorithms were developed to infer HIV-1 susceptibility to antiretrovirals from genotypic data. However, there is discordance between them, resulting in difficulties for clinical decisions about which treatment to use. Here, we developed ensemble classifiers integrating three interpretation algorithms: Agence Nationale de Recherche sur le SIDA (ANRS), Rega, and the genotypic resistance interpretation system from Stanford HIV Drug Resistance Database (HIVdb). Three approaches were applied to develop a classifier with a single resistance profile: stacked generalization, a simple plurality vote scheme and the selection of the interpretation system with the best performance. The strategies were compared with the Friedman's test and the performance of the classifiers was evaluated using the F-measure, sensitivity and specificity values. We found that the three strategies had similar performances for the selected antiretrovirals. For some cases, the stacking technique with naïve Bayes as the learning algorithm showed a statistically superior F-measure. This study demonstrates that ensemble classifiers can be an alternative tool for clinical decision-making since they provide a single resistance profile from the most commonly used resistance interpretation systems.
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21
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Shkreta L, Blanchette M, Toutant J, Wilhelm E, Bell B, Story BA, Balachandran A, Cochrane A, Cheung PK, Harrigan PR, Grierson DS, Chabot B. Modulation of the splicing regulatory function of SRSF10 by a novel compound that impairs HIV-1 replication. Nucleic Acids Res 2017; 45:4051-4067. [PMID: 27928057 PMCID: PMC5397194 DOI: 10.1093/nar/gkw1223] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 11/22/2016] [Indexed: 11/25/2022] Open
Abstract
We recently identified the 4-pyridinone-benzisothiazole carboxamide compound 1C8 as displaying strong anti-HIV-1 potency against a variety of clinical strains in vitro. Here we show that 1C8 decreases the expression of HIV-1 and alters splicing events involved in the production of HIV-1 mRNAs. Although 1C8 was designed to be a structural mimic of the fused tetracyclic indole compound IDC16 that targets SRSF1, it did not affect the splice site shifting activity of SRSF1. Instead, 1C8 altered splicing regulation mediated by SRSF10. Depleting SRSF10 by RNA interference affected viral splicing and, like 1C8, decreased expression of Tat, Gag and Env. Incubating cells with 1C8 promoted the dephosphorylation of SRSF10 and increased its interaction with hTra2β, a protein previously implicated in the control of HIV-1 RNA splicing. While 1C8 affects the alternative splicing of cellular transcripts controlled by SRSF10 and hTra2β, concentrations greater than those needed to inhibit HIV-1 replication were required to elicit significant alterations. Thus, the ability of 1C8 to alter the SRSF10-dependent splicing of HIV-1 transcripts, with minor effects on cellular splicing, supports the view that SRSF10 may be used as a target for the development of new anti-viral agents.
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Affiliation(s)
- Lulzim Shkreta
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Marco Blanchette
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Johanne Toutant
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Emmanuelle Wilhelm
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Brendan Bell
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Benjamin A Story
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Peter K Cheung
- BC Centre for Excellence in HIV/AIDS, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - David S Grierson
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
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Moscona R, Ram D, Wax M, Bucris E, Levy I, Mendelson E, Mor O. Comparison between next-generation and Sanger-based sequencing for the detection of transmitted drug-resistance mutations among recently infected HIV-1 patients in Israel, 2000-2014. J Int AIDS Soc 2017; 20:21846. [PMID: 28799325 PMCID: PMC5577736 DOI: 10.7448/ias.20.1.21846] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/22/2017] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Transmitted drug-resistance mutations (TDRM) may hamper successful anti-HIV-1 therapy and impact future control of the HIV-1 epidemic. Recently infected, therapy-naïve individuals are best suited for surveillance of such TDRM. In this study, TDRM, detected by next-generation sequencing (NGS) were compared to those identified by Sanger-based population sequencing (SBS) in recently infected HIV-1 patients. METHODS Historical samples from 80 recently infected HIV-1 patients, diagnosed between 2000 and 2014, were analysed by MiSeq (NGS) and ABI (SBS). DeepChek-HIV (ABL) was used for interpretation of the results. RESULTS Most patients were males (80%); Men who have sex with men (MSM) was the major transmission group (58.8%). Overall, TDRM were detected in 31.3% of patients by NGS and 8.8% by SBS, with SBS TDRM restricted to persons infected with subtype B. All SBS-detected TDRM were identified by NGS. The prevalence of TDRM impacting protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) was 11.3, 26.2 7.5%, respectively, in NGS analyses and 0, 3.8 and 5%, respectively, in SBS analyses. More patients with NGS and SBS TDRM were identified in 2008-2014 (37.2% or 13.9%, respectively) compared to 2000-2007 (24.3% or 2.7%, respectively), and a significantly greater number of these patients had multiple NGS TDRM. The most abundant, albeit, minor-frequency RT TDRM, were the K65R and D67N, while K103N, M184V and T215S were high-frequency mutations. Minor TDRM did not become a major variant in later samples and did not hinder successful treatment. CONCLUSIONS NGS can replace SBS for mutation detection and allows for the detection of low-frequency TDRM not identified by SBS. Although rates of TDRM in Israel continued to increase from 2000 to 2014, minor TDRM did not become major species. The need for ongoing surveillance of low-frequency TDRM should be revisited in a larger study.
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Affiliation(s)
- Roy Moscona
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Daniela Ram
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Marina Wax
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- School of Public Health, Tel Aviv University, Ramat-Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
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Abstract
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis.
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Affiliation(s)
- Charlotte J. Houldcroft
- Department of Infection, UK; and the Division of Biological Anthropology, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, University of Cambridge, Cambridge CB2 3QG, UK.,
- and the Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3QG, UK.,
| | - Mathew A. Beale
- Division of Infection and Immunity, University College London, London, WC1E 6BT UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
- and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
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24
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Piana C, Danhof M, Della Pasqua O. Impact of disease, drug and patient adherence on the effectiveness of antiviral therapy in pediatric HIV. Expert Opin Drug Metab Toxicol 2017; 13:497-511. [PMID: 28043170 DOI: 10.1080/17425255.2017.1277203] [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] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Maintaining effective antiretroviral treatment for life is a major problem in both resource-limited and resource-rich countries. Despite the progress observed in paediatric antiretroviral therapy, approximately 12% of children still experience treatment failure due to drug resistance, inadequate dosing and poor adherence. We explore the current status of antiretroviral therapy in children with focus on the interaction between disease, drug pharmacokinetics and patient behavior, all of which are strongly interconnected and determine treatment outcome. Areas covered: An overview is provided of the viral characteristics and available drug combinations aimed at the prevention of resistance. In this context, the role of patient adherence is scrutinized. A detailed assessment of factors affecting adherence is presented together with the main strategies to enhance treatment response in children. Expert opinion: Using modeling and simulation, a framework for characterizing the forgiveness of non-adherence for specific antiretroviral drugs in children is proposed in which information on pharmacokinetics, pharmacokinetic-pharmacodynamic relationships and viral dynamics is integrated. This approach represents an opportunity for the simplification of dosing regimens taking into account the interaction between these factors. Based on clinical trial simulation scenarios, we envisage the possibility of assessing the impact of variable adherence to antiretroviral drug combinations in HIV-infected children.
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Affiliation(s)
- Chiara Piana
- a Division of Pharmacology, Leiden Academic Centre for Drug Research , Leiden University , Leiden , The Netherlands
| | - Meindert Danhof
- a Division of Pharmacology, Leiden Academic Centre for Drug Research , Leiden University , Leiden , The Netherlands
| | - Oscar Della Pasqua
- b Clinical Pharmacology Modelling & Simulation , GlaxoSmithKline , Uxbridge , United Kingdom.,c Clinical Pharmacology & Therapeutics Group , University College London , London , United Kingdom
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25
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Casadellà M, Paredes R. Deep sequencing for HIV-1 clinical management. Virus Res 2016; 239:69-81. [PMID: 27818211 DOI: 10.1016/j.virusres.2016.10.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/10/2016] [Accepted: 10/18/2016] [Indexed: 02/05/2023]
Abstract
The emerging HIV-1 resistance epidemic is threatening the impressive global advances in HIV-1 infection treatment and prevention achieved in the last decade. Next-generation sequencing is improving our ability to understand, diagnose and prevent HIV-1 resistance, being increasingly cost-effective and more accessible. However, NGS still faces a number of limitations that need to be addressed to enable its widespread use. Here, we will review the main NGS platforms available for HIV-1 diagnosis, the factors affecting the clinical utility of NGS testing and the evidence supporting -or not- ultrasensitive genotyping over Sanger sequencing for routine HIV-1 diagnosis. Now that global HIV-1 eradication might be within our reach, making NGS accessible also to LMICs has become a priority. Reductions in sequencing costs, particularly in library preparation, and accessibility to low-cost, robust but simplified automated bioinformatic analyses of NGS data will remain essential to end the HIV-1 pandemic.
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Affiliation(s)
- Maria Casadellà
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Catalonia, Spain.
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Catalonia, Spain; Universitat de Vic - Central de Catalunya, Vic, Catalonia, Spain; HIV-1 Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
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26
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Ercan S. Docking and Molecular Dynamics Calculations of Some Previously Studied and newly Designed Ligands to Catalytic Core Domain of HIV-1 Integrase and an Investigation to Effects of Conformational Changes of Protein on Docking Results. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2016. [DOI: 10.18596/jotcsa.287327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Low-Frequency Drug Resistance in HIV-Infected Ugandans on Antiretroviral Treatment Is Associated with Regimen Failure. Antimicrob Agents Chemother 2016; 60:3380-97. [PMID: 27001818 DOI: 10.1128/aac.00038-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/11/2016] [Indexed: 12/27/2022] Open
Abstract
Most patients failing antiretroviral treatment in Uganda continue to fail their treatment regimen even if a dominant drug-resistant HIV-1 genotype is not detected. In a recent retrospective study, we observed that approximately 30% of HIV-infected individuals in the Joint Clinical Research Centre (Kampala, Uganda) experienced virologic failure with a susceptible HIV-1 genotype based on standard Sanger sequencing. Selection of minority drug-resistant HIV-1 variants (not detectable by Sanger sequencing) under antiretroviral therapy pressure can lead to a shift in the viral quasispecies distribution, becoming dominant members of the virus population and eventually causing treatment failure. Here, we used a novel HIV-1 genotyping assay based on deep sequencing (DeepGen) to quantify low-level drug-resistant HIV-1 variants in 33 patients failing a first-line antiretroviral treatment regimen in the absence of drug-resistant mutations, as screened by standard population-based Sanger sequencing. Using this sensitive assay, we observed that 64% (21/33) of these individuals had low-frequency (or minority) drug-resistant variants in the intrapatient HIV-1 population, which correlated with treatment failure. Moreover, the presence of these minority HIV-1 variants was associated with higher intrapatient HIV-1 diversity, suggesting a dynamic selection or fading of drug-resistant HIV-1 variants from the viral quasispecies in the presence or absence of drug pressure, respectively. This study identified low-frequency HIV drug resistance mutations by deep sequencing in Ugandan patients failing antiretroviral treatment but lacking dominant drug resistance mutations as determined by Sanger sequencing methods. We showed that these low-abundance drug-resistant viruses could have significant consequences for clinical outcomes, especially if treatment is not modified based on a susceptible HIV-1 genotype by Sanger sequencing. Therefore, we propose to make clinical decisions using more sensitive methods to detect minority HIV-1 variants.
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Read G, Ingersoll KS. Which Patient Characteristics Among Cocaine Users with HIV Relate to Drug Use and Adherence Outcomes Following a Dual-Focused Intervention? AIDS Behav 2016; 20:633-45. [PMID: 26142103 DOI: 10.1007/s10461-015-1119-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This is a secondary analysis of data from a randomized trial of dually-focused interventions for nonadherent HIV patients with cocaine use disorders (Ingersoll et al. in Drug Alcohol Depend 116(1-3):177-187, 2011). We examined the relationships among baseline demographic, psychological, psychiatric, and behavioral characteristics and 6-months post-study ART adherence, log viral load (VL), ASI Drug Composite Score, and days using cocaine. We used the SAS GLMSELECT procedure to build multivariate models of each post-study outcome. Post-study ART adherence was related to 2 psychological variables; while logVL was related to 2 drug-related behaviors. ASI Drug Composite score was related to 2 psychiatric disorders, 1 demographic, and 1 psychological variable; in contrast, days using cocaine related to 1 behavioral and 3 psychological variables. Analyses show clear, robust relationships among behavioral, psychological and psychiatric diagnosis factors with post-study ART adherence and cocaine use outcomes. Future ART adherence interventions for cocaine users should consider tailoring to these patient characteristics.
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Cheung PK, Horhant D, Bandy LE, Zamiri M, Rabea SM, Karagiosov SK, Matloobi M, McArthur S, Harrigan PR, Chabot B, Grierson DS. A Parallel Synthesis Approach to the Identification of Novel Diheteroarylamide-Based Compounds Blocking HIV Replication: Potential Inhibitors of HIV-1 Pre-mRNA Alternative Splicing. J Med Chem 2016; 59:1869-79. [PMID: 26878150 DOI: 10.1021/acs.jmedchem.5b01357] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A 256-compound library was evaluated in an anti-HIV screen to identify structural "mimics" of the fused tetracyclic indole compound 1 (IDC16) that conserve its anti-HIV activity without associated cytotoxicity. Four diheteroarylamide-type compounds, containing a common 5-nitroisobenzothiazole motif, were identified as active. In subsequent screens, the most potent compound 9 (1C8) was active against wild-type HIV-1IIIB (subtype B, X4-tropic) and HIV-1 97USSN54 (subtype A, R5-tropic) with EC50's of 0.6 and 0.9 μM, respectively. Compound 9 also inhibited HIV strains resistant to drugs targeting HIV reverse transcriptase, protease, integrase, and coreceptor CCR5 with EC50's ranging from 0.9 to 1.5 μM. The CC50 value obtained in a cytotoxicity assay for compound 9 was >100 μM, corresponding to a therapeutic index (CC50/EC50) of approximately 100. Further comparison studies revealed that, whereas the anti-HIV activity for compound 9 and the parent molecule 1 are similar, the cytotoxic effect for compound 9 was, as planned, markedly suppressed.
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Affiliation(s)
- Peter K Cheung
- British Columbia Centre for Excellence in HIV/AIDS , 608-1081 Burrard Street, Vancouver, British Columbia V6Z 1Y6, Canada
| | | | | | | | | | | | | | | | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS , 608-1081 Burrard Street, Vancouver, British Columbia V6Z 1Y6, Canada
| | - Benoit Chabot
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke , 3201, rue Jean-Mignault, Sherbrooke, Québec J1E 4K8 Canada
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HIV-1 genotypic drug resistance testing: digging deep, reaching wide? Curr Opin Virol 2015; 14:16-23. [DOI: 10.1016/j.coviro.2015.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 06/10/2015] [Accepted: 06/10/2015] [Indexed: 12/26/2022]
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31
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Adetokunboh O, Atibioke O, Balogun T, Oluwasanu M. Antiretroviral Treatment and Resistance Patterns in HIV-Infected Children. Curr Infect Dis Rep 2015; 17:502. [DOI: 10.1007/s11908-015-0502-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Protein/peptide-based entry/fusion inhibitors as anti-HIV therapies: challenges and future direction. Rev Med Virol 2015; 26:4-20. [DOI: 10.1002/rmv.1853] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/02/2015] [Accepted: 07/15/2015] [Indexed: 11/07/2022]
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33
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Kwon OK, Kim SS, Rhee JE, Kee MK, Park M, Oh HR, Choi JY. Drug susceptibility to etravirine and darunavir among Human Immunodeficiency Virus Type 1-derived pseudoviruses in treatment-experienced patients with HIV/AIDS in South Korea. Virol J 2015; 12:53. [PMID: 25879840 PMCID: PMC4404133 DOI: 10.1186/s12985-015-0283-7] [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: 09/29/2014] [Accepted: 03/19/2015] [Indexed: 11/25/2022] Open
Abstract
Background In South Korea, about 20 types of antiretroviral drugs are used in the treatment of patients with human immunodeficiency virus/acquired immune deficiency syndrome. Since 2010, raltegravir, etravirine, and darunavir have been spotlighted as new drugs for highly active antiretroviral therapy (HAART)-experienced adults with resistant HIV-1 in South Korea. In this study, we investigated potential susceptibility of pseudoviruses derived from treatment-experienced Korean patients to etravirine vs efavirenz and to darunavir vs amprenavir and indinavir using a modified single-round assay. Methods Pseudoviruses derived from nine treatment-experienced patients infected with HIV-1 were investigated by comparison with the wild-type strain pNL4-3. The 50% inhibitory concentration (IC50) values were calculated and drug susceptibility was compared. The intensity of genotypic drug resistance was classified based on the ‘SIR’ interpretation of the Stanford data base. Results Drug susceptibility was generally higher for etravirine and darunavir compared with efavirenz, amprenavir, and indinavir in pseudoviruses derived from treatment-experienced patients. Pseudoviruses derived from patients KRB4025 and KRB8014, who exhibited long-term use of protease inhibitors, showed an outside of tested drug concentration, especially for amprenavir and indinavir. However, they exhibited a lower fold-change in resistance to darunavir. Conclusions Etravirine and darunavir have been used in HAART since 2010 in South Korea. Therefore, these antiretroviral drugs together with other newly introduced antiretroviral drugs are interesting for the optimal treatment of patients with treatment failure. This study may help to find a more effective HAART in the case of HIV-1 infected patients that have difficulty being treated.
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Affiliation(s)
- Oh-Kyung Kwon
- Department of Immunology and Pathology, Division of AIDS, Korea National Institute of Health, Osong, Republic of Korea.
| | - Sung Soon Kim
- Department of Immunology and Pathology, Division of AIDS, Korea National Institute of Health, Osong, Republic of Korea.
| | - Jee Eun Rhee
- Department of Immunology and Pathology, Division of AIDS, Korea National Institute of Health, Osong, Republic of Korea.
| | - Mee-Kyung Kee
- Department of Immunology and Pathology, Division of AIDS, Korea National Institute of Health, Osong, Republic of Korea.
| | - Mina Park
- Department of Immunology and Pathology, Division of AIDS, Korea National Institute of Health, Osong, Republic of Korea.
| | - Hye-Ri Oh
- Department of Immunology and Pathology, Division of AIDS, Korea National Institute of Health, Osong, Republic of Korea.
| | - Ju-Yeon Choi
- Department of Immunology and Pathology, Division of AIDS, Korea National Institute of Health, Osong, Republic of Korea.
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Radchuk OM, Chentsova NP, Tukaiev SV. Outcome of antiretroviral treatment in patients with AIDS monoinfection and those co-infected with hepatitis B and C viruses and tuberculosis in Ukraine. Cent Eur J Public Health 2015; 22:143-6. [PMID: 25438388 DOI: 10.21101/cejph.a3850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Antiretroviral therapy reduces AIDS morbidity and mortality as well as decreases HIV transmission by reducing the viral load (VL). We aimed to determine the rate of immunological and virological failure that reflects antiretroviral treatment (ART) effectiveness among the patients of the Kyiv City AIDS Centre and may lead to ART switch in the future. In 59% of patients the prescribed ATR regimen was regarded as successful, in 37% as unsuccessful and 4% of patients were excluded for lacking sufficient follow-up time. Among the cases of unsuccessful ART, the largest part of patients was experiencing secondary immunological failure, on the second place was primary immunological failure. The temporal distribution of primary and secondary failures was also defined. It was shown that the number of patients with treatment failure increases steadily Drug resistance testing is able to reduce the number of unsuccessful ART regimens, but such testing is not a part of the routine testing in Ukraine.
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Jain (Pancholi) N, Gupta S, Sapre N, Sapre NS. In silico de novo design of novel NNRTIs: a bio-molecular modelling approach. RSC Adv 2015. [DOI: 10.1039/c4ra15478a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Six novel NNRTIs (DABO) with high efficacy are designed by assessing the interaction potential and structural requirements using chemometric analyses (SVM, BPNN and MLR) on structural descriptors.
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Affiliation(s)
| | - Swagata Gupta
- Department of Chemistry
- Govt. BLPPG College
- MHOW, India
| | - Neelima Sapre
- Department of Mathematics and Computational Sc
- SGSITS
- Indore, India
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Contribution of human immunodeficiency virus type 1 minority variants to reduced drug susceptibility in patients on an integrase strand transfer inhibitor-based therapy. PLoS One 2014; 9:e104512. [PMID: 25110880 PMCID: PMC4128663 DOI: 10.1371/journal.pone.0104512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
The role of HIV-1 minority variants on transmission, pathogenesis, and virologic failure to antiretroviral regimens has been explored; however, most studies of low-level HIV-1 drug-resistant variants have focused in single target regions. Here we used a novel HIV-1 genotypic assay based on deep sequencing, DEEPGEN (Gibson et al 2014 Antimicrob Agents Chemother 58∶2167) to simultaneously analyze the presence of minority variants carrying mutations associated with reduced susceptibility to protease (PR), reverse transcriptase (RT), and integrase strand transfer integrase inhibitors (INSTIs), as well as HIV-1 coreceptor tropism. gag-p2/NCp7/p1/p6/pol-PR/RT/INT and env/C2V3 PCR products were obtained from twelve heavily treatment-experienced patients experiencing virologic failure while participating in a 48-week dose-ranging study of elvitegravir (GS-US-183-0105). Deep sequencing results were compared with (i) virological response to treatment, (ii) genotyping based on population sequencing, (iii) phenotyping data using PhenoSense and VIRALARTS, and (iv) HIV-1 coreceptor tropism based on the phenotypic test VERITROP. Most patients failed the antiretroviral regimen with numerous pre-existing mutations in the PR and RT, and additionally newly acquired INSTI-resistance mutations as determined by population sequencing (mean 9.4, 5.3, and 1.4 PI- RTI-, and INSTI-resistance mutations, respectively). Interestingly, since DEEPGEN allows the accurate detection of amino acid substitutions at frequencies as low as 1% of the population, a series of additional drug resistance mutations were detected by deep sequencing (mean 2.5, 1.5, and 0.9, respectively). The presence of these low-abundance HIV-1 variants was associated with drug susceptibility, replicative fitness, and coreceptor tropism determined using sensitive phenotypic assays, enhancing the overall burden of resistance to all four antiretroviral drug classes. Further longitudinal studies based on deep sequencing tests will help to clarify (i) the potential impact of minority HIV-1 drug resistant variants in response to antiretroviral therapy and (ii) the importance of the detection of HIV minority variants in the clinical practice.
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Stanojevic M, Siljic M, Salemovic D, Pesic-Pavlovic I, Zerjav S, Nikolic V, Ranin J, Jevtovic D. Ten years survey of primary HIV-1 resistance in Serbia: the occurrence of multiclass resistance. AIDS Res Hum Retroviruses 2014; 30:634-41. [PMID: 24635515 DOI: 10.1089/aid.2013.0270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In Serbia, the first cases of HIV infection were reported in 1985, whereas antiretroviral (ARV) therapy has been in use since 1987. With this study we aimed to assess the occurrence and pattern of HIV resistance mutations among newly diagnosed patients in the period 2002-2011. The study prospectively included 181 adult patients. Genotypic HIV-1 drug resistance testing was performed and drug resistance was scored according to the 2009 WHO list for surveillance of drug resistance mutations (SDRMs). A bioinformatic approach was used to estimate the duration of infection by calculating the percentage of ambiguous basecalls per sequence, with a cutoff of 0.47% as the delimiter for recent infection. The overall prevalence of transmitted drug resistance (TDR) found in the study was 8.8% (16/181, 95% CI=5.5-13.8). Thirty-one percent of resistant samples contained multiple SDRMs. In particular, 5/16 patients with resistance carried viral strains with SDRMs to multiple ARV classes, hence one-third of resistant strains were multiclass resistant, including non-B strains. A total of 51.9% of samples (94/181) were classified as recent infection, with a significant increase in the second part of the study period. However, the prevalence of TDR in recent infection was 6.4% (6/94, 95% CI=2.9-13.2), not statistically different from that found in nonrecent infection. We showed a changing pattern of TDR mutations over the study period, with a substantial occurrence of multiclass resistance, across different HIV subtypes. Our results highlight the need for continued surveillance of primary resistance.
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Affiliation(s)
- Maja Stanojevic
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | - Marina Siljic
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | - Dubravka Salemovic
- Institute for Infectious and Tropical Diseases CCS, HIV/AIDS Unit, Belgrade, Serbia
| | - Ivana Pesic-Pavlovic
- Institute for Infectious and Tropical Diseases CCS, HIV/AIDS Unit, Belgrade, Serbia
| | - Sonja Zerjav
- Institute for Infectious and Tropical Diseases CCS, HIV/AIDS Unit, Belgrade, Serbia
| | - Valentina Nikolic
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | - Jovan Ranin
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
- Institute for Infectious and Tropical Diseases CCS, HIV/AIDS Unit, Belgrade, Serbia
| | - Djordje Jevtovic
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
- Institute for Infectious and Tropical Diseases CCS, HIV/AIDS Unit, Belgrade, Serbia
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Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use? Curr Infect Dis Rep 2014; 16:401. [DOI: 10.1007/s11908-014-0401-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism. Antimicrob Agents Chemother 2014; 58:2167-85. [PMID: 24468782 DOI: 10.1128/aac.02710-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
With 29 individual antiretroviral drugs available from six classes that are approved for the treatment of HIV-1 infection, a combination of different phenotypic and genotypic tests is currently needed to monitor HIV-infected individuals. In this study, we developed a novel HIV-1 genotypic assay based on deep sequencing (DeepGen HIV) to simultaneously assess HIV-1 susceptibilities to all drugs targeting the three viral enzymes and to predict HIV-1 coreceptor tropism. Patient-derived gag-p2/NCp7/p1/p6/pol-PR/RT/IN- and env-C2V3 PCR products were sequenced using the Ion Torrent Personal Genome Machine. Reads spanning the 3' end of the Gag, protease (PR), reverse transcriptase (RT), integrase (IN), and V3 regions were extracted, truncated, translated, and assembled for genotype and HIV-1 coreceptor tropism determination. DeepGen HIV consistently detected both minority drug-resistant viruses and non-R5 HIV-1 variants from clinical specimens with viral loads of ≥1,000 copies/ml and from B and non-B subtypes. Additional mutations associated with resistance to PR, RT, and IN inhibitors, previously undetected by standard (Sanger) population sequencing, were reliably identified at frequencies as low as 1%. DeepGen HIV results correlated with phenotypic (original Trofile, 92%; enhanced-sensitivity Trofile assay [ESTA], 80%; TROCAI, 81%; and VeriTrop, 80%) and genotypic (population sequencing/Geno2Pheno with a 10% false-positive rate [FPR], 84%) HIV-1 tropism test results. DeepGen HIV (83%) and Trofile (85%) showed similar concordances with the clinical response following an 8-day course of maraviroc monotherapy (MCT). In summary, this novel all-inclusive HIV-1 genotypic and coreceptor tropism assay, based on deep sequencing of the PR, RT, IN, and V3 regions, permits simultaneous multiplex detection of low-level drug-resistant and/or non-R5 viruses in up to 96 clinical samples. This comprehensive test, the first of its class, will be instrumental in the development of new antiretroviral drugs and, more importantly, will aid in the treatment and management of HIV-infected individuals.
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Li L, Sun G, Liang S, Li J, Li T, Wang Z, Liu W, Yang S, Liu Y, Wang X, Li J. Different distribution of HIV-1 subtype and drug resistance were found among treatment naïve individuals in Henan, Guangxi, and Yunnan province of China. PLoS One 2013; 8:e75777. [PMID: 24098398 PMCID: PMC3789720 DOI: 10.1371/journal.pone.0075777] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/20/2013] [Indexed: 11/30/2022] Open
Abstract
Yunnan, Guangxi and Henan are the provinces with the most severe HIV epidemic in China, which were also among the first group of areas providing free ART in 2004. However, little comprehensive data are available on prevalence of HIV subtype and baseline drug resistance in drug-naïve populations. In this study, 1746 treatment-naïve HIV-positive individuals were randomly selected from new-reported cases in Henan, Guangxi and Yunnan. Among of them, subtypes and drug resistance of 1159 strains were determined by amplifying and sequencing full-length pol genes. Significantly different distributions of HIV subtypes prevalent in three provinces were identified (P<0.01). CRF08_BC was found dominant in Yunnan (59.8%), while CRF01_AE was dominant in Guangxi (77.3%) and subtype B was dominant in Henan province (93.9%). The total prevalence of drug resistance was 7.1%. The highest prevalence of HIV drug resistance was found in Henan (12.2%), followed by Yunnan (5.6%) and Guangxi (3.3%). The results of this study suggest that genetic drug-resistance should be tested before initiation of ART in China, especially in Henan province. Furthermore, the prevalence of HIV drug resistant strains should be considered separately in different areas in China before the change of different free ART regimens.
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Affiliation(s)
- Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Guoqing Sun
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan, China
| | - Shujia Liang
- Guangxi Center for Disease Prevention and Control, Nanning, China
| | - Jianjian Li
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Wang
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan, China
| | - Wei Liu
- Guangxi Center for Disease Prevention and Control, Nanning, China
| | - Shaomin Yang
- Yunnan Provincial Hospital Infectious Disease, AIDS Care Center (YNACC), Kunming, Yunnan, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *E-mail:
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Rai D, Chen W, Tian Y, Chen X, Zhan P, De Clercq E, Pannecouque C, Balzarini J, Liu X. Design, synthesis and biological evaluation of 3-benzyloxy-linked pyrimidinylphenylamine derivatives as potent HIV-1 NNRTIs. Bioorg Med Chem 2013; 21:7398-405. [PMID: 24134904 DOI: 10.1016/j.bmc.2013.09.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
A novel series of 3-benzyloxy-linked pyrimidinylphenylamine derivatives (8a-8s) was designed, synthesized and evaluated for their in vitro anti-HIV activity in MT-4 cell cultures. Most of the compounds inhibited wild-type (wt) HIV-1 replication in the lower micromolar concentration range (EC(50)=0.05-35 μM) with high selectivity index (SI) values (ranged from 10 to >4870). In particular, 8h and 8g displayed excellent antiretroviral activity against wt HIV-1 with low cytotoxicity (EC(50)=0.07 μM, CC(50) >347 μM, SI >4870; EC50=0.05 μM, CC(50)=42 μM, SI=777, respectively), comparable to that of the marked drug nevirapine (EC(50)=0.113 μM, CC(50) >15 μM, SI >133). In order to confirm the binding target, 8h was selected to perform the anti-HIV-1 RT assay. Additionally, preliminary structure activity relationship (SAR) analysis and molecular docking studies of newly synthesized compounds were also discussed, as well as the predicted physicochemical properties.
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Affiliation(s)
- Diwakar Rai
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Educational Ministry of China), School of Pharmaceutical Sciences, Shandong University, No. 44 Wenhuaxi Road, Jinan 250012, China
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42
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Chen X, Li Y, Ding S, Balzarini J, Pannecouque C, De Clercq E, Liu H, Liu X. Discovery of Piperidine-Linked Pyridine Analogues as Potent Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors. ChemMedChem 2013; 8:1117-26. [DOI: 10.1002/cmdc.201300130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Indexed: 11/10/2022]
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Tremblay M, Bethell RC, Cordingley MG, DeRoy P, Duan J, Duplessis M, Edwards PJ, Faucher AM, Halmos T, James CA, Kuhn C, Lacoste JÉ, Lamorte L, LaPlante SR, Malenfant E, Minville J, Morency L, Morin S, Rajotte D, Salois P, Simoneau B, Tremblay S, Sturino CF. Identification of benzofurano[3,2-d]pyrimidin-2-ones, a new series of HIV-1 nucleotide-competing reverse transcriptase inhibitors. Bioorg Med Chem Lett 2013; 23:2775-80. [PMID: 23511023 DOI: 10.1016/j.bmcl.2013.02.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/31/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Screening of our sample collection led to the identification of a set of benzofurano[3,2-d]pyrimidine-2-one hits acting as nucleotide-competing HIV-1 reverse transcriptase inhibitiors (NcRTI). Significant improvement in antiviral potency was achieved when substituents were introduced at positions N1, C4, C7 and C8 on the benzofuranopyrimidone scaffold. The series was optimized from low micromolar enzymatic activity against HIV-1 RT and no antiviral activity to low nanomolar antiviral potency. Further profiling of inhibitor 30 showed promising overall in vitro properties and also demonstrated that its potency was maintained against viruses resistant to the other major classes of HIV-1 RT inhibitors.
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Affiliation(s)
- Martin Tremblay
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd, 2100 Cunard Street, Laval, Québec, Canada H7S 2G5.
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Buonaguro L, Tagliamonte M, Visciano ML, Tornesello ML, Buonaguro FM. Developments in virus-like particle-based vaccines for HIV. Expert Rev Vaccines 2013; 12:119-127. [PMID: 23414404 DOI: 10.1586/erv.12.152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Virus-like particles (VLPs) hold great promise for the development of effective and affordable vaccines. VLPs, indeed, are suitable for presentation and efficient delivery to antigen-presenting cells of linear as well as conformational antigens. This will ultimately result in a crosspresentation with both MHC class I and II molecules to prime CD4(+) T-helper and CD8(+) cytotoxic T cells. This review describes an update on the development and use of VLPs as vaccine approaches for HIV.
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Affiliation(s)
- Luigi Buonaguro
- Department of Experimental Oncology, Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori 'Fond Pascale', Via Mariano Semmola 142, 80131 Napoli, Italy
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Krentz HB, Ko K, Beckthold B, Gill MJ. The cost of antiretroviral drug resistance in HIV-positive patients. Antivir Ther 2013; 19:341-8. [DOI: 10.3851/imp2709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2013] [Indexed: 10/25/2022]
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46
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Kim J, Kwon J, Lee D, Jo S, Park DS, Choi J, Park E, Hwang JY, Ko Y, Choi I, Ju MK, Ahn J, Kim J, Han SJ, Kim TH, Cechetto J, Nam J, Ahn S, Sommer P, Liuzzi M, No Z, Lee J. Synthesis and biological evaluation of triazolothienopyrimidine derivatives as novel HIV-1 replication inhibitors. Bioorg Med Chem Lett 2013. [DOI: 10.1016/j.bmcl.2012.10.134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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Yin L, Liu L, Sun Y, Hou W, Lowe AC, Gardner BP, Salemi M, Williams WB, Farmerie WG, Sleasman JW, Goodenow MM. High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology 2012; 9:108. [PMID: 23244298 PMCID: PMC3531307 DOI: 10.1186/1742-4690-9-108] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 11/20/2012] [Indexed: 02/05/2023] Open
Abstract
Background Deep sequencing provides the basis for analysis of biodiversity of taxonomically similar organisms in an environment. While extensively applied to microbiome studies, population genetics studies of viruses are limited. To define the scope of HIV-1 population biodiversity within infected individuals, a suite of phylogenetic and population genetic algorithms was applied to HIV-1 envelope hypervariable domain 3 (Env V3) within peripheral blood mononuclear cells from a group of perinatally HIV-1 subtype B infected, therapy-naïve children. Results Biodiversity of HIV-1 Env V3 quasispecies ranged from about 70 to 270 unique sequence clusters across individuals. Viral population structure was organized into a limited number of clusters that included the dominant variants combined with multiple clusters of low frequency variants. Next generation viral quasispecies evolved from low frequency variants at earlier time points through multiple non-synonymous changes in lineages within the evolutionary landscape. Minor V3 variants detected as long as four years after infection co-localized in phylogenetic reconstructions with early transmitting viruses or with subsequent plasma virus circulating two years later. Conclusions Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.
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Affiliation(s)
- Li Yin
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, 2033 Mowry Road, PO Box 103633, Gainesville, FL 32610-3633, USA.
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Abstract
PURPOSE OF THE REVIEW Changing antiretroviral regimens and the introduction of new antiretroviral drugs have altered drug resistance patterns in human immunodeficiency virus type 1 (HIV-1). This review summarizes recent information on antiretroviral drug resistance. RECENT FINDINGS As tenofovir and abacavir have replaced zidovudine and stavudine in antiretroviral regimens, thymidine analog resistance mutations have become less common in patients failing antiretroviral therapy in developed countries. Similarly, the near universal use of ritonavir-boosted protease inhibitors (PI) in place of unboosted PIs has made the selection of PI resistance mutations uncommon in patients failing a first-line or second-line PI regimen. The challenge of treating patients with multidrug-resistant HIV-1 has largely been addressed by the advent of newer PIs, second-generation non-nucleoside reverse transcriptase inhibitors and drugs in novel classes, including integrase inhibitors and CCR5 antagonists. Resistance to these newer agents can emerge, however, resulting in the appearance of novel drug resistance mutations in the HIV-1 polymerase, integrase and envelope genes. SUMMARY New drugs make possible the effective treatment of multidrug-resistant HIV-1, but the activity of these drugs may be limited by the appearance of novel drug resistance mutations.
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Theys K, Deforche K, Vercauteren J, Libin P, van de Vijver DAMC, Albert J, Åsjö B, Balotta C, Bruckova M, Camacho RJ, Clotet B, Coughlan S, Grossman Z, Hamouda O, Horban A, Korn K, Kostrikis LG, Kücherer C, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stockl E, Riva C, Ruiz L, Liitsola K, Schmit JC, Schuurman R, Sönnerborg A, Stanekova D, Stanojevic M, Struck D, Van Laethem K, Wensing AMJ, Boucher CAB, Vandamme AM. Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients. Retrovirology 2012; 9:81. [PMID: 23031662 PMCID: PMC3487874 DOI: 10.1186/1742-4690-9-81] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The effect of drug resistance transmission on disease progression in the newly infected patient is not well understood. Major drug resistance mutations severely impair viral fitness in a drug free environment, and therefore are expected to revert quickly. Compensatory mutations, often already polymorphic in wild-type viruses, do not tend to revert after transmission. While compensatory mutations increase fitness during treatment, their presence may also modulate viral fitness and virulence in absence of therapy and major resistance mutations. We previously designed a modeling technique that quantifies genotypic footprints of in vivo treatment selective pressure, including both drug resistance mutations and polymorphic compensatory mutations, through the quantitative description of a fitness landscape from virus genetic sequences. RESULTS Genotypic correlates of viral load and CD4 cell count were evaluated in subtype B sequences from recently diagnosed treatment-naive patients enrolled in the SPREAD programme. The association of surveillance drug resistance mutations, reported compensatory mutations and fitness estimated from drug selective pressure fitness landscapes with baseline viral load and CD4 cell count was evaluated using regression techniques. Protease genotypic variability estimated to increase fitness during treatment was associated with higher viral load and lower CD4 cell counts also in treatment-naive patients, which could primarily be attributed to well-known compensatory mutations at highly polymorphic positions. By contrast, treatment-related mutations in reverse transcriptase could not explain viral load or CD4 cell count variability. CONCLUSIONS These results suggest that polymorphic compensatory mutations in protease, reported to be selected during treatment, may improve the replicative capacity of HIV-1 even in absence of drug selective pressure or major resistance mutations. The presence of this polymorphic variation may either reflect a history of drug selective pressure, i.e. transmission from a treated patient, or merely be a result of diversity in wild-type virus. Our findings suggest that transmitted drug resistance has the potential to contribute to faster disease progression in the newly infected host and to shape the HIV-1 epidemic at a population level.
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Affiliation(s)
- Kristof Theys
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Jurgen Vercauteren
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Jan Albert
- Clinical Microbiology, Karolinska University Hospital and Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Birgitta Åsjö
- Section for Microbiology and Immunology, Gade institute, University of Bergen, Bergen, Norway
| | | | - Marie Bruckova
- National Institute of Public Health, Prague, Czech Republic
| | - Ricardo J Camacho
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
- Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Bonaventura Clotet
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari “Germans Trias i Pujol”, Badalona, Spain
| | | | - Zehava Grossman
- Sheba Medical Center, Tel-Hashomer, and School of Public Health, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Andrzei Horban
- Warsaw Medical University and Hospital for Infectious Diseases, Warsaw, Poland
| | - Klaus Korn
- Institut für Klinische und Molekulare Virologie, University of Erlangen, Erlangen, Germany
| | | | | | | | - Dimitrios Paraskevis
- National Retrovirus Reference Center, Department of Hygiene Epidemiology of Medical Statistics, University of Athens, Medical School, Athens, Greece
| | | | | | | | - Lidia Ruiz
- irsiCaixa AIDS Research Institute & Lluita contra la SIDA Foundation, Hospital Universitari “Germans Trias i Pujol”, Badalona, Spain
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Jean-Claude Schmit
- Centre Hospitalier de Luxembourg and Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Anders Sönnerborg
- Divisions of Infectious Diseases and Clinical Virology, Karolinska Institutet, Stockholm, Sweden
| | | | - Maja Stanojevic
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Daniel Struck
- Centre Hospitalier de Luxembourg and Centre de Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Kristel Van Laethem
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Annemarie MJ Wensing
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Charles AB Boucher
- Department of Virology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherland
| | - Anne-Mieke Vandamme
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
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Novel two-round phenotypic assay for protease inhibitor susceptibility testing of recombinant and primary HIV-1 isolates. J Clin Microbiol 2012; 50:3909-16. [PMID: 23015664 DOI: 10.1128/jcm.01636-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antiretroviral drug susceptibility tests facilitate therapeutic management of HIV-1-infected patients. Although genotyping systems are affordable, inaccuracy in the interpretation of complex mutational patterns may limit their usefulness. Currently available HIV-1 phenotypic assays are based on the generation of recombinant viruses in which the specific viral gene of interest, derived from a patient plasma sample, is cloned into a susceptible genetic viral backbone prior to in vitro drug susceptibility evaluation. Nevertheless, in the case of protease inhibitors, not only are mutations in the HIV-1 protease-coding region involved in resistance, but the role of Gag in drug susceptibility has also recently been reported. In order to avoid the inherent limitations resulting from partial cloning of the viral genome, we designed and evaluated a new experimental strategy to test the in vitro susceptibility of primary viral isolates to protease inhibitors. Our protocol, which is based on a two-round infection protocol using the reporter TZM-bl cell line, showed a good correlation with genotypic resistance prediction and with the Antivirogram phenotypic assay, in both protease-recombinant viruses and primary viral isolates. The protocol is suitable for any HIV-1 subtype and enables rapid in-house measurement of protease inhibitor susceptibility, thus making it possible to evaluate the concomitant effects of both patient-derived gag and protease-coding regions.
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