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Burdorf RM, Zhou S, Amon C, Long N, Hill CS, Adams L, Tegha G, Chagomerana MB, Jumbe A, Maliwichi M, Wallie S, Li Y, Swanstrom R, Hosseinipour MC. Impact of Low-Frequency Human Immunodeficiency Virus Type 1 Drug Resistance Mutations on Antiretroviral Therapy Outcomes. J Infect Dis 2024; 230:86-94. [PMID: 39052733 PMCID: PMC11272071 DOI: 10.1093/infdis/jiae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND The association between low-frequency human immunodeficiency virus type 1 (HIV-1) drug resistance mutations (DRMs) and treatment failure (TF) is controversial. We explore this association using next-generation sequencing (NGS) methods that accurately sample low-frequency DRMs. METHODS We enrolled women with HIV-1 in Malawi who were either antiretroviral therapy (ART) naive (cohort A), had ART failure (cohort B), or had discontinued ART (cohort C). At entry, cohorts A and C began a nonnucleoside reverse transcriptase inhibitor-based regimen and cohort B started a protease inhibitor-based regimen. We used Primer ID MiSeq to identify regimen-relevant DRMs in entry and TF plasma samples, and a Cox proportional hazards model to calculate hazard ratios (HRs) for entry DRMs. Low-frequency DRMs were defined as ≤20%. RESULTS We sequenced 360 participants. Cohort B and C participants were more likely to have TF than cohort A participants. The presence of K103N at entry significantly increased TF risk among A and C participants at both high and low frequency, with HRs of 3.12 (95% confidence interval [CI], 1.58-6.18) and 2.38 (95% CI, 1.00-5.67), respectively. At TF, 45% of participants showed selection of DRMs while in the remaining participants there was an apparent lack of selective pressure from ART. CONCLUSIONS Using accurate NGS for DRM detection may benefit an additional 10% of patients by identifying low-frequency K103N mutations.
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Affiliation(s)
- Rachel M Burdorf
- Lineberger Comprehensive Cancer Center
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | | | - Nathan Long
- Lineberger Comprehensive Cancer Center
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | | | - Lily Adams
- Lineberger Comprehensive Cancer Center
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | | | - Maganizo B Chagomerana
- UNC Project–Malawi, Lilongwe
- Department of Medicine, University of North Carolina at Chapel Hill
| | | | | | | | - Yijia Li
- Department of Medicine, University of Pittsburgh Medical Center, Pennsylvania
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill
| | - Mina C Hosseinipour
- UNC Project–Malawi, Lilongwe
- Department of Medicine, University of North Carolina at Chapel Hill
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Raymond S, Jeanne N, Vellas C, Nicot F, Saune K, Ranger N, Latour J, Carcenac R, Harter A, Delobel P, Izopet J. HIV-1 genotypic resistance testing using single molecule real-time sequencing. J Clin Virol 2024; 174:105717. [PMID: 39068746 DOI: 10.1016/j.jcv.2024.105717] [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: 04/26/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND HIV-1 resistance testing is recommended in clinical management and next-generation sequencing (NGS) methods are now available in many virology laboratories. OBJECTIVES To evaluate the diagnostic performance of Long-Read Single Molecule Real-time (SMRT) sequencing (Sequel, PacBio) for HIV-1 polymerase genotyping. STUDY DESIGN 111 prospective clinical samples (83 plasma and 28 leukocyte-enriched blood fraction) were analyzed for routine HIV-1 resistance genotyping using Sanger sequencing, Vela NGS, and SMRT sequencing. We developed a SMRT sequencing protocol and a bio-informatics pipeline to infer antiretroviral resistance on both haplotype and variant calling approaches. RESULTS The polymerase was successfully sequenced by the three platforms in 98 % of plasma RNA samples for viral loads above 4 log copies/mL. The success rate decreased to 83 % using Sanger or Vela sequencing and to 67 % using SMRT sequencing for viral loads of 3 to 4 log copies/mL. Sensitivities of 50 %, 54 % and 61 % were obtained using SMRT, Vela, and Sanger sequencing, respectively, in cellular DNA from patients with prolonged undetectable plasma HIV-1 RNA. Ninety-eight percent of resistance-associated mutations (RAMs) identified with Sanger sequencing were detected using SMRT sequencing. Furthermore, 91 % of RAMs (> 5 % threshold) identified with Vela NGS were detected using SMRT sequencing. RAM quantification using Vela and SMRT sequencing was well correlated (Spearman correlation ρ = 0.82; P < 0.0001). CONCLUSIONS SMRT sequencing of the full-length HIV-1 polymerase appeared performant for characterizing HIV-1 genotypic resistance on both RNA and DNA clinical samples. Long-read sequencing is a new tool for mutation haplotyping and resistance analysis.
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Affiliation(s)
- Stéphanie Raymond
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France.
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Camille Vellas
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Karine Saune
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Noémie Ranger
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Justine Latour
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Pierre Delobel
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Jacques Izopet
- INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse, France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
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Mariani C, Borgonovo F, Gerbi M, Rizzardini G, Capetti AF. Unexpected CD4 decay, hidden adherence gaps, resilience, and the need for long-acting therapy in a single HIV outpatients' cohort. AIDS Care 2024; 36:864-869. [PMID: 38170878 DOI: 10.1080/09540121.2023.2298768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
This single-centre, single-cohort study examines hidden non-adherence to antiretroviral therapy in a setting of persistent optimal viral suppression but concordant absolute and percent CD4 decay by >10% from the previous test. After the finding of important drug holidays in two virologically suppressed patients, between January 2021 and January 2022 all PLWH who fulfilled CD4 decay criteria were asked for how long therapy was interrupted, how many days before re-testing CD4 and HIV RNA was it resumed and the reason for interruption. Of 668 HIV-infected subjects, 61 fulfilled the pre-specified criteria for significant CD4 decay and 15 (2.25% of the total, 25% of the CD4 decay group) admitted long-lasting treatment interruptions, compensated by treatment resumption before the subsequent testing. Eleven treatment interruptions exceeded 28 days, and none was shorter than 15 days. CD4 recovery was worse at 6 months in non-adherent subjects (-0.5 vs + 16/mmc, p < 0.0001) and in non adherence vs immune decay time-related with COVID-19 (0 vs + 22/mmc, p < 0.0001). Reasons for interrupting treatment were travel, psychological, poverty-related, addiction and sentimental sphere problems. Long-acting regimens, with stringent control of precision in timely administration, may protect PLWH from damaging their health status and possibly transmit HIV.
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Affiliation(s)
- Chiara Mariani
- First Division of Infectious Diseases, Luigi Sacco Hospital, Milano, Italy
| | - Fabio Borgonovo
- First Division of Infectious Diseases, Luigi Sacco Hospital, Milano, Italy
| | - Martina Gerbi
- First Division of Infectious Diseases, Luigi Sacco Hospital, Milano, Italy
| | - Giuliano Rizzardini
- First Division of Infectious Diseases, Luigi Sacco Hospital, Milano, Italy
- School of Medicine, Faculty of Health Sciences, University of the Whitwatersrand, Johannesburg, South Africa
| | - Amedeo F Capetti
- First Division of Infectious Diseases, Luigi Sacco Hospital, Milano, Italy
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Nematadzira TG, Murnane PM, Odiase OJ, Bacchetti P, Okochi H, Tallerico R, Chanaiwa VM, Vhembo T, Mutambanengwe-Jacob MT, Louie A, Chipato T, Gandhi M, Stranix-Chibanda L. Antiretroviral Therapy Adherence During and Postbreastfeeding Cessation Measured by Tenofovir Levels in Hair. J Acquir Immune Defic Syndr 2022; 91:237-241. [PMID: 35952357 PMCID: PMC9561228 DOI: 10.1097/qai.0000000000003076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND We examined change in antiretroviral treatment (ART) adherence after breastfeeding (BF) cessation using hair tenofovir (TFV) concentrations as an objective metric of medication consumption. METHODS A subset of postpartum women in Zimbabwe randomized in IMPAACT PROMISE to take ART while BF and post-BF cessation had hair TFV measured longitudinally. Using linear mixed-effect models, we estimated differences in hair TFV levels after BF cessation, accounting for trends in levels over time regardless of BF status and change in slope after breastfeeding cessation. We also estimated the relative risk of viremia (>50 copies/mL) per doubling of hair TFV concentration. RESULTS Among 55 women (median age 26, interquartile range 24-29 years), hair TFV levels (n = 305) were available for a median of 9 visits per woman between 3 and 29 months postpartum. Hair TFV levels ranged from undetected to 0.25 ng/mg (median 0.04 ng/mg). Controlling for trends since delivery [decline of 2.2% per month, 95% confidence interval (CI): -5.3 to 1.0], TFV levels averaged 24.4% higher (95% CI: -5.1 to 63.1) post-BF cessation than during BF, with no change in slope (0.0% per month, 95% CI: -3.8 to 3.9). Postpartum, 42% of women were ever viremic. Higher TFV levels were strongly protective; relative risk of viremia per doubling of TFV was 0.52 (95% CI: 0.43 to 0.63; P < 0.0001). CONCLUSIONS Leveraging an objective metric of ART use, we observed modestly declining adherence across the postpartum period, but no additional decline associated with breastfeeding cessation. High viremia frequency and varying postpartum TFV levels observed highlight the importance of enhanced adherence support with viral load monitoring among postpartum women.
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Affiliation(s)
| | - Pamela M. Murnane
- Institute for Global Health Sciences, University of California-San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California-San Francisco, San Francisco, CA
| | - Osamuedeme J. Odiase
- Hair Analytical Laboratory, University of California-San Francisco, San Francisco, CA; and
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California-San Francisco, San Francisco, CA
| | - Hideaki Okochi
- Hair Analytical Laboratory, University of California-San Francisco, San Francisco, CA; and
| | - Regina Tallerico
- Hair Analytical Laboratory, University of California-San Francisco, San Francisco, CA; and
| | - Vongai M. Chanaiwa
- University of Zimbabwe-Clinical Trials Research Centre, Harare, Zimbabwe
| | - Tichaona Vhembo
- University of Zimbabwe-Clinical Trials Research Centre, Harare, Zimbabwe
| | | | - Alexander Louie
- Hair Analytical Laboratory, University of California-San Francisco, San Francisco, CA; and
| | - Tsungai Chipato
- University of Zimbabwe-Clinical Trials Research Centre, Harare, Zimbabwe
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Monica Gandhi
- Hair Analytical Laboratory, University of California-San Francisco, San Francisco, CA; and
| | - Lynda Stranix-Chibanda
- University of Zimbabwe-Clinical Trials Research Centre, Harare, Zimbabwe
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
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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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HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
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Shorter Time to Discontinuation Due to Treatment Failure in People Living with HIV Switched to Dolutegravir Plus Either Rilpivirine or Lamivudine Compared with Integrase Inhibitor-Based Triple Therapy in a Large Spanish Cohort. Infect Dis Ther 2022; 11:1177-1192. [PMID: 35399147 PMCID: PMC9124284 DOI: 10.1007/s40121-022-00630-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/18/2022] [Indexed: 11/27/2022] Open
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High Level of Pre-Treatment HIV-1 Drug Resistance and Its Association with HLA Class I-Mediated Restriction in the Pumwani Sex Worker Cohort. Viruses 2022; 14:v14020273. [PMID: 35215866 PMCID: PMC8879707 DOI: 10.3390/v14020273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/08/2023] Open
Abstract
Background: We analyzed the prevalence of pre-antiretroviral therapy (ART) drug resistance mutations (DRMs) in a Kenyan population. We also examined whether host HLA class I genes influence the development of pre-ART DRMs. Methods: The HIV-1 proviral DNAs were amplified from blood samples of 266 ART-naïve women from the Pumwani Sex Worker cohort of Nairobi, Kenya using a nested PCR method. The amplified HIV genomes were sequenced using next-generation sequencing technology. The prevalence of pre-ART DRMs was investigated. Correlation studies were performed between HLA class I alleles and HIV-1 DRMs. Results: Ninety-eight percent of participants had at least one DRM, while 38% had at least one WHO surveillance DRM. M184I was the most prevalent clinically important variant, seen in 37% of participants. The DRMs conferring resistance to one or more integrase strand transfer inhibitors were also found in up to 10% of participants. Eighteen potentially relevant (p < 0.05) positive correlations were found between HLA class 1 alleles and HIV drug-resistant variants. Conclusions: High levels of HIV drug resistance were found in all classes of antiretroviral drugs included in the current first-line ART regimens in Africa. The development of DRMs may be influenced by host HLA class I-restricted immunity.
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Abstract
HIV-1 is genetically heterogeneous, having different subtypes and circulating recombinant forms (CRFs). HIV-1 genotyping is used to determine drug resistance profiles and is based on the use of a mixture of consensus and degenerate primers targeting the pol gene. However, the use of this type of primers is associated with either PCR bias or PCR failure. Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) can detect and identify unknown and distantly related gene sequences by PCR. CODEHOPs designed using different HIV-1 subtypes and CRFs were evaluated for HIV-1 genotyping by Sanger and MinION sequencing. A total of 321 plasma samples were used for the validation of CODEHOP-mediated HIV-1 genotyping. CODEHOP-mediated PCR showed 100% sensitivity and specificity, with limits of detection and genotyping below 200 copies/ml. The head-to-head evaluation of CODEHOP-mediated PCR and standard PCR showed 97 to 98% and 82 to 84% PCR success rates, respectively. There was 100% agreement between the CODEHOP and the reference method in the drug resistance profiles determined by Sanger-based sequencing. Using MinION sequencing, the CODEHOP-mediated PCR scheme resulted in better depth of genome coverage and detection of more drug resistance variants in the protease and reverse transcriptase genes than the standard amplification scheme. The overall prevalences of drug resistance mutations were 17.1% in treatment-experienced patients and 1.2% in treatment-naive patients. They were mainly associated with resistance to reverse transcriptase inhibitors and were linked to virological failure and the patient’s treatment history. Findings from this study suggest that the performance of HIV-1 genotyping is improved by using CODEHOP-mediated PCR. IMPORTANCE HIV-1 drug resistance is the main cause of treatment failure. Regular surveillance of resistance-associated mutations in HIV-1 genomes is essential for the optimal management of HIV-1 infections. Due to HIV-1’s genetic diversity, different HIV-1 genotypes are circulating worldwide. Standard primers used in the amplification of HIV-1 RNA have not been designed to cover all HIV-1 genotypes and are the main cause of amplification and drug resistance test failure. In this study, new sets of PCR primers targeting the protease, reverse transcriptase, and integrase genes were designed using the CODEHOP approach. They were compared to primers recommended in part by WHO for drug resistance testing using in-house PCR. Unsuccessful HIV-1 RNA amplification was less likely to occur with CODEHOP primers, leading to fewer test failures and lower cost. Furthermore, CODEHOP primers were more effective than standard primers for the detection of minority resistant variants by MinION sequencing.
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Wagner GJ, Hoffman R, Linnemayr S, Schneider S, Ramirez D, Gordon K, Seelam R, Ghosh-Dastidar B. START (Supporting Treatment Adherence Readiness through Training) Improves Both HIV Antiretroviral Adherence and Viral Reduction, and is Cost Effective: Results of a Multi-site Randomized Controlled Trial. AIDS Behav 2021; 25:3159-3171. [PMID: 33811266 DOI: 10.1007/s10461-021-03188-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2021] [Indexed: 12/11/2022]
Abstract
The START (Supporting Treatment Adherence Readiness through Training) intervention was examined for its effects on ART adherence and virologic suppression relative to usual care. A sample of 176 clients about to start or restart ART were randomized (83 to START, 93 to usual care) at HIV clinics in the Los Angeles area. Primary outcomes included electronically monitored dose-taking adherence and HIV viral load; primary end points were months 6 and 24, with group differences examined using nonresponse-weighted means or proportions, effect sizes, and significance testing. Item nonresponse was addressed using multiple imputation. 166 (94.3%) participants started ART, of whom 124 (74.7%) were still in care at month 6, and 90 (54.2%) at month 24. In comparison to the usual care control group, the START group had higher dose-taking adherence at month 6 (86.2% vs. 71.6%, d = 0.56, p = 0.01), which was sustained through month 24 (86.0% vs. 61.1%, d =1.01, p < 0.0001). While rates of undetectable viral load did not differ between groups at month 6 or 24, the mean reduction in viral load (log10 copies/mm3) at month 24 was significantly greater in the intervention arm (3.0 vs. 2.7; d = 0.40, p = 0.047). An estimated cost of $132 per person was needed to obtain a 10% increase in dose-taking adherence over 24 months from the intervention. These findings suggest that START is cost effective in producing a medium to large effect on dose-taking adherence that is durable over 24 months, and a modest long-term effect on viral reduction.Trial registration Clinicaltrials.gov NCT02329782 (registered December 22, 2014).
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Affiliation(s)
- Glenn J Wagner
- RAND Corporation, 1776 Main St, Santa Monica, CA, 90407, USA.
| | - Risa Hoffman
- UCLA, Department of Medicine, Los Angeles, CA, USA
| | | | - Stefan Schneider
- Long Beach Education and Research Consultants, Long Beach, CA, USA
| | - Daniel Ramirez
- Long Beach Education and Research Consultants, Long Beach, CA, USA
| | - Kyle Gordon
- UCLA, Department of Medicine, Los Angeles, CA, USA
| | - Rachana Seelam
- RAND Corporation, 1776 Main St, Santa Monica, CA, 90407, USA
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Stecher C, Linnemayr S. Promoting antiretroviral therapy adherence habits: a synthesis of economic and psychological theories of habit formation. AIDS 2021; 35:711-716. [PMID: 33306553 PMCID: PMC9207816 DOI: 10.1097/qad.0000000000002792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Siedner MJ, Moorhouse MA, Simmons B, de Oliveira T, Lessells R, Giandhari J, Kemp SA, Chimukangara B, Akpomiemie G, Serenata CM, Venter WDF, Hill A, Gupta RK. Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase. Nat Commun 2020; 11:5922. [PMID: 33262331 PMCID: PMC7708638 DOI: 10.1038/s41467-020-19801-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/28/2020] [Indexed: 12/05/2022] Open
Abstract
Little is known about the impact of pretreatment drug resistance (PDR) on the efficacy of second generation integrase inhibitors. We sequenced pretreatment plasma specimens from the ADVANCE trial (NCT03122262). Our primary outcome was 96-week virologic success, defined as a sustained viral load <1000 copies/mL from 12 weeks onwards, <200 copies/mL from 24 weeks onwards, and <50 copies/mL after 48 weeks. Here we report how this outcome was impacted by PDR, defined by the World Health Organization (WHO) mutation list. Of 1053 trial participants, 874 (83%) have successful sequencing, including 289 (33%) randomized to EFV-based therapy and 585 (67%) randomized to DTG-based therapy. Fourteen percent (122/874) have ≥1 WHO-defined mutation, of which 98% (120/122) are NNRTI mutations. Rates of virologic suppression are lower in the total cohort among those with PDR 65% (73/112) compared to those without PDR (85% [605/713], P < 0.001), and for those on EFV-based treatment (60% [12/20] vs 86% [214/248], P = 0.002) and for those on DTG-based treatment (61/92 [66%] vs 84% [391/465] P < 0.001, P for interaction by regimen 0.49). Results are similar in multivariable models adjusted for clinical characteristics and adherence. NNRTI resistance prior to treatment is associated with long-term failure of integrase inhibitor-containing first-line regimens, and portends high rates of first-line failure in sub Saharan Africa.
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Affiliation(s)
- Mark J Siedner
- Africa Health Research Institute, KwaZulu-Natal, South Africa.
- Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- University of KwaZulu-Natal, Durban, South Africa.
| | - Michelle A Moorhouse
- Ezintsha, Wits Reproductive Health and HIV Institute, University of Witwatersrand, Johannesburg, South Africa
| | - Bryony Simmons
- Department of Infectious Disease, Imperial College, London, UK
| | - Tulio de Oliveira
- University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Richard Lessells
- University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Jennifer Giandhari
- University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | | | - Benjamin Chimukangara
- University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Godspower Akpomiemie
- Ezintsha, Wits Reproductive Health and HIV Institute, University of Witwatersrand, Johannesburg, South Africa
| | - Celicia M Serenata
- Ezintsha, Wits Reproductive Health and HIV Institute, University of Witwatersrand, Johannesburg, South Africa
| | - Willem D F Venter
- Ezintsha, Wits Reproductive Health and HIV Institute, University of Witwatersrand, Johannesburg, South Africa
| | | | - Ravindra K Gupta
- Africa Health Research Institute, KwaZulu-Natal, South Africa.
- University of KwaZulu-Natal, Durban, South Africa.
- University of Cambridge, Cambridge, UK.
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Brooks RA, Nieto O, Swendeman D, Myers J, Lepe RM, Cabral A, Kao U, Donohoe T, Comulada WS. Qualitative Evaluation of Social Media and Mobile Technology Interventions Designed to Improve HIV Health Outcomes for Youth and Young Adults Living With HIV: A HRSA SPNS Initiative. Health Promot Pract 2020; 21:693-704. [PMID: 32757839 PMCID: PMC7646559 DOI: 10.1177/1524839920938704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Youth and young adults living with HIV (YYALH) are less likely to be engaged in HIV care, adhere to their medications, and achieve viral suppression compared to older adult populations. In the United States, the majority of YYALH belong to racial/ethnic, sexual, and gender minority groups. HIV care interventions are needed that specifically target YYALH and that exploit the use of social media and mobile technology (SMMT) platforms, where youth and young adults have a ubiquitous presence. We conducted a qualitative evaluation of SMMT interventions included in a Health Resources and Services Administration Special Projects of National Significance initiative designed to improve medical care engagement, retention, and medication adherence to achieve viral suppression among YYALH. However, in this study, only young adults living with HIV (YALH) ages 18 to 34 years participated. A total of 48 YALH were interviewed. The data were analyzed using thematic analysis and revealed three main themes supporting the usefulness of the SMMT interventions, which included (1) acceptability of SMMT interventions in managing HIV care with subthemes of medical information accessibility, reminders, and self-efficacy; (2) feelings of support and personal connection afforded by SMMT interventions; and (3) SMMT interventions help to alleviate negative feelings about status and mitigate HIV-related stigma. A few participants identified problems with using their respective intervention, primarily related to the functionality of the technologies. Overall, findings from our qualitative evaluation suggest that SMMT-based interventions have the potential to increase engagement and retention in care, support YALH in adhering to medication, and help them adjust to their diagnosis.
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Affiliation(s)
| | - Omar Nieto
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Janet Myers
- University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Uyen Kao
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Thomas Donohoe
- University of California, Los Angeles, Los Angeles, CA, USA
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14
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Martin IB, Read S, Harrigan R, Gomez MP. Treatment Experience and Repeat Pregnancy Impact the Effectiveness of Non-Nucleoside Reverse Transcription Inhibitor-Highly Active Antiretroviral Therapy for the Prevention of Mother to Child Transmission of Human Immunodeficiency Virus. AIDS Res Hum Retroviruses 2020; 36:681-687. [PMID: 32408754 DOI: 10.1089/aid.2019.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-nucleoside reverse transcription inhibitor (NNRTI)-containing antiretroviral therapy (ART) for the prevention of mother to child transmission (PMTCT) of human immunodeficiency virus (HIV) has led to dramatic reductions in perinatal HIV infection in resource-constrained settings. Nonetheless, PMTCT programs are complicated by repeat pregnancies, in which long-term or repeat exposures to PMTCT regimens over time may lead to the acquisition of HIV drug resistance mutations, and consequent treatment failure. In this study, we retrospectively assessed the effectiveness of the NNRTI-based PMTCT protocol from 2008 to 2010 in The Bahamas National HIV/AIDS Program. We show that women who had been in repeat pregnancies and those who were already prescribed ART at conception were at increased risk of virologic failure, relative to treatment-inexperienced women and primigravida, respectively (AOR 3.1, 95% CI: 1.3-7.1, p = .008 and AOR 5.0, 95% CI: 1.8-14.1, p = .002). In addition, women undergoing treatment at conception were more likely to possess HIVDR mutations relative to treatment-naive women (AOR 447.1, 95% CI: 17.9-11,173.5, p = .001). Therefore, individual treatment history is a key metric determining the effectiveness of current and future PMTCT interventions. The implications of this to PMTCT programmatic success in light of the most recent WHO guidelines are discussed.
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Affiliation(s)
| | - Stanley Read
- Department of Paediatrics, University of Toronto Hospital for Sick Kids, Toronto, Canada
| | - Richard Harrigan
- Research Laboratory, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - M. Perry Gomez
- Reference Lab, The Bahamas Ministry of Health, Nassau, Bahamas
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15
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Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping. Viruses 2020; 12:v12070694. [PMID: 32605062 PMCID: PMC7411816 DOI: 10.3390/v12070694] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) is increasingly used for HIV-1 drug resistance genotyping. NGS methods have the potential for a more sensitive detection of low-abundance variants (LAV) compared to standard Sanger sequencing (SS) methods. A standardized threshold for reporting LAV that generates data comparable to those derived from SS is needed to allow for the comparability of data from laboratories using NGS and SS. Ten HIV-1 specimens were tested in ten laboratories using Illumina MiSeq-based methods. The consensus sequences for each specimen using LAV thresholds of 5%, 10%, 15%, and 20% were compared to each other and to the consensus of the SS sequences (protease 4-99; reverse transcriptase 38-247). The concordance among laboratories' sequences at different thresholds was evaluated by pairwise sequence comparisons. NGS sequences generated using the 20% threshold were the most similar to the SS consensus (average 99.6% identity, range 96.1-100%), compared to 15% (99.4%, 88.5-100%), 10% (99.2%, 87.4-100%), or 5% (98.5%, 86.4-100%). The average sequence identity between laboratories using thresholds of 20%, 15%, 10%, and 5% was 99.1%, 98.7%, 98.3%, and 97.3%, respectively. Using the 20% threshold, we observed an excellent agreement between NGS and SS, but significant differences at lower thresholds. Understanding how variation in NGS methods influences sequence quality is essential for NGS-based HIV-1 drug resistance genotyping.
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16
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Chen NY, Kao SW, Liu ZH, Wu TS, Tsai CL, Lin HH, Wong WW, Chang YY, Chen SS, Ku SWW. Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection. Int J Infect Dis 2020; 93:182-191. [PMID: 32061862 DOI: 10.1016/j.ijid.2020.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The clinical utilisation of deep sequencing in HIV treatment has been hindered due to its unknown correlation with standard Sanger genotyping and the undetermined value of minority drug resistance mutation (DRM) detection. OBJECTIVES To compare deep sequencing performance to standard Sanger genotyping with clinical samples, in an effort to delineate the correlation between the results from the two methods and to find the optimal deep sequencing threshold for clinical utilisation. METHODS We conducted a retrospective study using stored plasma collected from August 2014 to March 2018 for HIV genotyping with the commercial Sanger genotyping kit. Samples with available Sanger genotyping reports were further deep sequenced. Drug resistance was interpreted according to the Stanford HIV drug resistance database algorithm. RESULTS At 15-25% minority detection thresholds, 9-15% cases had underestimated DRMs by Sanger sequencing. The concordance between the Sanger and deep sequencing reports was 68-82% in protease-reverse transcriptase region and 88-97% in integrase region at 5-25% thresholds. The undetected drug resistant minority variants by Sanger sequencing contributed to the lower negative predictive value of Sanger genotyping in cases harbouring DRMs. CONCLUSIONS Use of deep sequencing improved detection of antiretroviral resistance mutations especially in cases with virological failure or previous treatment interruption. Deep sequencing with 10-15% detection thresholds may be considered a suitable substitute for Sanger sequencing on antiretroviral DRM detection.
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Affiliation(s)
- Nan-Yu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Shu-Wei Kao
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Zhuo-Hao Liu
- Department of Neurosurgery, Chang Gung Memorial Hospital Linkou Branch, Taiwan
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taiwan
| | - Hsi-Hsun Lin
- General Clinical Research Centre, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Public Health, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wing-Wai Wong
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yea-Yuan Chang
- Division of Infectious Diseases, Department of Internal Medicine, National Yang-Ming University Hospital, Yilan, Taiwan; Institute of Clinical Medicine and AIDS Prevention and Research Centre, National Yang-Ming University, Taipei, Taiwan; Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taiwan
| | - Shu-Sheng Chen
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Stephane Wen-Wei Ku
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taiwan.
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17
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Matías-Florentino M, Chaillon A, Ávila-Ríos S, Mehta SR, Paz-Juárez HE, Becerril-Rodríguez MA, del Arenal-Sánchez SJ, Piñeirúa-Menéndez A, Ruiz V, Iracheta-Hernández P, Macías-González I, Tena-Sánchez J, Badial-Hernández F, González-Rodríguez A, Reyes-Terán G. Pretreatment HIV drug resistance spread within transmission clusters in Mexico City. J Antimicrob Chemother 2020; 75:656-667. [PMID: 31819984 PMCID: PMC7021100 DOI: 10.1093/jac/dkz502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pretreatment HIV drug resistance (HIVDR) to NNRTIs has consistently increased in Mexico City during the last decade. OBJECTIVES To infer the HIV genetic transmission network in Mexico City to describe the dynamics of the local HIV epidemic and spread of HIVDR. PATIENTS AND METHODS HIV pol sequences were obtained by next-generation sequencing from 2447 individuals before initiation of ART at the largest HIV clinic in Mexico City (April 2016 to June 2018). Pretreatment HIVDR was estimated using the Stanford algorithm at a Sanger-like threshold (≥20%). Genetic networks were inferred with HIV-TRACE, establishing putative transmission links with genetic distances <1.5%. We examined demographic associations among linked individuals with shared drug resistance mutations (DRMs) using a ≥ 2% threshold to include low-frequency variants. RESULTS Pretreatment HIVDR reached 14.8% (95% CI 13.4%-16.2%) in the cohort overall and 9.6% (8.5%-10.8%) to NNRTIs. Putative links with at least one other sequence were found for 963/2447 (39%) sequences, forming 326 clusters (2-20 individuals). The inferred network was assortative by age and municipality (P < 0.001). Clustering individuals were younger [adjusted OR (aOR) per year = 0.96, 95% CI 0.95-0.97, P < 0.001] and less likely to include women (aOR = 0.46, 95% CI 0.28-0.75, P = 0.002). Among clustering individuals, 175/963 (18%) shared DRMs (involving 66 clusters), of which 66/175 (38%) shared K103N/S (24 clusters). Eight municipalities (out of 75) harboured 65% of persons sharing DRMs. Among all persons sharing DRMs, those sharing K103N were younger (aOR = 0.93, 95% CI 0.88-0.98, P = 0.003). CONCLUSIONS Our analyses suggest age- and geographically associated transmission of DRMs within the HIV genetic network in Mexico City, warranting continuous monitoring and focused interventions.
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Affiliation(s)
- Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Antoine Chaillon
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Sanjay R Mehta
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Héctor E Paz-Juárez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Manuel A Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Silvia J del Arenal-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Alicia Piñeirúa-Menéndez
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Verónica Ruiz
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Patricia Iracheta-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Israel Macías-González
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Jehovani Tena-Sánchez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Florentino Badial-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Andrea González-Rodríguez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
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18
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Behavioral Economics Incentives to Support HIV Treatment Adherence (BEST): Protocol for a randomized controlled trial in Uganda. Trials 2020; 21:9. [PMID: 31900193 PMCID: PMC6942278 DOI: 10.1186/s13063-019-3795-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 10/11/2019] [Indexed: 11/30/2022] Open
Abstract
Background Many HIV-positive patients do not appropriately adhere to their antiretroviral medication (ART). This leads to higher viral loads and greater probability of HIV transmission. Present bias—a tendency to give in to short-term temptations at the expense of long-term outcomes—is a potential driver of low adherence. In this study we test a novel intervention rooted in behavioral economics that is designed to overcome present bias and increase ART adherence. Methods/design We will enroll 330 HIV-positive patients at Mildmay Hospital in Kampala, Uganda, into a 2-year randomized controlled trial. Participants will be randomized to one of three groups. The first intervention group (T1, n = 110) will be eligible for small lottery prizes based on timely clinic visits and demonstration of viral suppression. Group 2 (T2, n = 110) will be eligible for the same lottery prizes conditional on high adherence measured by a medication event management system (MEMS) cap. The control group (n = 110) will receive the usual standard of care. Adherence will be measured continuously throughout the intervention period and for 12 months post-intervention to evaluate effect persistence. Surveys will be conducted at baseline and then every 6 months. Viral loads will be measured annually. Primary outcomes are whether the viral load is detectable and MEMS-measured adherence. Secondary outcomes are the log-transformed viral load as a continuous measure and a binary measure for whether the person took at least 90% of their ART pills. Discussion Our study is one of the first to investigate the effectiveness of lottery incentives for improving ART adherence, and in addition, it compares the relative efficacy of using electronically measured adherence versus viral load to determine lottery eligibility. MEMS caps are relatively costly, whereas viral load testing is now part of routine clinical care in Uganda. BEST will test whether directly incentivizing viral suppression (which can be implemented using readily available clinic data) is as effective as incentivizing electronically measured adherence. Cost-effectiveness analyses of the two implementation modes will also be performed. Trial registration ClinicalTrials.gov, NCT03494777. Registered on 11 April 2018.
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19
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Raymond S, Nicot F, Pallier C, Bellecave P, Maillard A, Trabaud MA, Morand-Joubert L, Rodallec A, Amiel C, Mourez T, Bocket L, Beby-Defaux A, Bouvier-Alias M, Lambert-Niclot S, Charpentier C, Malve B, Mirand A, Dina J, Le Guillou-Guillemette H, Marque-Juillet S, Signori-Schmuck A, Barin F, Si-Mohamed A, Avettand Fenoel V, Roussel C, Calvez V, Saune K, Marcelin AG, Rodriguez C, Descamps D, Izopet J. Impact of Human Immunodeficiency Virus Type 1 Minority Variants on the Virus Response to a Rilpivirine-Based First-line Regimen. Clin Infect Dis 2019; 66:1588-1594. [PMID: 29244143 DOI: 10.1093/cid/cix1070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Background Minority resistant variants of human immunodeficiency virus type 1 (HIV-1) could influence the virological response to treatment based on nonnucleoside reverse transcriptase inhibitors (NNRTIs). Data on minority rilpivirine-resistant variants are scarce. This study used next-generation sequencing (NGS) to identify patients harboring minority resistant variants to nucleos(t)ide reverse transcriptase inhibitors and NNRTIs and to assess their influence on the virological response (VR). Methods All the subjects, 541 HIV-1-infected patients started a first-line regimen containing rilpivirine. VR was defined as a HIV-1 RNA load <50 copies/mL at month 6 with continued suppression at month 12. NGS was performed at baseline (retrospectively) on the 454 GS-FLX platform (Roche). Results NGS revealed resistance-associated mutations accounting for 1% to <5% of variants in 17.2% of samples, for 5%-20% in 5.7% of samples, and for >20% in 29% of samples. We identified 43 (8.8%) and 36 (7.4%) patients who harbored rilpivirine-resistant variants with a 1% sensitivity threshold according to the French National Agency for Research on AIDS and Viral Hepatitis and Stanford algorithms, respectively. The VR was 96.9% at month 12. Detection of minority rilpivirine resistant variants was not associated with virological failure (VF). Multivariate analysis indicated that VF at month 12 was associated with a CD4 count <250 cells/µL at baseline, a slower decrease in viral load at month 3, and rilpivirine resistance at baseline using the Stanford algorithm with a 20% threshold. Conclusions Minority resistant variants had no impact on the VR of treatment-naive patients to a rilpivirine-based regimen.
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Affiliation(s)
- Stéphanie Raymond
- Institut national de la santé et de la recherche médicale (INSERM).,Université de Toulouse, Université Paul Sabatier, Physiopathology Center of Toulouse-Purpan
| | - Florence Nicot
- Laboratoire de Virologie, Centre Hospitalier Universitaire (CHU) de Toulouse
| | | | | | | | - Mary Anne Trabaud
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon
| | | | | | | | | | | | | | | | | | - Charlotte Charpentier
- Infection, Antimicrobials, Modelling, Evolution, Unité Mixte de Recherche 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Assistance Publique-Hôpitaux de Paris.,Laboratoire de Virologie, Hôpital Bichat-Claude Bernard
| | | | | | | | | | | | | | | | | | | | | | - Vincent Calvez
- Laboratoire de Virologie, Hôpital de la Pitié-Salpêtrière
| | - Karine Saune
- Institut national de la santé et de la recherche médicale (INSERM).,Université de Toulouse, Université Paul Sabatier, Physiopathology Center of Toulouse-Purpan
| | | | | | - Diane Descamps
- Infection, Antimicrobials, Modelling, Evolution, Unité Mixte de Recherche 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Assistance Publique-Hôpitaux de Paris.,Laboratoire de Virologie, Hôpital Bichat-Claude Bernard
| | - Jacques Izopet
- Institut national de la santé et de la recherche médicale (INSERM).,Université de Toulouse, Université Paul Sabatier, Physiopathology Center of Toulouse-Purpan
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20
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Raymond S, Nicot F, Carcenac R, Lefebvre C, Jeanne N, Saune K, Delobel P, Izopet J. HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform. J Antimicrob Chemother 2019; 73:1152-1157. [PMID: 29444253 DOI: 10.1093/jac/dky003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/29/2017] [Indexed: 11/12/2022] Open
Abstract
Objectives To evaluate the diagnostic performance of the Vela next-generation sequencing (NGS) system in conjunction with the Sentosa SQ HIV Genotyping Assay for genotyping HIV-1. Methods Plasma RNA was extracted and templates prepared with the Sentosa SX instrument before sequencing the HIV-1 polymerase on the Sentosa SQ301 Sequencer (PGM IonTorrent). The Vela NGS System was compared with direct sequencing and the 454 GS-FLX (Roche) and MiSeq (Illumina) systems for genotypic resistance testing on clinical samples. Results The Vela NGS system detected majority resistance mutations in subtype B and CRF02-AG samples at 500 copies/mL and minority variants with a sensitivity of 5% at 100 000 copies/mL. The Vela NGS system and direct sequencing identified resistance mutations with 97% concordance in 46 clinical samples. Vela identified 1/20 of the 1%-5% mutations identified by 454, 5/12 of the 5%-20% mutations and 60/61 of the >20% mutations. Vela identified 3/14 of the 1%-5% mutations identified by MiSeq, 0/2 of the 5%-20% mutations and 47/47 of the >20% mutations. The resistance mutation quantifications by Vela and 454 were concordant (bias: 2.31%), as were those by Vela and MiSeq (bias: 1.06%). Conclusions The Vela NGS system provides automated nucleic acid extraction, PCR reagent distribution, library preparation and bioinformatics analysis. The analytical performance was very good when compared with direct sequencing, but was less sensitive than two other NGS platforms for detecting minority variants.
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Affiliation(s)
- Stéphanie Raymond
- INSERM, U1043, Toulouse F-31300, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Caroline Lefebvre
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Karine Saune
- INSERM, U1043, Toulouse F-31300, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
| | - Pierre Delobel
- INSERM, U1043, Toulouse F-31300, France.,Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse F-31300, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse F-31300, France
| | - Jacques Izopet
- INSERM, U1043, Toulouse F-31300, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse F-31300, France
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Hassan AS, Bibby DF, Mwaringa SM, Agutu CA, Ndirangu KK, Sanders EJ, Cane PA, Mbisa JL, Berkley JA. Presence, persistence and effects of pre-treatment HIV-1 drug resistance variants detected using next generation sequencing: A Retrospective longitudinal study from rural coastal Kenya. PLoS One 2019; 14:e0210559. [PMID: 30759103 PMCID: PMC6373901 DOI: 10.1371/journal.pone.0210559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 12/27/2018] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The epidemiology of HIV-1 drug resistance (HIVDR) determined by Sanger capillary sequencing, has been widely studied. However, much less is known about HIVDR detected using next generation sequencing (NGS) methods. We aimed to determine the presence, persistence and effect of pre-treatment HIVDR variants detected using NGS in HIV-1 infected antiretroviral treatment (ART) naïve participants from rural Coastal Kenya. METHODS In a retrospective longitudinal study, samples from HIV-1 infected participants collected prior [n = 2 time-points] and after [n = 1 time-point] ART initiation were considered. An ultra-deep amplicon-based NGS assay, calling for nucleotide variants at >2.0% frequency of viral population, was used. Suspected virologic failure (sVF) was defined as a one-off HIV-1 viral load of >1000 copies/ml whilst on ART. RESULTS Of the 50 eligible participants, 12 (24.0% [95% CI: 13.1-38.2]) had at least one detectable pre-treatment HIVDR variant against Protease Inhibitors (PIs, n = 6 [12%]), Nucleoside Reverse Transcriptase Inhibitors (NRTIs, n = 4 [8.0%]) and Non-NRTIs (n = 3 [6.0%]). Overall, 15 pre-treatment resistance variants were detected (frequency, range: 2.3-92.0%). A positive correlation was observed between mutation frequency and absolute load for NRTI and/or NNRTI variants (r = 0.761 [p = 0.028]), but not for PI variants (r = -0.117 [p = 0.803]). Participants with pre-treatment NRTI and/or NNRTI resistance had increased odds of sVF (OR = 6.0; 95% CI = 1.0-36.9; p = 0.054). CONCLUSIONS Using NGS, pre-treatment resistance variants were common, though observed PI variants were unlikely transmitted, but rather probably generated de novo. Even when detected from a low frequency, pre-treatment NRTI and/or NNRTI resistance variants may adversely affect treatment outcomes.
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Affiliation(s)
| | - David F. Bibby
- Virus Reference Department, Public Health England, London, United Kingdom
| | | | | | | | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, United Kingdom
| | - Patricia A. Cane
- Virus Reference Department, Public Health England, London, United Kingdom
| | - Jean L. Mbisa
- Virus Reference Department, Public Health England, London, United Kingdom
| | - James A. Berkley
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, United Kingdom
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22
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Fedonin GG, Fantin YS, Favorov AV, Shipulin GA, Neverov AD. VirGenA: a reference-based assembler for variable viral genomes. Brief Bioinform 2019; 20:15-25. [PMID: 28968771 PMCID: PMC6488938 DOI: 10.1093/bib/bbx079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Characterization of the within-host genetic diversity of viral pathogens is required for selection of effective treatment of some important viral infections, e.g. HIV, HBV and HCV. Despite the technical ability of detection, there are conflicting data regarding the clinical significance of low-frequency variants, partially because of the difficulty of their distinguishing from experimental artifacts. The issue of cross-contamination is relevant for all highly sensitive techniques, including deep sequencing: even trace contamination leads to a significant increase of false positives in identified SNVs. Determination of infections by multiple genotypes of some viruses, the incidence of which can be considerable, especially in risk groups, is also clinically significant in some cases. We developed a new viral reference-guided assembler, VirGenA, that can separate mixtures of strains of different intraspecies genetic groups (genotypes, subtypes, clades, etc.) and assemble a separate consensus sequence for each group in a mixture. It produced long assemblies for mixture components of extremely low frequencies (<1%) allowing detection of cross-contamination of samples by divergent genotypes. We tested VirGenA on both clinical and simulated data. On both types of data, VirGenA shows better or similar results than the existing de novo assemblers. Cross-platform implementation (including source code) is freely available at https://github.com/gFedonin/VirGenA/releases.
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Affiliation(s)
- Gennady G Fedonin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Yury S Fantin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Alexnader V Favorov
- Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University
| | - German A Shipulin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Alexey D Neverov
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
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23
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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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van Zyl G, Bale MJ, Kearney MF. HIV evolution and diversity in ART-treated patients. Retrovirology 2018; 15:14. [PMID: 29378595 PMCID: PMC5789667 DOI: 10.1186/s12977-018-0395-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/18/2018] [Indexed: 12/21/2022] Open
Abstract
Characterizing HIV genetic diversity and evolution during antiretroviral therapy (ART) provides insights into the mechanisms that maintain the viral reservoir during ART. This review describes common methods used to obtain and analyze intra-patient HIV sequence data, the accumulation of diversity prior to ART and how it is affected by suppressive ART, the debate on viral replication and evolution in the presence of ART, HIV compartmentalization across various tissues, and mechanisms for the emergence of drug resistance. It also describes how CD4+ T cells that were likely infected with latent proviruses prior to initiating treatment can proliferate before and during ART, providing a renewable source of infected cells despite therapy. Some expanded cell clones carry intact and replication-competent proviruses with a small fraction of the clonal siblings being transcriptionally active and a source for residual viremia on ART. Such cells may also be the source for viral rebound after interrupting ART. The identical viral sequences observed for many years in both the plasma and infected cells of patients on long-term ART are likely due to the proliferation of infected cells both prior to and during treatment. Studies on HIV diversity may reveal targets that can be exploited in efforts to eradicate or control the infection without ART.
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Affiliation(s)
- Gert van Zyl
- Division of Medical Virology, Stellenbosch University and NHLS Tygerberg, Cape Town, South Africa
| | - Michael J Bale
- HIV Dynamic and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA
| | - Mary F Kearney
- HIV Dynamic and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA.
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25
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Stella-Ascariz N, Arribas JR, Paredes R, Li JZ. The Role of HIV-1 Drug-Resistant Minority Variants in Treatment Failure. J Infect Dis 2017; 216:S847-S850. [PMID: 29207001 DOI: 10.1093/infdis/jix430] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) drug resistance genotyping is recommended to help in the selection of antiretroviral therapy and to prevent virologic failure. There are several ultrasensitive assays able to detect HIV-1 drug-resistance minority variants (DRMVs) not detectable by standard population sequencing-based HIV genotyping assays. Presence of these DRMVs has been shown to be clinically relevant, but its impact does not appear to be uniform across drug classes. In this review, we summarize key evidence for the clinical impact of DRMVs across drug classes for both antiretroviral treatment-naive and antiretroviral treatment-experienced patients, and highlight areas where more supporting evidence is needed.
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Affiliation(s)
| | - José Ramón Arribas
- HIV Unit, Internal Medicine Service, Hospital Universitario La Paz-IdiPAZ
| | - Roger Paredes
- HIV Unit and irsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona and Universitat de Vic-UCC, Spain
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School
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26
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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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27
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Moderate levels of pre-therapy drug resistance (PDR) in a generalised epidemic: time for better first-line ART? AIDS 2017; 31:2387-2391. [PMID: 28857824 DOI: 10.1097/qad.0000000000001629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND The WHO-recommended first-line antiretroviral therapy (ART) as a fixed dose combination (FDC) of efavirenz (EFV) and tenofovir disoproxil fumarate (TDF) with lamivudine (3TC) or emtricitabine (FTC) has been preferred in the large scale unprecedented ART roll out in Southern Africa. Models and recent reports suggest that pre-ART
HIV drug resistance (PDR) is increasing with high treatment coverage. METHOD We therefore investigated PDR and any local transmission clusters in a setting where high treatment coverage was further enhanced by universal test and treat (UTT). Surveillance drug resistance mutations (SDRMs) were identified with an in-house PCR and population sequencing method and calibrated population resistance (CPR) tool. RESULTS Of 60 patients, six (10%) had an SDRM mutation: five (8.3%) had nonnucleoside reverse transcriptase (NNRT) mutations, one had an nucleos(t)ide reverse transcriptase inhibitor mutation and none had protease inhibitor (PI) mutations. Phylogenetic analysis revealed no large transmission clusters. CONCLUSION An increase to the current moderate PDR levels and the better tolerability and durability, may support a recent drive to avail FDC integrase strand transfer inhibitor (ISTI)-based regimens as the new preferred first-line ART in the Southern African region for individual benefit and to contribute to limiting transmission of infection and drug resistant virus.
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28
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Gag P2/NC and pol genetic diversity, polymorphism, and drug resistance mutations in HIV-1 CRF02_AG- and non-CRF02_AG-infected patients in Yaoundé, Cameroon. Sci Rep 2017; 7:14136. [PMID: 29074854 PMCID: PMC5658410 DOI: 10.1038/s41598-017-14095-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/29/2017] [Indexed: 12/21/2022] Open
Abstract
In HIV-1 subtype-B, specific mutations in Gag cleavage sites (CS) are associated with treatment failure, with limited knowledge among non-B subtypes. We analyzed non-B HIV-1 gag and pol (protease/reverse-transcriptase) sequences from Cameroonians for drug resistance mutations (DRMs) in the gag P2/NC CS, and pol major DRMs. Phylogeny of the 141 sequences revealed a high genetic diversity (12 subtypes): 67.37% CRF02_AG versus 32.6% non-CRF02_AG. Overall, 7.3% transmitted and 34.3% acquired DRMs were found, including M184V, thymidine analogue mutations (T215F, D67N, K70R, K219Q), NNRTIs (L100I, Y181C, K103N, V108I, Y188L), and PIs (V82L). Twelve subjects [10 with HIV-1 CRF02_AG, 8 treatment-naïve and 4 on 3TC-AZT-NVP] showed 3 to 4 mutations in the Gag P2/NC CS: S373Q/T/A, A374T/S/G/N, T375S/A/N/G, I376V, G381S, and R380K. Subjects with or without Gag P2/NC CS mutations showed no significant difference in viral loads. Treatment-naïve subjects harboring NRTI-DRMs had significantly lower CD4 cells than those with NRTI-DRMs on ART (p = 0.042). Interestingly, two subjects had major DRMs to NRTIs, NNRTIs, and 4 mutations in the Gag P2/NC CS. In this prevailing CRF02_AG population with little exposure to PIs (~3%), mutations in the Gag P2/NC CS could increase the risk of treatment failure if there is increased use of PIs-based therapy.
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Linnemayr S, Huang H, Luoto J, Kambugu A, Thirumurthy H, Haberer JE, Wagner G, Mukasa B. Text Messaging for Improving Antiretroviral Therapy Adherence: No Effects After 1 Year in a Randomized Controlled Trial Among Adolescents and Young Adults. Am J Public Health 2017; 107:1944-1950. [PMID: 29048966 DOI: 10.2105/ajph.2017.304089] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES To assess the effectiveness of Short Message Service (SMS) reminder messages on antiretroviral and cotrimoxazole prophylaxis adherence among HIV-positive youths as well as the relative effectiveness of SMS with and without a response option. METHODS Eligible HIV-positive patients aged 15 to 22 years at 2 HIV clinics in Kampala, Uganda, participated in a year-long parallel individual-randomized controlled trial and were assigned in a 1-to-1-to-1 ratio to a weekly SMS message group, weekly SMS message with response option group, or a usual-care control group. RESULTS We enrolled 332 participants. Electronically measured mean adherence was 67% in the control group, 64% in the 1-way SMS group (95% confidence interval [CI] = 0.77, 1.14), and 61% in the 2-way SMS group (95% CI = 0.75, 1.12) in an intent-to-treat analysis. Results for secondary outcomes and complete-case analysis were similarly statistically insignificant across groups. CONCLUSIONS Despite previous evidence that interventions using SMS reminders can promote antiretroviral therapy adherence, this study shows that they are not always effective in achieving behavior change. More research is needed to find out for whom, and under what conditions, they can be beneficial. TRIAL REGISTRATION ClinicalTrials.gov identifier: NCT00830622.
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Affiliation(s)
- Sebastian Linnemayr
- Sebastian Linnemayr, Jill Luoto, and Glenn Wagner are with the RAND Corporation, Santa Monica, CA. Haijing Huang is with the Pardee RAND Graduate School, Santa Monica. Andrew Kambugu is with Infectious Diseases Institute and Makerere University, Kampala, Uganda. Harsha Thirumurthy is with Department of Health Policy and Management and Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Jessica E. Haberer is with Massachusetts General Hospital Center for Global Health and Harvard Medical School, Boston, MA. Barbara Mukasa is with Mildmay Uganda, Kampala
| | - Haijing Huang
- Sebastian Linnemayr, Jill Luoto, and Glenn Wagner are with the RAND Corporation, Santa Monica, CA. Haijing Huang is with the Pardee RAND Graduate School, Santa Monica. Andrew Kambugu is with Infectious Diseases Institute and Makerere University, Kampala, Uganda. Harsha Thirumurthy is with Department of Health Policy and Management and Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Jessica E. Haberer is with Massachusetts General Hospital Center for Global Health and Harvard Medical School, Boston, MA. Barbara Mukasa is with Mildmay Uganda, Kampala
| | - Jill Luoto
- Sebastian Linnemayr, Jill Luoto, and Glenn Wagner are with the RAND Corporation, Santa Monica, CA. Haijing Huang is with the Pardee RAND Graduate School, Santa Monica. Andrew Kambugu is with Infectious Diseases Institute and Makerere University, Kampala, Uganda. Harsha Thirumurthy is with Department of Health Policy and Management and Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Jessica E. Haberer is with Massachusetts General Hospital Center for Global Health and Harvard Medical School, Boston, MA. Barbara Mukasa is with Mildmay Uganda, Kampala
| | - Andrew Kambugu
- Sebastian Linnemayr, Jill Luoto, and Glenn Wagner are with the RAND Corporation, Santa Monica, CA. Haijing Huang is with the Pardee RAND Graduate School, Santa Monica. Andrew Kambugu is with Infectious Diseases Institute and Makerere University, Kampala, Uganda. Harsha Thirumurthy is with Department of Health Policy and Management and Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Jessica E. Haberer is with Massachusetts General Hospital Center for Global Health and Harvard Medical School, Boston, MA. Barbara Mukasa is with Mildmay Uganda, Kampala
| | - Harsha Thirumurthy
- Sebastian Linnemayr, Jill Luoto, and Glenn Wagner are with the RAND Corporation, Santa Monica, CA. Haijing Huang is with the Pardee RAND Graduate School, Santa Monica. Andrew Kambugu is with Infectious Diseases Institute and Makerere University, Kampala, Uganda. Harsha Thirumurthy is with Department of Health Policy and Management and Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Jessica E. Haberer is with Massachusetts General Hospital Center for Global Health and Harvard Medical School, Boston, MA. Barbara Mukasa is with Mildmay Uganda, Kampala
| | - Jessica E Haberer
- Sebastian Linnemayr, Jill Luoto, and Glenn Wagner are with the RAND Corporation, Santa Monica, CA. Haijing Huang is with the Pardee RAND Graduate School, Santa Monica. Andrew Kambugu is with Infectious Diseases Institute and Makerere University, Kampala, Uganda. Harsha Thirumurthy is with Department of Health Policy and Management and Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Jessica E. Haberer is with Massachusetts General Hospital Center for Global Health and Harvard Medical School, Boston, MA. Barbara Mukasa is with Mildmay Uganda, Kampala
| | - Glenn Wagner
- Sebastian Linnemayr, Jill Luoto, and Glenn Wagner are with the RAND Corporation, Santa Monica, CA. Haijing Huang is with the Pardee RAND Graduate School, Santa Monica. Andrew Kambugu is with Infectious Diseases Institute and Makerere University, Kampala, Uganda. Harsha Thirumurthy is with Department of Health Policy and Management and Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Jessica E. Haberer is with Massachusetts General Hospital Center for Global Health and Harvard Medical School, Boston, MA. Barbara Mukasa is with Mildmay Uganda, Kampala
| | - Barbara Mukasa
- Sebastian Linnemayr, Jill Luoto, and Glenn Wagner are with the RAND Corporation, Santa Monica, CA. Haijing Huang is with the Pardee RAND Graduate School, Santa Monica. Andrew Kambugu is with Infectious Diseases Institute and Makerere University, Kampala, Uganda. Harsha Thirumurthy is with Department of Health Policy and Management and Gillings School of Global Public Health at the University of North Carolina at Chapel Hill. Jessica E. Haberer is with Massachusetts General Hospital Center for Global Health and Harvard Medical School, Boston, MA. Barbara Mukasa is with Mildmay Uganda, Kampala
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HIV-1 Drug Resistance by Ultra-Deep Sequencing Following Short Course Zidovudine, Single-Dose Nevirapine, and Single-Dose Tenofovir with Emtricitabine for Prevention of Mother-to-Child Transmission. J Acquir Immune Defic Syndr 2017; 73:384-389. [PMID: 27327263 PMCID: PMC5172515 DOI: 10.1097/qai.0000000000001116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Supplemental Digital Content is Available in the Text. Antiretroviral drug resistance following pMTCT strategies remains a significant problem. With rapid advancements in next generation sequencing technologies, there is more focus on HIV drug-resistant variants of low frequency, or the so-called minority variants. In South Africa, AZT monotherapy for pMTCT, similar to World Health Organization option A, has been used since 2008. In 2010, a single dose of co-formulated TDF/FTC was included in the strategy for prevention of resistance conferred by single-dose nevirapine (sd NVP). The study was conducted in KwaZulu-Natal, South Africa, among pMTCT participants who received AZT monotherapy from 14 weeks of gestation, intrapartum AZT and sd NVP, and postpartum sd TDF/FTC. Twenty-six specimens collected at 6 weeks post-delivery were successfully sequenced using 454 ultra-deep sequencing. Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance was detected in 17 of 26 (65%) patients, 2 (7%) had Thymidine analogue mutations, and 3 (11%) had K65R. Of the 17 patients with NNRTI resistance, 11 (65%) had high-level NNRTI resistance, whereas 6 (35%) had intermediate NNRTI resistance. The levels of NNRTI resistance are much higher than would be expected, given the inclusion of antepartum AZT and postpartum TDF/FTC. This high level of NNRTI resistance could impact future NNRTI-containing treatment for a large proportion of pMTCT-exposed women. The detection of Thymidine analogue mutations highlights the need to understand the clinical impact of these on AZT-containing antiretroviral treatment in women exposed to AZT monotherapy.
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Steegen K, Carmona S, Bronze M, Papathanasopoulos MA, van Zyl G, Goedhals D, MacLeod W, Sanne I, Stevens WS. Moderate Levels of Pre-Treatment HIV-1 Antiretroviral Drug Resistance Detected in the First South African National Survey. PLoS One 2016; 11:e0166305. [PMID: 27907009 PMCID: PMC5132262 DOI: 10.1371/journal.pone.0166305] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/26/2016] [Indexed: 11/29/2022] Open
Abstract
Background In order to assess the level of transmitted and/or pre-treatment antiretroviral drug resistance to HIV-1, the World Health Organization (WHO) recommends that regular surveys are conducted. This study’s objective was to assess the frequency of HIV-1 antiretroviral drug resistance in patients initiating antiretroviral treatment (ART) in the public sector throughout South Africa. Methods A prospective cross-sectional survey was conducted using probability proportional to size sampling. This method ensured that samples from each province were proportionally collected, based on the number of patients receiving ART in each region. Samples were collected between March 2013 and October 2014. Pol sequences were obtained using RT-PCR and Sanger sequencing and submitted to the Stanford Calibrated Population Resistance tool v6.0. Results A total of 277 sequences were available for analysis. Most participants were female (58.8%) and the median age was 34 years (IQR: 29–42). The median baseline CD4-count was 149 cells/mm3 (IQR: 62–249) and, based on self-reporting, participants had been diagnosed as HIV-positive approximately 44 days prior to sample collection (IQR: 23–179). Subtyping revealed that 98.2% were infected with HIV-1 subtype C. Overall, 25 out of 277 patients presented with ≥1 surveillance drug resistance mutation (SDRM, 9.0%, 95% CI: 6.1–13.0%). Non-nucleoside reverse transcriptase inhibitor (NNRTI) mutations were the most numerous mutations detected (n = 23). Only two patients presented with a protease inhibitor (PI) mutation. In four patients ≥4 SDRMs were detected, which might indicate that these patients were not truly ART-naïve or were infected with a multi-resistant virus. Conclusions These results show that the level of antiretroviral drug resistance in ART-naïve South Africans has reached moderate levels, as per the WHO classification. Therefore, regular surveys of pre-treatment drug resistance levels in all regions of South Africa is highly recommended to monitor the changing levels of pre-treatment antiretroviral drug resistance.
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Affiliation(s)
- Kim Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Sergio Carmona
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Michelle Bronze
- National Health Laboratory Services, Johannesburg, South Africa
| | - Maria A. Papathanasopoulos
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Gert van Zyl
- National Health Laboratory Services, Johannesburg, South Africa
- Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa
| | - Dominique Goedhals
- National Health Laboratory Services, Johannesburg, South Africa
- Department of Medical Microbiology and Virology, University of the Free State, Bloemfontein, South Africa
| | - William MacLeod
- Center for Global Health and Development, Boston University School of Public Health, Boston, Massachusetts, United States of America
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ian Sanne
- Right to Care, Johannesburg, South Africa
| | - Wendy S. Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
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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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Darcissac E, Nacher M, Adriouch L, Berlioz-Arthaud A, Boukhari R, Couppié P, Djossou F, Donato D, El Guedj M, Lavergne A, Papot E, Pouliquen JF, Tanguy E, Vantilcke V, Lacoste V. HIV-1 Pol Gene Polymorphism and Antiretroviral Resistance Mutations in Treatment-Naive Adult Patients in French Guiana Between 2006 and 2012. AIDS Res Hum Retroviruses 2016; 32:801-11. [PMID: 27009561 DOI: 10.1089/aid.2016.0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Little information is available on the molecular epidemiologic profile of HIV-1 in French Guiana, the French department with the highest HIV/AIDS incidence. To follow the evolution of HIV-1 diversity, we carried out a molecular analysis of HIV-1 isolates from 305 treatment-naive patients between 2006 and 2012. Protease and reverse-transcriptase sequences were obtained for subtype characterization, polymorphism analysis, and identification of drug resistance mutations. Of 305 HIV-1 strains, 95.1% were subtype B viruses. The overall prevalence of transmitted drug-resistance mutations (TDRMs) was 4.6% (14/305), ranging from 1.9% to 7.1% depending on the year. This study shows a low level of HIV-1 genetic diversity and a moderate prevalence of TDRMs with no evidence of an increasing trend over the study period. Nevertheless, the strong genetic polymorphism observed on both genes may be of concern for long-term treatment of people living with HIV-1 and thus deserves continuous monitoring.
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Affiliation(s)
- Edith Darcissac
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Mathieu Nacher
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
- Centre d'Investigation Clinique—Epidemiologie Clinique (CIC-EC) Antilles Guyane, INSERM CIE 802, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Leila Adriouch
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Alain Berlioz-Arthaud
- Laboratoire de Biologie Médicale, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Rachida Boukhari
- Service de Biologie Médicale, Centre Hospitalier de l'Ouest Guyanais “Franck Joly,” Saint Laurent du Maroni, Guyane Française
| | - Pierre Couppié
- Service de Dermatologie, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Felix Djossou
- Unité des Maladies Infectieuses et Tropicales, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Damien Donato
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Myriam El Guedj
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Emmanuelle Papot
- Service de Dermatologie, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Jean-François Pouliquen
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Edouard Tanguy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Vincent Vantilcke
- Hôpital de Jour Adultes, Centre Hospitalier de l'Ouest Guyanais “Franck Joly,” Saint Laurent du Maroni, Guyane Française
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
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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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Hawkins C, Ulenga N, Liu E, Aboud S, Mugusi F, Chalamilla G, Sando D, Aris E, Carpenter D, Fawzi W. HIV virological failure and drug resistance in a cohort of Tanzanian HIV-infected adults. J Antimicrob Chemother 2016; 71:1966-74. [PMID: 27076106 DOI: 10.1093/jac/dkw051] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/05/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES There are few data on ART failure rates and drug resistance from Tanzania, where there is a wide diversity of non-B HIV subtypes. We assessed rates and predictors of virological failure in HIV-infected Tanzanians and describe drug resistance patterns in a subgroup of these patients. METHODS ART-naive, HIV-1-infected adults enrolled in a randomized controlled trial between November 2006 and 2008 and on ≥24 weeks of first-line NNRTI-containing ART were included. Population-based genotyping of HIV-1 protease and reverse transcriptase was performed on stored plasma from patients with virological failure (viral load >1000 copies/mL at ≥24 weeks of ART) and at baseline, where available. RESULTS A total of 2403 patients [median (IQR) age 37 (32-43) years; 70% female] were studied. The median (IQR) baseline CD4+ T cell count was 128 (62-190) cells/μL. Predominant HIV subtypes were A, C and D (92.2%). The overall rate of virological failure was 14.9% (95% CI 13.2%-16.1%). In adjusted analyses, significant predictors of virological failure were lower CD4+ T cell count (P = 0.01) and non-adherence to ART (P < 0.01). Drug resistance mutations were present in 87/115 samples (75.7%); the most common were M184V/I (52.2%) and K103N (35%). Thymidine analogue mutations were uncommon (5.2%). The prevalence of mutations in 45 samples pre-ART was 22%. CONCLUSIONS High levels of early ART failure and drug resistance were observed among Tanzanian HIV-1-infected adults enrolled in a well-monitored study. Initiating treatment early and ensuring optimal adherence are vital for the success and durability of first-line ART in these settings.
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Affiliation(s)
- Claudia Hawkins
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nzovu Ulenga
- Management and Development for Health, Dar es Salaam, Tanzania Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Enju Liu
- Departments of Nutrition, Epidemiology, Biostatistics, and Global Health and Population, Harvard School of Public Health, Boston, MA, USA
| | - Said Aboud
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ferdinand Mugusi
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - David Sando
- Management and Development for Health, Dar es Salaam, Tanzania
| | - Eric Aris
- Management and Development for Health, Dar es Salaam, Tanzania
| | | | - Wafaie Fawzi
- Department of Global Health and Population, Harvard School of Public Health, Boston, MA, USA
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Van Dyke RB, Patel K, Kagan RM, Karalius B, Traite S, Meyer WA, Tassiopoulos KK, Seage GR, Seybolt LM, Burchett S, Hazra R, Lurie RH, Yogev R, Sanders MA, Malee K, Hunter S, Shearer W, Paul M, Cooper N, Harris L, Purswani M, Baig M, Cintron A, Puga A, Navarro S, Garvie P, Blood J, Burchett S, Karthas N, Kammerer B, Wiznia A, Burey M, Nozyce M, Dieudonne A, Bettica L, Adubato S, Chen J, Bulkley MG, Ivey L, Grant M, Knapp K, Allison K, Wilkins M, Acevedo-Flores M, Rios H, Olivera V, Silio M, Jones M, Sirois P, Spector S, Norris K, Nichols S, McFarland E, Katai A, Dunn J, Paul S, Scott G, Bryan P, Willen E. Antiretroviral Drug Resistance Among Children and Youth in the United States With Perinatal HIV. Clin Infect Dis 2016; 63:133-137. [PMID: 27056398 DOI: 10.1093/cid/ciw213] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/28/2016] [Indexed: 11/13/2022] Open
Abstract
Among 234 US youths with perinatal human immunodeficiency virus, 75% had antiretroviral resistance, substantially higher than that of the reference laboratory overall (36%-44%). Resistance to newer antiretrovirals and to all antiretrovirals in a class was uncommon. The only factor independently associated with future resistance was a higher peak viral load.
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Affiliation(s)
- Russell B Van Dyke
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Kunjal Patel
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ron M Kagan
- Focus Diagnostics, a Quest Diagnostics Subsidiary, San Juan Capistrano, California
| | - Brad Karalius
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Shirley Traite
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | | | - George R Seage
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lorna M Seybolt
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans
| | - Sandra Burchett
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Rohan Hazra
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland
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Bezabhe WM, Chalmers L, Bereznicki LR, Peterson GM. Adherence to Antiretroviral Therapy and Virologic Failure: A Meta-Analysis. Medicine (Baltimore) 2016; 95:e3361. [PMID: 27082595 PMCID: PMC4839839 DOI: 10.1097/md.0000000000003361] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The often cited need to achieve ≥95% (nearly perfect) adherence to antiretroviral therapy (ART) for successful virologic outcomes in HIV may present a barrier to initiation of therapy in the early stages of HIV. This meta-analysis synthesized 43 studies (27,905 participants) performed across >26 countries, to determine the relationship between cut-off point for optimal adherence to ART and virologic outcomes. Meta-analysis was performed using a random-effect model to calculate pooled odds ratios with corresponding 95% confidence intervals. The mean rate of patients reporting optimal adherence was 63.4%. Compared with suboptimal adherence, optimal adherence was associated with a lower risk of virologic failure (0.34; 95% CI: 0.26-0.44). There were no significant differences in the pooled odds ratios among different optimal adherence thresholds (≥98-100%, ≥95%, ≥80-90%). Study design (randomized controlled trial vs observational study) (regression coefficient 0.74, 95% CI: 0.04-1.43, P < 0.05) and study region (developing vs developed countries; regression coefficient 0.56, 95% CI: 0.01-1.12, P < 0.05) remained as independent predictors of between-study heterogeneity, with more patients with optimal adherence from developing countries or randomized controlled trials experiencing virologic failure. The threshold for optimal adherence to achieve better virologic outcomes appears to be wider than the commonly used cut-off point (≥95% adherence). The cut-off point for optimal adherence could be redefined to a slightly lower level to encourage the prescribing ART at an early stage of HIV infection.
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HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China. PLoS One 2016; 11:e0149215. [PMID: 26895182 PMCID: PMC4760947 DOI: 10.1371/journal.pone.0149215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
Objective Determine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF). Methods 29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels. Results DS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×104 c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1–4% and 24 (60%) at levels of 5–19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS. Conclusions DS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects.
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Tambuyzer L, Thys K, Hoogstoel A, Nijs S, Tomaka F, Opsomer M, De Meyer S, Vingerhoets J. Assessment of etravirine resistance in HIV-1-infected paediatric patients using population and deep sequencing: final results of the PIANO study. Antivir Ther 2015; 21:317-27. [PMID: 26566161 DOI: 10.3851/imp3011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND We assessed etravirine resistance in treatment-experienced, HIV-1-infected children (n=41)/adolescents (n=60) who received twice-daily etravirine 5.2 mg/kg and a background regimen (boosted protease inhibitor plus nucleoside/nucleotide reverse transcriptase inhibitors, optional enfuvirtide/raltegravir) in a Phase II, open-label, multicentre trial (PIANO). METHODS In addition to phenotypes, viral genotypes were assessed by population and deep sequencing (PS and DS) in virological failures (VFs; baseline and end point) and responders (baseline). Minority resistance-associated mutations (RAMs) were defined as those with frequencies above 1% and not detected with PS. RESULTS By week 48, 41/101 (40.6%) patients experienced VF; 17/41 (41.5%) VFs and 22/54 (40.8%) responders had ≥1 baseline etravirine RAM by PS, mainly A98G, K101E, V106I and G190A. Baseline minority etravirine RAMs (n) were detected in 8/40 VFs (V90I [2], A98G [1], L100I [1], V106I [1], E138G [1] and Y181C [2]) and 5/38 responders (V90I [3], A98G [1], V106I [1] and E138G [1]). The most frequent emerging non-nucleoside reverse transcriptase inhibitor RAMs detected by PS (≥3 VFs; n) were the etravirine RAMs Y181C (8), V90I (3), L100I (3) and E138A (3). In 15 of 29 (51.7%) VFs with baseline DS/PS and end point PS data, ≥1 emerging etravirine RAM was detected by PS, which was not detected at baseline by DS in most cases (12/15 [80.0%]). In 10/26 (38.5%) VFs with baseline/end point DS data, ≥1 additional emerging minority etravirine RAM was detected. CONCLUSIONS Patterns of etravirine resistance in adults, adolescents and children experiencing VF are similar. The presence of minority etravirine RAMs at baseline was not consistently associated with treatment failure. ClinicalTrials.gov: NCT00665847.
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Van Eygen V, Thys K, Van Hove C, Rimsky LT, De Meyer S, Aerssens J, Picchio G, Vingerhoets J. Deep sequencing analysis of HIV-1 reverse transcriptase at baseline and time of failure in patients receiving rilpivirine in the phase III studies ECHO and THRIVE. J Med Virol 2015; 88:798-806. [PMID: 26412111 DOI: 10.1002/jmv.24395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 11/10/2022]
Abstract
Minority variants (1.0-25.0%) were evaluated by deep sequencing (DS) at baseline and virological failure (VF) in a selection of antiretroviral treatment-naïve, HIV-1-infected patients from the rilpivirine ECHO/THRIVE phase III studies. Linkage between frequently emerging resistance-associated mutations (RAMs) was determined. DS (llIumina®) and population sequencing (PS) results were available at baseline for 47 VFs and time of failure for 48 VFs; and at baseline for 49 responders matched for baseline characteristics. Minority mutations were accurately detected at frequencies down to 1.2% of the HIV-1 quasispecies. No baseline minority rilpivirine RAMs were detected in VFs; one responder carried 1.9% F227C. Baseline minority mutations associated with resistance to other non-nucleoside reverse transcriptase inhibitors (NNRTIs) were detected in 8/47 VFs (17.0%) and 7/49 responders (14.3%). Baseline minority nucleoside/nucleotide reverse transcriptase inhibitor (NRTI) RAMs M184V and L210W were each detected in one VF (none in responders). At failure, two patients without NNRTI RAMs by PS carried minority rilpivirine RAMs K101E and/or E138K; and five additional patients carried other minority NNRTI RAMs V90I, V106I, V179I, V189I, and Y188H. Overall at failure, minority NNRTI RAMs and NRTI RAMs were found in 29/48 (60.4%) and 16/48 VFs (33.3%), respectively. Linkage analysis showed that E138K and K101E were usually not observed on the same viral genome. In conclusion, baseline minority rilpivirine RAMs and other NNRTI/NRTI RAMs were uncommon in the rilpivirine arm of the ECHO and THRIVE studies. DS at failure showed emerging NNRTI resistant minority variants in seven rilpivirine VFs who had no detectable NNRTI RAMs by PS.
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Affiliation(s)
| | - Kim Thys
- Janssen Infectious Diseases BVBA, Beerse, Belgium
| | | | | | | | | | - Gaston Picchio
- Janssen Research and Development, Titusville, New Jersey
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Abstract
PURPOSE OF REVIEW The review discusses new technologies for the sensitive detection of HIV drug resistance, with a focus on applications in antiretroviral treatment (ART)-naïve populations. RECENT FINDINGS Conventional sequencing is well established for detecting HIV drug resistance in routine care and guides optimal treatment selection in patients starting ART. Access to conventional sequencing is nearly universal in Western countries, but remains limited in Asia, Latin America, and Africa. Technological advances now allow detection of resistance with greatly improved sensitivity compared with conventional sequencing, variably increasing the yield of resistance testing in ART-naïve populations. There is strong cumulative evidence from retrospective studies that sensitive detection of resistant mutants in baseline plasma samples lacking resistance by conventional sequencing more than doubles the risk of virological failure after starting efavirenz-based or nevirapine-based ART. SUMMARY Sensitive resistance testing methods are mainly confined to research applications and in this context have provided great insight into the dynamics of drug resistance development, persistence, and transmission. Adoption in care settings is becoming increasingly possible, although important challenges remain. Platforms for diagnostic use must undergo technical improvements to ensure good performance and ease of use, and clinical validation is required to ensure utility.
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Clinical value of ultradeep HIV-1 genotyping and tropism testing in late presenters with advanced disease. AIDS 2015; 29:1493-504. [PMID: 26244389 DOI: 10.1097/qad.0000000000000748] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE This article aims to investigate if the detection of preexisting drug-resistant minority variant (DRMV) and/or X4 HIV-1 variants could improve the efficacy of first-line combined antiretroviral therapy (ART) in late presenters. DESIGN Post-hoc, combined analysis of two open-label, prospective, randomized clinical trials comparing first-line ART with efavirenz (EFV) vs. ritonavir-boosted protease inhibitor (PI/r)-based regimens in ART-naive, HIV-1-infected patients, with CD4 T-cell counts less than 100 cells/μl and wild-type HIV-1 by bulk sequencing. METHODS Pre-ART samples were reanalyzed for the presence of DRMVs and X4 HIV-1 using 454 sequencing. Kaplan-Meier curves and Cox regression were used to evaluate the association between X4 HIV and DRMVs and risk of virological failure. RESULTS From 141 evaluable patients, 57 received EFV, and 84 received PI/r, including first-line ART. Median pre-ART CD4 T-cell counts and HIV-1 RNA levels were 39 cells/μl and 257 424 copies/ml, respectively; 35.5% of patients had X4 HIV variants. Detection of DRMVs leading to an ART-specific cumulative HIVdb score of at least 10 increased the risk of virological failure in patients initiating EFV [log-rank P = 0.048, hazard ratio = 4.3 (95% confidence interval: 0.8, 25.0), P = 0.074], but not in those starting PI/r. Presence of X4 HIV did not affect virological outcomes, but was associated with impaired CD4 T-cell count recovery over 2 years (214 vs. 315 cells/μl with X4 vs. R5 HIV-1 tropism, respectively, P = 0.017). CONCLUSION Accounting for preexisting DRMVs may improve the outcomes of first-line nonnucleoside reverse transcriptase inhibitor-based ART in late presenters with advanced immune suppression. Presence of X4 HIV-1 at diagnosis predicts impaired immune restoration under ART.
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Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, Rinke de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CAB, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HHM, van de Vijver DAMC, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JPA, Vandamme AM, Shafer RW. Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. PLoS Med 2015; 12:e1001810. [PMID: 25849352 PMCID: PMC4388826 DOI: 10.1371/journal.pmed.1001810] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 02/27/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes. METHODS AND FINDINGS We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05-1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06-1.25), North America (OR = 1.19; 95% CI: 1.12-1.26), Europe (OR = 1.07; 95% CI: 1.01-1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12-1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92-1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs—K101E, K103N, Y181C, and G190A—accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling. CONCLUSIONS Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen.
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Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, California, United States of America. Leuven—University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Jose Luis Blanco
- Hospital Clinic Universitari-Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Michael R Jordan
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Jonathan Taylor
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Philippe Lemey
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Vici Varghese
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Raph L Hamers
- Department of Global Health and Internal Medicine, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | | | - Tobias F Rinke de Wit
- Department of Global Health and Internal Medicine, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | | | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Radko Avi
- Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Santiago Avila-Rios
- National Institute of Respiratory Diseases, Centre for Research in Infectious Diseases, Mexico City, Mexico
| | - Pascal O Bessong
- HIV/AIDS & Global Health Research Programme, Department of Microbiology, University of Venda, Thohoyandou, South Africa
| | - James I Brooks
- National HIV and Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Charles A B Boucher
- Department of Viroscience, Erasmus Medical Centre, Erasmus University, Rotterdam, Netherlands
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael P Busch
- Blood Systems Research Institute, San Francisco, California, United States of America
| | | | - Marie-Laure Chaix
- Laboratoire de Virologie, Hôpital Saint Louis, Université Paris Diderot, INSERM U941, Paris, France
| | - Bum Sik Chin
- Center for Infectious Diseases, National Medical Center, Seoul, Republic of Korea
| | | | - Cillian F De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Anne Derache
- Department of Virology, Pitie-Salpetriere Hospital, Paris, France
| | - Diane Descamps
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris Hôpital Bichat-Claude Bernard, INSERM UMR 1137, Université Paris Diderot, Paris, France
| | - Alaka K Deshpande
- Department of Medicine, Grant Medical College and Sir Jamshedjee Jeejeebhoy Group of Hospitals, Mumbai, India
| | - Cyrille F Djoko
- Global Viral Cameroon, Intendance Round About, EMAT/CRESAR, Yaoundé, Cameroon
| | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Herve Fleury
- Laboratoire de Virologie, Centre Hospitalier Universitaire de Bordeaux, CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Pierre Frange
- Microbiology Department, Hôpital Necker-Enfants Malades, Paris, France
| | - Seiichiro Fujisaki
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Junko Hattori
- National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Africa Holguin
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Gillian M Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Hiroshi Ichimura
- Department of Viral Infection and International Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - David Katzenstein
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | | | - Jerome H Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sung Soon Kim
- Division of AIDS, Korea National Institute of Health, Osong, Chungcheongbuk-do, Republic of Korea
| | - Yanpeng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Irja Lutsar
- Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Kee Peng Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ramesh S Paranjape
- National AIDS Research Institute, Indian Council of Medical Research, Pune, India
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, 34394 Montpellier, France; Computational Biology Institute, Montpellier, France
| | - Mario Poljak
- Institute of Microbiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Matt A Price
- Department of Medical Affairs, International AIDS Vaccine Initiative, New York, New York, United States of America; Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, California, United States of America
| | | | - Gustavo Reyes-Terán
- National Institute of Respiratory Diseases, Centre for Research in Infectious Diseases, Mexico City, Mexico
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | | | - Davey M Smith
- University of California San Diego, La Jolla, California, United States of America
| | | | - Vincent V Soriano
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain
| | | | - Maja Stanojevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Wataru Sugiura
- National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | | | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hong-Ha M Truong
- Department of Medicine, University of California, San Francisco, California, United States of America
| | | | - Nicole Vidal
- Institut de Recherche pour le Développement, University of Montpellier 1, Montpellier, France
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rongge Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Gonzalo Yebra
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - John P A Ioannidis
- Stanford Prevention Research Center, Department of Medicine, Stanford University, Stanford, California, United States of America; Meta-Research Innovation Center at Stanford, Stanford University, Stanford, California, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium; Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, California, United States of America
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DeJesus E, Fätkenheuer G, Orrell C, Wang C, Jones J, Craig C, Tawadrous M, Heera J. Efficacy and safety of lersivirine versus etravirine for the treatment of HIV-1 infection in patients with prior non-nucleoside reverse transcriptase inhibitor (NNRTI) use and evidence of NNRTI resistance: a randomized phase 2B trial. HIV CLINICAL TRIALS 2014; 15:209-17. [PMID: 25350959 DOI: 10.1310/hct1505-209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To assess the efficacy and safety of lersivirine versus etravirine in patients with HIV-1 and prior non-nucleoside reverse transcriptase inhibitor (NNRTI) use and evidence of NNRTI resistance. METHODS In this 96-week, phase 2b study, 97 patients were randomized and treated with lersivirine 750 mg qd (n = 31), lersivirine 1,000 mg qd (n = 32), and etravirine 200 mg bid (n = 34), plus one optimized nucleoside reverse transcriptase inhibitor and darunavir/ritonavir 600/100 mg bid. The primary endpoint was the percentage of patients with HIV-1 RNA <50 copies/mL at week 24. RESULTS At week 24, HIV-1 RNA <50 copies/mL was achieved by fewer patients receiving lersivirine 750 mg (48.4%) and 1,000 mg (43.8%) qd compared with etravirine 200 mg qd (67.7%) (intention to treat [ITT], missing/switch/discontinuation equals failure [MSDF]). At week 48, HIV-1 RNA <50 copies/mL and <400 copies/mL were also achieved by fewer patients receiving lersivirine 750 mg (41.9% and 41.9%, respectively) and 1,000 mg (31.3% and 34.4%, respectively) qd compared with etravirine 200 mg bid (61.8% and 70.6%, respectively) (ITT, MSDF). Least squares means (SE) change from baseline in log transformed HIV-1 RNA at week 48 was -1.42 (0.27) and -0.95 (0.28) copies/mL for lersivirine 750 mg and 1,000 mg qd, respectively, versus -2.02 (0.26) copies/mL for etravirine 200 mg bid (ITT). Lersivirine and etravirine were generally safe and well-tolerated. CONCLUSIONS Lersivirine 750 mg and 1,000 mg qd was associated with lower rates of viral suppression at week 24 and week 48 versus etravirine in patients with prior NNRTI use and evidence of NNRTI resistance. No new safety signals were detected.
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Affiliation(s)
| | - Gerd Fätkenheuer
- First Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Catherine Orrell
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Faculty of Health Sciences, Cape Town, South Africa
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Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure. J Clin Virol 2014; 62:48-53. [PMID: 25542470 DOI: 10.1016/j.jcv.2014.11.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/22/2014] [Accepted: 11/08/2014] [Indexed: 11/21/2022]
Abstract
BACKGROUND Next generation sequencing (NGS) allows the detection of minor variant HIV drug resistance mutations (DRMs). However data from new NGS platforms after Prevention-of-Mother-to-Child-Transmission (PMTCT) regimen failure are limited. OBJECTIVE To compare major and minor variant HIV DRMs with Illumina MiSeq and Life Technologies Ion Personal Genome Machine (PGM) in infants infected despite a PMTCT regimen. STUDY DESIGN We conducted a cross-sectional study of NGS for detecting DRMs in infants infected despite a zidovudine (AZT) and Nevirapine (NVP) regimen, before initiation of combination antiretroviral therapy. Sequencing was performed on PCR products from plasma samples on PGM and MiSeq platforms. Bioinformatic analyses were undertaken using a codon-aware version of the Smith-Waterman mapping algorithm and a mixture multinomial error filtering statistical model. RESULTS Of 15 infants, tested at a median age of 3.4 months after birth, 2 (13%) had non-nucleoside reverse transcriptase inhibitor (NNRTI) DRMs (K103N and Y181C) by bulk sequencing, whereas PGM detected 4 (26%) and MiSeq 5 (30%). NGS enabled the detection of additional minor variant DRMs in the infant with K103N. Coverage and instrument quality scores were higher with MiSeq, increasing the confidence of minor variant calls. CONCLUSIONS NGS followed by bioinformatic analyses detected multiple minor variant DRMs in HIV-1 RT among infants where PMTCT failed. The high coverage of MiSeq and high read quality improved the confidence of identified DRMs and may make this platform ideal for minor variant detection.
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Minority drug-resistant HIV-1 variants in treatment naïve East-African and Caucasian patients detected by allele-specific real-time PCR. PLoS One 2014; 9:e111042. [PMID: 25333961 PMCID: PMC4205091 DOI: 10.1371/journal.pone.0111042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/28/2014] [Indexed: 11/19/2022] Open
Abstract
Objective To assess the presence of two major non-nucleoside reverse transcriptase inhibitors (NNRTI) drug resistance mutations (DRMs), Y181C and K103N, in minor viral quasispecies of treatment naïve HIV-1 infected East-African and Swedish patients by allele-specific polymerase chain reaction (AS-PCR). Methods Treatment naïve adults (n = 191) with three epidemiological backgrounds were included: 92 Ethiopians living in Ethiopia; 55 East-Africans who had migrated to Sweden; and 44 Caucasians living in Sweden. The pol gene was analysed by standard population sequencing and by AS-PCR for the detection of Y181C and K103N. Results The Y181C was detected in the minority quasispecies of six Ethiopians (6.5%), in two Caucasians (4.5%), and in one East-African (1.8%). The K103N was detected in one East- African (1.8%), by both methods. The proportion of mutants ranged from 0.25% to 17.5%. Additional DRMs were found in all three treatment naïve patient groups by population sequencing. Conclusions Major NNRTI mutations can be found by AS-PCR in minor quasispecies of treatment naïve HIV-1 infected Ethiopians living in Ethiopia, in East-African and Caucasian patients living in Sweden in whom population sequencing reveal wild-type virus only. Surveys with standard sequencing are likely to underestimate transmitted drug resistance and the presence of resistant minor quasispecies in treatment naïve patients should be topic for future large scale studies.
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Cozzi-Lepri A, Noguera-Julian M, Di Giallonardo F, Schuurman R, Däumer M, Aitken S, Ceccherini-Silberstein F, D'Arminio Monforte A, Geretti AM, Booth CL, Kaiser R, Michalik C, Jansen K, Masquelier B, Bellecave P, Kouyos RD, Castro E, Furrer H, Schultze A, Günthard HF, Brun-Vezinet F, Paredes R, Metzner KJ. Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing. J Antimicrob Chemother 2014; 70:930-40. [PMID: 25336166 PMCID: PMC4319483 DOI: 10.1093/jac/dku426] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objectives It is still debated if pre-existing minority drug-resistant HIV-1 variants (MVs) affect the virological outcomes of first-line NNRTI-containing ART. Methods This Europe-wide case–control study included ART-naive subjects infected with drug-susceptible HIV-1 as revealed by population sequencing, who achieved virological suppression on first-line ART including one NNRTI. Cases experienced virological failure and controls were subjects from the same cohort whose viraemia remained suppressed at a matched time since initiation of ART. Blinded, centralized 454 pyrosequencing with parallel bioinformatic analysis in two laboratories was used to identify MVs in the 1%–25% frequency range. ORs of virological failure according to MV detection were estimated by logistic regression. Results Two hundred and sixty samples (76 cases and 184 controls), mostly subtype B (73.5%), were used for the analysis. Identical MVs were detected in the two laboratories. 31.6% of cases and 16.8% of controls harboured pre-existing MVs. Detection of at least one MV versus no MVs was associated with an increased risk of virological failure (OR = 2.75, 95% CI = 1.35–5.60, P = 0.005); similar associations were observed for at least one MV versus no NRTI MVs (OR = 2.27, 95% CI = 0.76–6.77, P = 0.140) and at least one MV versus no NNRTI MVs (OR = 2.41, 95% CI = 1.12–5.18, P = 0.024). A dose–effect relationship between virological failure and mutational load was found. Conclusions Pre-existing MVs more than double the risk of virological failure to first-line NNRTI-based ART.
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Affiliation(s)
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA IrsiCaixa i Unitat VIH, Universitat Autònoma de Barcelona, Universitat de Vic, Catalonia, Spain
| | - Francesca Di Giallonardo
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Rob Schuurman
- Department of Virology, University Medical Centre, Utrecht, The Netherlands
| | - Martin Däumer
- Institut für Immunologie und Genetik, Kaiserslautern, Germany
| | - Sue Aitken
- Department of Virology, University Medical Centre, Utrecht, The Netherlands
| | | | - Antonella D'Arminio Monforte
- Department of Health Sciences, Clinic of Infectious Diseases, 'San Paolo' Hospital, University of Milan, Milan, Italy
| | - Anna Maria Geretti
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Clare L Booth
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Claudia Michalik
- Competence Network for HIV/AIDS, Bochum, Germany and Clinic for Dermatology, Venerology and Allergology of the Ruhr-Universität, Bochum, Germany Clinical Trial Centre (ZKS), University of Cologne, Cologne, Germany
| | - Klaus Jansen
- Competence Network for HIV/AIDS, Bochum, Germany and Clinic for Dermatology, Venerology and Allergology of the Ruhr-Universität, Bochum, Germany
| | - Bernard Masquelier
- Laboratoire de Virologie, CHU de Bordeaux and MFP-UMR5234, Université Bordeaux 2, Bordeaux, France
| | - Pantxika Bellecave
- Laboratoire de Virologie, CHU de Bordeaux and MFP-UMR5234, Université Bordeaux 2, Bordeaux, France
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Erika Castro
- Addiction Medicine, Service of Community Psychiatry, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Roger Paredes
- Institut de Recerca de la SIDA IrsiCaixa i Unitat VIH, Universitat Autònoma de Barcelona, Universitat de Vic, Catalonia, Spain
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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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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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Pou C, Noguera-Julian M, Pérez-Álvarez S, García F, Delgado R, Dalmau D, Álvarez-Tejado M, Gonzalez D, Sayada C, Chueca N, Pulido F, Ibáñez L, Rodríguez C, Casadellà M, Santos JR, Ruiz L, Clotet B, Paredes R. Improved prediction of salvage antiretroviral therapy outcomes using ultrasensitive HIV-1 drug resistance testing. Clin Infect Dis 2014; 59:578-88. [PMID: 24879788 DOI: 10.1093/cid/ciu287] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The clinical relevance of ultrasensitive human immunodeficiency virus type 1 (HIV-1) genotypic resistance testing in antiretroviral treatment (ART)-experienced individuals remains unknown. METHODS This was a retrospective, multicentre, cohort study in ART-experienced, HIV-1-infected adults who initiated salvage ART including, at least 1 ritonavir-boosted protease inhibitor, raltegravir or etravirine. Presalvage ART Sanger and 454 sequencing of plasma HIV-1 were used to generate separate genotypic sensitivity scores (GSS) using the HIVdb, ANRS, and REGA algorithms. Virological failure (VF) was defined as 2 consecutive HIV-1 RNA levels ≥200 copies/mL at least 12 weeks after salvage ART initiation, whereas subjects remained on the same ART. The ability of Sanger and 454-GSS to predict VF was assessed by receiver operating characteristic (ROC) curves and survival analyses. RESULTS The study included 132 evaluable subjects; 28 (21%) developed VF. Using HIVdb, 454 predicted VF better than Sanger sequencing in the ROC curve analysis (area under the curve: 0.69 vs 0.60, Delong test P = .029). Time to VF was shorter for subjects with 454-GSS < 3 vs 454-GSS ≥ 3 (Log-rank P = .003) but not significantly different between Sanger-GSS < 3 and ≥3. Factors independently associated with increased risk of VF in multivariate Cox regression were a 454-GSS < 3 (HR = 4.6, 95 CI, [1.5, 14.0], P = .007), and the number of previous antiretrovirals received (HR = 1.2 per additional drug, 95 CI, [1.1, 1.3], P = .001). Equivalent findings were obtained with the ANRS and REGA algorithms. CONCLUSIONS Ultrasensitive HIV-1 genotyping improves GSS-based predictions of virological outcomes of salvage ART relative to Sanger sequencing. This may improve the clinical management of ART-experienced subjects living with HIV-1. CLINICAL TRIALS REGISTRATION NCT01346878.
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Affiliation(s)
- Christian Pou
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic
| | - Susana Pérez-Álvarez
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Federico García
- Microbiology and Molecular Biology Department, Hospital Universitario San Cecilio, Granada
| | - Rafael Delgado
- Laboratory of Molecular Microbiology, Instituto de Investigación Biomedica Hospital 12 de Octubre (i + 12), Madrid
| | - David Dalmau
- HIV/AIDS Department, Hospital Universitari MútuaTerrassa Universitat de Barcelona, Terrassa
| | | | | | - Chalom Sayada
- ABL SA, Barcelona, Spain ABL SA, Luxembourg, Luxembourg
| | - Natalia Chueca
- Microbiology and Molecular Biology Department, Hospital Universitario San Cecilio, Granada
| | - Federico Pulido
- Laboratory of Molecular Microbiology, Instituto de Investigación Biomedica Hospital 12 de Octubre (i + 12), Madrid
| | - Laura Ibáñez
- HIV/AIDS Department, Hospital Universitari MútuaTerrassa
| | - Cristina Rodríguez
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Maria Casadellà
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - José R Santos
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Lidia Ruiz
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute - HIVACAT, Hospital Universitari Germans Trias i Pujol, Badalona Universitat Autònoma de Barcelona, Cerdanyola del Vallès Universitat de Vic-Universitat Central de Catalunya, Vic HIV Unit, Internal Medicine Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
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