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Planinić A, Begovac J, Rokić F, Šimičić P, Oroz M, Jakovac K, Vugrek O, Zidovec-Lepej S. Characterization of Human Immunodeficiency Virus-1 Transmission Clusters and Transmitted Drug-Resistant Mutations in Croatia from 2019 to 2022. Viruses 2023; 15:2408. [PMID: 38140649 PMCID: PMC10747707 DOI: 10.3390/v15122408] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection is challenging due to the highly diverse HIV-genome. We investigated the genetic diversity and prevalence of transmitted drug resistance (TDR) followed by phylogenetic analysis in 270 HIV-1 infected, treatment-naïve individuals from Croatia in the period 2019-2022. The results of this research confirmed a high overall prevalence of TDR of 16.7%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTIs (NNRTIs), and protease inhibitors (PIs) was found in 9.6%, 7.4%, and 1.5% of persons, respectively. No resistance to integrase strand-transfer inhibitors (INSTIs) was found. Phylogenetic analysis revealed that 173/229 sequences (75.5%) were part of transmission clusters, and the largest identified was T215S, consisting of 45 sequences. Forward transmission was confirmed in several clusters. We compared deep sequencing (DS) with Sanger sequencing (SS) on 60 randomly selected samples and identified additional surveillance drug resistance mutations (SDRMs) in 49 of them. Our data highlight the need for baseline resistance testing in treatment-naïve persons. Although no major INSTIs were found, monitoring of SDRMs to INSTIs should be continued due to the extensive use of first- and second-generation INSTIs.
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Affiliation(s)
- Ana Planinić
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
| | - Josip Begovac
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Filip Rokić
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Petra Šimičić
- Department of Oncology and Nuclear Medicine, Sestre Milosrdnice University Hospital Center, 10000 Zagreb, Croatia;
| | - Maja Oroz
- Cytogenetic Laboratory, Department of Obstetrics and Gynecology, Clinical Hospital Sveti Duh, 10000 Zagreb, Croatia;
| | - Katja Jakovac
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Oliver Vugrek
- Ruđer Bošković Institute, 10000 Zagreb, Croatia; (F.R.); (K.J.); (O.V.)
| | - Snjezana Zidovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases Dr. Fran Mihaljević, 10000 Zagreb, Croatia;
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2
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Hui S, Chen F, Li Y, Cui Y, Zhang J, Zhang L, Yang Y, Liu Y, Zhao Y, Lv F. Factors Associated With Newly HIV Infection and Transmitted Drug Resistance Among Men Who Have Sex With Men in Harbin, P.R. China. Front Public Health 2022; 10:860171. [PMID: 35719611 PMCID: PMC9201057 DOI: 10.3389/fpubh.2022.860171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
Background This study aimed to evaluate HIV incidence, factors associated with HIV incidence and transmitted drug resistance (TDR) among newly infected men who have sex with men (MSM) in Harbin, P.R. China. Methods A cohort study was conducted among MSM in Harbin during 2013 and 2018, with a follow-up frequency of every 6 months. Blood samples from MSM were tested for HIV antibodies, RNA was extracted from plasma, and the pol gene was sequenced, and genotypic drug-resistance analyses were performed. Results From 2013 to 2018, the overall rate of HIV incidence was 3.55/100 PY. Syphilis infection, unprotected sex with men in the past 6 months, and unawareness of HIV/AIDS knowledge were risk factors for HIV seroconversion. The distribution of HIV genotypes was as follows: CRF01_AE, 57.1%; CRF07_BC, 28.5%; CRF55_01B, 2.0%; B, 8.2%. The prevalence of transmitted drug resistance was 4.08%. Conclusion HIV incidence in MSM in Harbin is moderately high, and transmitted drug resistance exists in the population.
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Affiliation(s)
- Shan Hui
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China.,Heilongjiang Provincial Center for Disease Control and Prevention, Harbin, China
| | - Fangfang Chen
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Li
- Heilongjiang Provincial Center for Disease Control and Prevention, Harbin, China
| | - Yan Cui
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jinhui Zhang
- Jixi Municipal Center for Disease Control and Prevention, Harbin, China
| | - Ling Zhang
- Harbin Municipal Center for Disease Control and Prevention, Harbin, China
| | - Yisi Yang
- Harbin Municipal Center for Disease Control and Prevention, Harbin, China
| | - Yanlin Liu
- Harbin Municipal Center for Disease Control and Prevention, Harbin, China
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Fan Lv
- Chinese Center for Disease Control and Prevention, Beijing, China
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3
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Guo C, Wu Y, Zhang Y, Liu X, Li A, Gao M, Zhang T, Wu H, Chen G, Huang X. Transmitted Drug Resistance in Antiretroviral Therapy-Naive Persons With Acute/Early/Primary HIV Infection: A Systematic Review and Meta-Analysis. Front Pharmacol 2021; 12:718763. [PMID: 34899288 PMCID: PMC8652085 DOI: 10.3389/fphar.2021.718763] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background: The widespread use of antiretroviral therapy (ART) has raised concerns about the emergence of HIV transmitted drug resistance (TDR). Acute HIV infection (AHI) was the most appropriate time to detect the spread of TDR. In this meta-analysis, our purpose was to evaluate the level of TDR in ART-naive patients with primary HIV infection (PHI)/AHI/early HIV infection (EHI) and to describe the critical drug-resistant mutations. Methods: We systematically searched the literature between January 1, 2008, and April 30, 2021, in PubMed, Web of Science, Embase, and the Cochrane Library. To evaluate the overall prevalence of TDR, we extracted raw data and analyzed prevalence estimates using Stata SE. Results: The data of this meta-analysis come from 12 observational studies, covering 3,558 ART-naive individuals with PHI, AHI, or EHI. The overall prevalence of HIV-TDR is 9.3% (95% CI: 6.8%–11.8%, I2 = 81.1%, in 11 studies). The prevalence of resistance by drug class is the highest for the nonnucleoside reverse transcriptase inhibitors (NNRTIs) at 5.7% (95% CI: 2.9%–8.5%, I2 = 96.6%, in 11 studies), followed by nucleoside reverse transcriptase inhibitors (NRTIs) at 3.4% (95% CI: 1.8%–5.0%, I2 = 86.3%, in 10 studies) and protease inhibitors (PIs) at 3.3% (95% CI: 2.7%–3.9%, I2 = 15.6%, in 10 studies). The prevalence of TDR to integrase inhibitors (INIs) is 0.3% (95% CI: 0.1%–0.7%, I2 = 95.9%, in three studies), which is the lowest among all antiretroviral drugs. Conclusion: The overall prevalence of TDR is at a moderate level among AHI patients who have never received ART. This emphasizes the importance of baseline drug resistance testing for public health surveillance and guiding the choice of ART. In addition, the prevalence of TDR to NNRTIs is the highest, while the TDR to INIs is the lowest. This may guide the selection of clinical antiretroviral drugs.
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Affiliation(s)
- Chunxiang Guo
- Department of Dermatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yaxin Wu
- Center for Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yang Zhang
- Center for Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xinchao Liu
- Department of Infectious Disease, Peking Union Medical College Hospital, Beijing, China
| | - Aixin Li
- Center for Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Meixia Gao
- Center for Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Tong Zhang
- Center for Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Hao Wu
- Center for Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Guanzhi Chen
- Department of Dermatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaojie Huang
- Center for Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
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4
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Muccini C, Pinyakorn S, Sirivichayakul S, Kroon E, Sacdalan C, Crowell TA, Trichavaroj R, Ananworanich J, Vasan S, Phanuphak N, Colby DJ, on behalf of the RV254 Study Group. Brief Report: Prevalence Trend of Transmitted Drug Resistance in a Prospective Cohort of Thai People With Acute HIV Infection. J Acquir Immune Defic Syndr 2021; 87:1173-1177. [PMID: 34229330 PMCID: PMC8260960 DOI: 10.1097/qai.0000000000002718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND The greater availability of different antiretroviral therapy regimens in developing countries may influence the emergence of transmitted drug resistance (TDR). People with acute HIV infection (AHI) represent the best opportunity for real-time monitoring of TDR. This study assessed the TDR prevalence trends over time in a Thai cohort of predominantly men who have sex with men (MSM) with AHI. METHODS At the time of RV254/SEARCH010 study (NCT00796146) enrollment and before starting ART, HIV genotyping was used to identify mutations in the reverse transcriptase and protease genes. Testing for TDR mutations was obtained by a validated in-house method with TRUGENE assay in a subset. Genotype sequences were analyzed using the Stanford University HIV Drug Resistance Database. RESULTS Genotyping was performed for 573 participants with AHI. Their median age was 26 years (interquartile range 22-31), 97.4% were men, and 94.1% were MSM. Overall TDR prevalence was 7.0%, declining from 12.5% in 2009-2010 to 4.8% in 2017-2018. A declining resistance prevalence to nonnucleoside reverse transcriptase inhibitor emerged from 9.4% in 2009-2010 to 3.5% in 2017-2018 and to nucleoside reverse transcriptase inhibitor from 6.3% to 2.1%. Protease inhibitor resistance showed a decreased TDR level from 3.1% in 2009-2010 to 1.4% in 2017-2018. CONCLUSIONS We report an encouraging declining trend in TDR prevalence in a Thai cohort of mainly MSM from 2009 to 2018; in 2017-2018, we observed a low TDR prevalence according to the World Health Organization definition.
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Affiliation(s)
- Camilla Muccini
- Vita-Salute San Raffaele University, Milan, Italy
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Suteeraporn Pinyakorn
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sunee Sirivichayakul
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Eugene Kroon
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Trevor A. Crowell
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rapee Trichavaroj
- Institute of HIV Research and Innovation, Bangkok, Thailand
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences _ US Component, Bangkok, Thailand
| | - Jintanat Ananworanich
- Department of Global Health, the University of Amsterdam, Amsterdam, The Netherlands
| | - Sandhya Vasan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | - Donn J. Colby
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Institute of HIV Research and Innovation, Bangkok, Thailand
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5
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Baxter JD, Dunn D, Tostevin A, Marvig RL, Bennedbaek M, Cozzi-Lepri A, Sharma S, Kozal MJ, Gompels M, Pinto AN, Lundgren J. Transmitted HIV-1 drug resistance in a large international cohort using next-generation sequencing: results from the Strategic Timing of Antiretroviral Treatment (START) study. HIV Med 2021; 22:360-371. [PMID: 33369017 PMCID: PMC8049964 DOI: 10.1111/hiv.13038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/11/2020] [Accepted: 11/10/2020] [Indexed: 01/13/2023]
Abstract
OBJECTIVES The aim of this analysis was to characterize transmitted drug resistance (TDR) in Strategic Timing of Antiretroviral Treatment (START) study participants by next-generation sequencing (NGS), a sensitive assay capable of detecting low-frequency variants. METHODS Stored plasma from participants with entry HIV RNA > 1000 copies/mL were analysed by NGS (Illumina MiSeq). TDR was based on the WHO 2009 surveillance definition with the addition of reverse transcriptase (RT) mutations T215N and E138K, and integrase strand transfer inhibitor (INSTI) surveillance mutations (Stanford HIVdb). Drug resistance mutations (DRMs) detected at three thresholds are reported: > 2%, 5% and 20% of the viral population. RESULTS Between 2009 and 2013, START enrolled 4684 antiretroviral therapy (ART)-naïve individuals in 35 countries. Baseline NGS data at study entry were available for 2902 participants. Overall prevalence rates of TDR using a detection threshold of 2%/5%/20% were 9.2%/5.6%/3.2% for nucleoside reverse transcriptase inhibitors (NRTIs), 9.2%/6.6%/4.9% for non-NRTIs, 11.4%/5.5%/2.4% for protease inhibitors (PIs) and 3.5%/1.6%/0.1% for INSTI DRMs and varied by geographic region. Using the 2% detection threshold, individual DRMs with the highest prevalence were: PI M46IL (5.5%), RT K103NS (3.5%), RT G190ASE (3.1%), T215ISCDVEN (2.5%), RT M41L (2.2%), RT K219QENR (1.7%) and PI D30N (1.6%). INSTI DRMs were detected almost exclusively below the 20% detection threshold, most commonly Y143H (0.4%), Q148R (0.4%) and T66I (0.4%). CONCLUSIONS Use of NGS in this study population resulted in the detection of a large proportion of low-level variants which would not have been detected by traditional Sanger sequencing. Global surveillance studies utilizing NGS should provide a more comprehensive assessment of TDR prevalence in different regions of the world.
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Affiliation(s)
- J D Baxter
- Cooper University Hospital/Cooper Medical School of Rowan University, Camden, NJ, USA
| | - D Dunn
- Institute for Global Health, UCL, London, UK
| | - A Tostevin
- Institute for Global Health, UCL, London, UK
| | - R L Marvig
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - M Bennedbaek
- Copenhagen HIV Programme, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - S Sharma
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - M J Kozal
- Yale University School of Medicine, New Haven, CT, USA
| | - M Gompels
- North Bristol NHS Trust, Westbury on Trym, UK
| | - A N Pinto
- The Kirby Institute, University of New South Wales, Sydney, Australia
| | - J Lundgren
- Copenhagen HIV Programme, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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6
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Efficacy, pharmacokinetics and neurocognitive performance of dual, NRTI-sparing antiretroviral therapy in acute HIV-infection. AIDS 2020; 34:1923-1931. [PMID: 32773474 DOI: 10.1097/qad.0000000000002652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate penetration of antiretrovirals into compartments and efficacy of a dual, NRTI-sparing regimen in acute HIV infection (AHI). DESIGN Single-arm, open-label pilot study of participants with AHI initiating ritonavir-boosted darunavir 800 mg once daily and etravirine 400 mg once daily or 200 mg twice daily within 30 days of AHI diagnosis. METHODS Efficacy was defined as HIV RNA less than 200 copies/ml by week 24. Optional sub-studies included pharmacokinetics analysis from genital fluids (weeks 0-4, 12, 48), cerebrospinal fluid (CSF) (weeks 2-4, 24 and 48) and endoscopic biopsies (weeks 4-12 and 36-48). Neuropsychological performance was assessed at weeks 0, 24 and 48. RESULTS Fifteen AHI participants were enrolled. Twelve (80%) participants achieved HIV RNA less than 200 copies/ml by week 24. Among 12 participants retained through week 48, nine (75%) remained suppressed to less than 50 copies/ml. The median time from ART initiation to suppression less than 200 and less than 50 copies/ml was 59 and 86 days, respectively. The penetration ratios for etravirine and darunavir in gut associated lymphoid tissue were 19.2 and 3.05, respectively. Most AHI participants achieving viral suppression experienced neurocognitive improvement. Of the three participants without overall improvement in neurocognitive functioning as measured by impairment ratings (more than two tests below 1 SD), two had virologic failure. CONCLUSION NRTI-sparing ART started during AHI resulted in rapid viral suppression similar to NRTI-based regimens. More novel and compact two-drug treatments for AHI should be considered. Early institution of ART during AHI appears to improve overall neurocognitive function and may reduce the risk of subsequent neurocognitive impairment. CLINICALTRIALS.GOV:: NCT00855413.
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7
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Crowell TA, Kijak GH, Sanders-Buell E, O'Sullivan AM, Kokogho A, Parker ZF, Lawlor J, Polyak CS, Adebajo S, Nowak RG, Baral SD, Robb ML, Charurat ME, Ake JA, Ndembi N, Tovanabutra S. Transmitted, pre-treatment and acquired antiretroviral drug resistance among men who have sex with men and transgender women living with HIV in Nigeria. Antivir Ther 2020; 24:595-601. [PMID: 32125280 DOI: 10.3851/imp3342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND Across sub-Saharan Africa, men who have sex with men (MSM) and transgender women (TGW) have disproportionately poor HIV treatment outcomes. Stigma and criminalization create barriers to health-care engagement and adherence to antiretroviral therapy (ART), potentially promoting the development of HIV drug resistance (HIVDR). We evaluated transmitted, pre-treatment and acquired HIVDR among MSM and TGW in Lagos and Abuja, Nigeria. METHODS Adults with HIV RNA ≥1,000 copies/ml in the TRUST/RV368 cohort, including incident cases diagnosed via 3-monthly screening, underwent HIVDR testing using the Sanger sequencing method. Major mutations conferring resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) were identified from the 2017 IAS-USA list. World Health Organization surveillance drug resistance mutations (SDRMs) were identified in ART-naive participants. RESULTS From March 2013 to June 2017, 415 participants with median age 24 (interquartile range [IQR] 21-27) years, CD4+ T-cell count 370 (IQR 272-502) cells/mm3, and HIV RNA 4.73 (IQR 4.26-5.15) log10 copies/ml underwent HIVDR testing. SDRMs were observed in 36 of 373 ART-naive participants (9.7%, 95% confidence interval [95% CI 6.8, 13.1%]), including 8 of 39 incident cases (20.5%, [95% CI] 9.3, 36.5%). Among 42 ART-experienced participants, NNRTI resistance was detected in 18 (42.9%, 95% CI 27.7, 59.0%) and NRTI resistance in 10 (23.8%, 95% CI 12.0, 39.4%). No PI resistance was detected. CONCLUSIONS The high prevalence of transmitted and acquired drug resistance among Nigerian MSM and TGW living with HIV suggests the need for programmatic solutions to improve uninterrupted access to ART and timely switch to second-line regimens in cases of viral failure.
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Affiliation(s)
- Trevor A Crowell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gustavo H Kijak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,Present address: GSK Vaccines, Rockville, MD, USA
| | - Eric Sanders-Buell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Anne Marie O'Sullivan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Afoke Kokogho
- US Army Medical Research Directorate-Africa, Nairobi, Kenya.,HJF Medical Research International, Abuja, Nigeria
| | - Zahra F Parker
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,US Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - John Lawlor
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Christina S Polyak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | - Rebecca G Nowak
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Stefan D Baral
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Manhattan E Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julie A Ake
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.,Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
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8
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Crowell TA, Danboise B, Parikh A, Esber A, Dear N, Coakley P, Kasembeli A, Maswai J, Khamadi S, Bahemana E, Iroezindu M, Kiweewa F, Owuoth J, Freeman J, Jagodzinski LL, Malia JA, Eller LA, Tovanabutra S, Peel SA, Ake JA, Polyak CS. Pretreatment and Acquired Antiretroviral Drug Resistance Among Persons Living With HIV in Four African Countries. Clin Infect Dis 2020; 73:e2311-e2322. [PMID: 32785695 PMCID: PMC8492117 DOI: 10.1093/cid/ciaa1161] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Emerging HIV drug resistance (HIVDR) could jeopardize the success of standardized HIV management protocols in resource-limited settings. We characterized HIVDR among antiretroviral therapy (ART)-naive and experienced participants in the African Cohort Study (AFRICOS). METHODS From January 2013 to April 2019, adults with HIV-1 RNA >1000 copies/mL underwent ART history review and HIVDR testing upon enrollment at 12 clinics in Uganda, Kenya, Tanzania, and Nigeria. We calculated resistance scores for specific drugs and tallied major mutations to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) using Stanford HIVDB 8.8 and SmartGene IDNS software. For ART-naive participants, World Health Organization surveillance drug resistance mutations (SDRMs) were noted. RESULTS HIVDR testing was performed on 972 participants with median age 35.7 (interquartile range [IQR] 29.7-42.7) years and median CD4 295 (IQR 148-478) cells/mm3. Among 801 ART-naive participants, the prevalence of SDRMs was 11.0%, NNRTI mutations 8.2%, NRTI mutations 4.7%, and PI mutations 0.4%. Among 171 viremic ART-experienced participants, NNRTI mutation prevalence was 83.6%, NRTI 67.8%, and PI 1.8%. There were 90 ART-experienced participants with resistance to both efavirenz and lamivudine, 33 (36.7%) of whom were still prescribed these drugs. There were 10 with resistance to both tenofovir and lamivudine, 8 (80.0%) of whom were prescribed these drugs. CONCLUSIONS Participants on failing ART regimens had a high burden of HIVDR that potentially limited the efficacy of standardized first- and second-line regimens. Management strategies that emphasize adherence counseling while delaying ART switch may promote drug resistance and should be reconsidered.
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Affiliation(s)
- Trevor A Crowell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Brook Danboise
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ajay Parikh
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Allahna Esber
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Nicole Dear
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Peter Coakley
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Alex Kasembeli
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kericho, Kenya
| | - Jonah Maswai
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kericho, Kenya
| | - Samoel Khamadi
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Mbeya, Tanzania
| | - Emmanuel Bahemana
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Mbeya, Tanzania
| | - Michael Iroezindu
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Abuja, Nigeria
| | | | - John Owuoth
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kisumu, Kenya
| | - Joanna Freeman
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Linda L Jagodzinski
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jennifer A Malia
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Leigh Ann Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sheila A Peel
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Julie A Ake
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Christina S Polyak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
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9
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Su B, Zheng X, Liu Y, Liu L, Xin R, Lu H, Huang C, Bai L, Mammano F, Zhang T, Wu H, Sun L, Dai L. Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes. J Antimicrob Chemother 2020; 74:1408-1416. [PMID: 30668734 DOI: 10.1093/jac/dky561] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/24/2018] [Accepted: 12/10/2018] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Ultra-deep sequencing (UDS) is a powerful tool for exploring the impact on virological outcome of minority variants with low frequencies, some even <1% of the virus population. Here, we compared HIV-1 minority variants at baseline, through plasma RNA and PBMC DNA analyses, and the dominant variants at the virological failure (VF) point, to evaluate the impact of minority drug-resistant variants (MDRVs) on virological outcomes. METHODS Single-molecule real-time sequencing (SMRTS) was performed on baseline RNA and DNA. The Stanford HIV-1 drug resistance database was used for the identification and evaluation of drug resistance-associated mutations (DRAMs). RESULTS We classified 50 patients into virological success (VS) and VF groups. We found that the rates of reverse transcriptase inhibitor (RTI) DRAMs determined by SMRTS did not differ significantly within or between groups, whether based on RNA or DNA analyses. There was no significant difference in the level of resistance to specific drugs between groups, in either DNA or RNA analyses, except for the DNA-based analysis of lamivudine, for which there was a trend towards a higher prevalence of intermediate/high-level resistance in the VF group. The RNA MDRVs corresponded to DNA MDRVs, except for M100I and Y188H. Sequencing from DNA appeared to be more sensitive than from RNA to detect MDRVs. CONCLUSIONS Detection of pretreatment minority HIV-1 RTI-resistant variants by UDS showed that MDRVs at baseline were not significantly associated with virological outcome. However, HIV-1 DNA sequencing by UDS was useful for detecting pretreatment drug resistance mutations in patients, potentially affecting virological responses, suggesting a potential clinical relevance for ultra-deep DNA sequencing.
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Affiliation(s)
- Bin Su
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | | | - Yan Liu
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Lifeng Liu
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Ruolei Xin
- Institute for AIDS/STD Control and Prevention, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hongyan Lu
- Institute for AIDS/STD Control and Prevention, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Chun Huang
- Institute for AIDS/STD Control and Prevention, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lishi Bai
- Institute for AIDS/STD Control and Prevention, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Fabrizio Mammano
- INSERM U941, Genetics and Ecology of Viruses, Hospital Saint Louis, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Tong Zhang
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Hao Wu
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for HIV/AIDS Research, Beijing, China
| | - Lijun Sun
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Lili Dai
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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10
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Aulicino PC, Zapiola I, Kademian S, Valle MM, Fernandez Giuliano S, Toro R, Barbas G, Cañizal AM, Mayon P, Golemba MD, Ortiz de Zarate M, Corazza MS, Cudola A, Mecikovsky D, Bologna R, Mangano A, Sen L. Pre-treatment drug resistance and HIV-1 subtypes in infants from Argentina with and without exposure to antiretroviral drugs for prevention of mother-to-child transmission. J Antimicrob Chemother 2020; 74:722-730. [PMID: 30517632 DOI: 10.1093/jac/dky486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES To assess the prevalence and patterns of pre-treatment HIV drug resistance (PDR) and HIV-1 subtype in infants from Argentina with exposure to different antiretroviral drugs (ARVs) for the prevention of mother-to-child transmission (PMTCT). PATIENTS AND METHODS HIV-1 genotyping was performed in 115 infants (median age = 2.3 months) born between 2007 and 2014 to screen for drug resistance mutations (DRMs) before starting first-line ART. HIV-1 subtype was characterized by phylogenetic and recombination analysis. RESULTS Overall, DRMs were found in 34 of 115 infants (PDR level 30% to any ARV, 3.5% to PIs, 12% to NRTIs and 22% to NNRTIs). Of the 115 infants, 22 (19.1%) were ARV-unexposed. Another 93 were ARV-exposed: 28 (24.3%) to short-course zidovudine monotherapy ARV prophylaxis; 25 (21.7%) to nevirapine-based ARV prophylaxis; 12 (10.4%) to perinatal infant zidovudine prophylaxis + maternal combination ART with NNRTIs; and 28 (24.3%) to perinatal infant zidovudine prophylaxis+maternal combination ART with PIs. Transmitted drug resistance among ARV-unexposed infants was 32% (5% to PIs, 9% to NRTIs and 18% to NNRTIs). ART-exposed infants showed multi-class ARV resistance. Importantly, vertical transmission of a triple-class-resistant virus was confirmed in one case. Patterns of DRMs predicted high-level resistance to NNRTIs in a similar and high proportion (>50%) of infants with at least one DRM independently of ARV exposure. BF recombinants were found in 74%, subtype B in 20%, subtype C in 3% and novel AG and AB recombinants in 3%. CONCLUSIONS PDR in HIV-1-infected children from Argentina is among the highest reported, jeopardizing successful lifelong suppressive ART as well as the efficacy of current PMTCT regimens.
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Affiliation(s)
- Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | - Ines Zapiola
- Unidad de Virología, Hospital de Infecciosas "Francisco J. Muñiz", Buenos Aires, Argentina
| | - Silvia Kademian
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - María M Valle
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | | | - Rosana Toro
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Gabriela Barbas
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - Ana M Cañizal
- Unidad de Virología, Hospital de Infecciosas "Francisco J. Muñiz", Buenos Aires, Argentina
| | - Paula Mayon
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Marcelo D Golemba
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | | | - Marisa S Corazza
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Analía Cudola
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - Débora Mecikovsky
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Rosa Bologna
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
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11
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Analysis of HIV-1 diversity, primary drug resistance and transmission networks in Croatia. Sci Rep 2019; 9:17307. [PMID: 31754119 PMCID: PMC6872562 DOI: 10.1038/s41598-019-53520-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/31/2019] [Indexed: 01/23/2023] Open
Abstract
Molecular epidemiology of HIV-1 infection in treatment-naive HIV-1 infected persons from Croatia was investigated. We included 403 persons, representing 92.4% of all HIV-positive individuals entering clinical care in Croatia in 2014–2017. Overall prevalence of transmitted drug resistance (TDR) was estimated at 16.4%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside RTI (NNRTIs) and protease inhibitors (PIs) was found in 11.4%, 6.7% and 2.5% of persons, respectively. Triple-class resistance was determined in 2.2% of individuals. In addition, a single case (1.0%) of resistance to integrase strand-transfer inhibitors (InSTIs) was found. Deep sequencing was performed on 48 randomly selected samples and detected additional TDR mutations in 6 cases. Phylogenetic inference showed that 347/403 sequences (86.1%) were part of transmission clusters and identified forward transmission of resistance in Croatia, even that of triple-class resistance. The largest TDR cluster of 53 persons with T215S was estimated to originate in the year 1992. Our data show a continuing need for pre-treatment HIV resistance testing in Croatia. Even though a low prevalence of resistance to InSTI was observed, surveillance of TDR to InSTI should be continued.
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12
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Kagan RM, Dunn KJ, Snell GP, Nettles RE, Kaufman HW. Trends in HIV-1 Drug Resistance Mutations from a U.S. Reference Laboratory from 2006 to 2017. AIDS Res Hum Retroviruses 2019; 35:698-709. [PMID: 31169022 DOI: 10.1089/aid.2019.0063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Trends in resistance to antiretroviral drugs for HIV-1 may inform clinical support and drug development. We evaluated drug resistance mutation (DRM) trends for nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI), protease inhibitor (PI), and integrase strand transfer inhibitor (INSTI) in a large U.S. reference laboratory database. DRMs with a Stanford HIV Drug Resistance Database mutation score ≥10 from deidentified subtype B NRTI/NNRTI/PI specimens (2006-2017; >10,000/year) and INSTI specimens (2010-2017; >1,000/year) were evaluated. Sequences with NRTI, NNRTI, or PI single- or multiclass DRMs declined from 48.9% to 39.3%. High-level dual- and triple-class resistance declined from 43.3% (2006) to 17.1% (2017), while sequences with only single-class DRMs increased from 40.0% to 52.9%. The prevalence of DRMs associated with earlier treatment regimens declined, while prevalence of some DRMs associated with newer regimens increased. M184V/I decreased from 48.3% to 29.4%. K103N/S/T declined from 42.5% in 2012 to 36.4% in 2017. Rilpivirine and etravirine DRMs E138A/Q/R and E138K increased from 4.9% and 0.4% to 9.7% and 1.7%, respectively. Sequences with ≥1 darunavir DRM declined from 18.1% to 4.8% by 2017. INSTI DRM Q148H/K/R declined from 39.3% (2010) to 13.8% (2017). Prevalence of elvitegravir-associated DRMs T66A/I/K, E92Q, S147G, and the dolutegravir-associated DRM R263K increased. For a subset of patients with serial testing, 50% (2,646/5,290) of those who initially had no reportable DRM subsequently developed ≥1 DRM for NRTI/NNRTI/PI and 49.7% (159/320) for INSTI. These trends may inform the need for baseline genotypic resistance testing. The detection of treatment-emergent DRMs in serially tested patients confirms the value of genotypic testing following virologic failure.
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Affiliation(s)
- Ron M. Kagan
- Quest Diagnostics Infectious Disease, San Juan Capistrano, California
| | - Keith J. Dunn
- Janssen Scientific Affairs, LLC, Titusville, New Jersey
| | - Gregg P. Snell
- Quest Diagnostics Medical Informatics, Needham, Massachusetts
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13
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Giacomelli A, Fabbiani M, De Benedetto I, Nozza S, Focà E, Celesia BM, Marchetti G, Mussini C, Antinori A, d'Ettorre G, Madeddu G, Bandera A, Muscatello A, Rusconi S. Impact of genotypic susceptibility score on cART outcomes during primary HIV infection. J Med Virol 2019; 91:1891-1895. [PMID: 31199538 DOI: 10.1002/jmv.25517] [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: 01/31/2019] [Accepted: 06/03/2019] [Indexed: 11/12/2022]
Abstract
To assess the impact of genotypic susceptibility score (GSS) on combined antiretroviral therapy (cART) outcomes during primary HIV infection (PHI) we retrospectively enrolled patients with PHI diagnosed between 2008 and 2015 at 9/24 Italian Network ACuTe HIV InfectiON centers. One hundred-seventy-six patients were enrolled. Of these, 55 (32.9%) patients started with more than three drugs and 11 (7.2%) started with a GSS < 3. Regimen's GSS (per 1 point increase) (adjusted odds ratio [aOR], 4.82; 95% confidence interval [CI], 1.62-14.28; P = .005) and baseline HIV-RNA (per 1 log10 increase) (aOR, 2.02; 95% CI, 1.09-3.73; P = .025) resulted associated with early cART initiation. In conclusion, regimen's GSS resulted to be associated to the time to cART initiation during PHI.
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Affiliation(s)
- Andrea Giacomelli
- Divisione Malattie Infettive, DIBIC Luigi Sacco, Università degli Studi di Milano, Milan, Italy
| | | | - Ilaria De Benedetto
- Divisione Malattie Infettive, Ospedale Amedeo di Savoia, Università di Torino, Turin, Italy
| | - Silvia Nozza
- Divisione Malattie Infettive, Ospedale San Raffaele IRCCS, Università Vita-Salute, Milan, Italy
| | - Emanuele Focà
- Divisione Malattie Infettive, Spedali Civili, Università degli Studi di Brescia, Brescia, Italy
| | | | - Giulia Marchetti
- Divisione Malattie Infettive, Dipartimento di Scienze della Salute, Università degli Studi di Milano
| | - Cristina Mussini
- Divisione Malattie Infettive, Università degli Studi di Modena e Reggio Emilia, Modena
| | - Andrea Antinori
- U.O.C. Immunodeficienze virali, Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani, IRCCS, Roma
| | | | - Giordano Madeddu
- Divisione Malattie Infettive, Università degli Studi di Sassari, Italy
| | - Alessandra Bandera
- Divisione Malattie Infettive IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano
| | - Antonio Muscatello
- Divisione Malattie Infettive IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano
| | - Stefano Rusconi
- Divisione Malattie Infettive, DIBIC Luigi Sacco, Università degli Studi di Milano, Milan, Italy
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14
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Hauser A, Kusejko K, Johnson LF, Wandeler G, Riou J, Goldstein F, Egger M, Kouyos RD. Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa. PLoS Comput Biol 2019; 15:e1007083. [PMID: 31233494 PMCID: PMC6611642 DOI: 10.1371/journal.pcbi.1007083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 07/05/2019] [Accepted: 05/06/2019] [Indexed: 11/19/2022] Open
Abstract
The scale-up of antiretroviral therapy (ART) in South Africa substantially reduced AIDS-related deaths and new HIV infections. However, its success is threatened by the emergence of resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTI). The MARISA (Modelling Antiretroviral drug Resistance In South Africa) model presented here aims at investigating the time trends and factors driving NNRTI resistance in South Africa. MARISA is a compartmental model that includes the key aspects of the local HIV epidemic: continuum of care, disease progression, and gender. The dynamics of NNRTI resistance emergence and transmission are then added to this framework. Model parameters are informed using data from HIV cohorts participating in the International epidemiology Databases to Evaluate AIDS (IeDEA) and literature estimates, or fitted to UNAIDS estimates. Using this novel approach of triangulating clinical and resistance data from various sources, MARISA reproduces the time trends of HIV in South Africa in 2005–2016, with a decrease in new infections, undiagnosed individuals, and AIDS-related deaths. MARISA captures the dynamics of the spread of NNRTI resistance: high levels of acquired drug resistance (ADR, in 83% of first-line treatment failures in 2016), and increasing transmitted drug resistance (TDR, in 8.1% of ART initiators in 2016). Simulation of counter-factual scenarios reflecting alternative public health policies shows that increasing treatment coverage would have resulted in fewer new infections and deaths, at the cost of higher TDR (11.6% in 2016 for doubling the treatment rate). Conversely, improving switching to second-line treatment would have led to lower TDR (6.5% in 2016 for doubling the switching rate) and fewer new infections and deaths. Implementing drug resistance testing would have had little impact. The rapid ART scale-up and inadequate switching to second-line treatment were the key drivers of the spread of NNRTI resistance in South Africa. However, even though some interventions could have substantially reduced the level of NNRTI resistance, no policy including NNRTI-based first line regimens could have prevented this spread. Thus, by combining epidemiological data on HIV in South Africa with biological data on resistance evolution, our modelling approach identified key factors driving NNRTI resistance, highlighting the need of alternative first-line regimens. Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI) threatens the long-term success of antiretroviral therapy (ART) roll-out in South Africa. We developed a compartmental model integrating the local HIV epidemiology with biological mechanisms of drug resistance. A first dimension of the model accounts for the continuum of care: infection, diagnosis, first-line treatment with suppression or failure, and second-line treatment. Other dimensions include: disease progression (CD4 counts), gender, and acquisition and transmission of NNRTI resistance. Whenever possible, we informed the parameters using the data available from local cohorts. Other parameters were informed using literature or UNAIDS estimates. The model captured the rise of NNRTI resistance during the period. We assessed the impact of counter-factual scenarios reflecting alternative countrywide policies during the period 2005 to 2016, considering either increasing ART coverage, improving management of treatment failure, broadening ART eligibility, or implementing drug resistance testing before ART initiation. We identified key drivers of the NNRTI resistance epidemic: large-scale ART roll-out and insufficient monitoring of first-line treatment failure. The model also suggested that no policy including NNRTI-based first line regimens could have prevented the spread of NNRTI resistance.
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Affiliation(s)
- Anthony Hauser
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Leigh F. Johnson
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, South Africa
| | - Gilles Wandeler
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Fardo Goldstein
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, South Africa
| | - Roger D. Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
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15
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Lagi F, Baldin G, Colafigli M, Capetti A, Madeddu G, Kiros ST, Di Giambenedetto S, Sterrantino G. Viro-immunological efficacy and tolerability of dolutegravir-based regimens compared to regimens based on other integrase strand inhibitors, protease inhibitors or non-nucleoside reverse transcriptase inhibitors in patients with acute HIV-1 infection: A multicenter retrospective cohort study. Int J Antimicrob Agents 2019; 54:487-490. [PMID: 31195121 DOI: 10.1016/j.ijantimicag.2019.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/10/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVES The aim of this study was to compare the tolerability and viro-immunological efficacy of dolutegravir-based regimens (DTG group) with regimens based on EVG, RAL, PI or NNRTI (NODTG group) in patients with acute HIV-1 infections (AHI). METHODS All patients diagnosed with AHI and on antiretroviral therapy (ART) between January 2015 and December 2017 from five centers in Italy were included and followed-up to 30th April 2018. AHI was defined by the presence of the positive p24 antigen with negative or indeterminate western blot. RESULTS Forty-three patients were enrolled: 20 in the DTG group, 23 in the NODTG group. Nine patients (20.9%; four in the DTG group, five in the NODTG group) were prescribed a four-drug regimen. In the cohort, 81.4% were Italian and 83.7% were male, with a median age of 41 years (interquartile range [IQR] 31-48). Median time between HIV diagnosis and ART initiation was 12 days (IQR 5-28). Seven patients harbored a virus with transmitted mutations at baseline (16.2%), all were in the DTG group (P=0.005). All patients had undetectable HIV-RNA at the end of follow-up except two patients, one of whom had 57 copies and one who was lost to follow-up. In Kaplan-Meier analysis, time to virological suppression was similar in the two groups (log rank: P= 0.7155). After achieving virological suppression, four patients stopped ART because of toxicity: two on DTG, two on EVG for neurological and gastrointestinal toxicity, respectively. CONCLUSION In our setting, ART in AHI is started very early. DTG showed good viro-immunological efficacy even in the presence of NRTI-transmitted mutations. DTG interruptions were rare.
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Affiliation(s)
- F Lagi
- Infectious Disease Unit, Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Firenze, (Italy)
| | - G Baldin
- Institute of Clinical Infectious Diseases, Fondazione Policlinico Universitario A. Gemelli IRCCS, Catholic University of the Sacred Heart, L. go Agostino Gemelli, 8 - 00168, Rome (Italy)
| | - M Colafigli
- Infectious Dermatology and Allergology Unit, IFO S. Gallicano Institute (IRCCS), via Elio Chianesi, 53 - 00144, Rome, (Italy)
| | - A Capetti
- Division of Infectious Diseases, Department of Infectious Diseases, Luigi Sacco University Hospital, via Giovanni Battista Grassi, 74, 20157, Milan, (Italy)
| | - G Madeddu
- Unit of Infectious Diseases, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Viale San Pietro, 10- 07100 Sassari, (Italy)
| | - S Tekle Kiros
- Infectious Disease Unit, Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Firenze, (Italy)
| | - S Di Giambenedetto
- Institute of Clinical Infectious Diseases, Fondazione Policlinico Universitario A. Gemelli IRCCS, Catholic University of the Sacred Heart, L. go Agostino Gemelli, 8 - 00168, Rome (Italy)
| | - G Sterrantino
- Infectious Disease Unit, Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134, Firenze, (Italy).
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16
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New antiretroviral agent use affects prevalence of HIV drug resistance in clinical care populations. AIDS 2018; 32:2593-2603. [PMID: 30134298 DOI: 10.1097/qad.0000000000001990] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE To estimate the prevalence of HIV drug resistance over time and identify risk factors for multiclass resistance. DESIGN Prospective clinical cohort of HIV-infected patients at the University of North Carolina. METHODS Among antiretroviral therapy (ART)-experienced patients in care 2000-2016, we estimated annual prevalences of cumulative resistance, defined as at least one major mutation by drug class. Clinical data and multiple imputation were used when genotypic data were missing, and mutations were carried forward in time. We estimated resistance odds ratios comparing characteristics of patients in care in 2016. RESULTS A total of 3682 patients contributed 23 169 person-years. Prevalence of at least one major resistance mutation, irrespective of viral suppression, peaked in 2005 with 49% (95% confidence interval 46, 52) and decreased to 38% (35, 40) in 2016. Resistance to nucleoside reverse transcriptase inhibitors, protease inhibitors, and nonnucleoside reverse transcriptase inhibitors also peaked in 2005-2007 and decreased to 28 (26, 31), 14 (12, 16), and 27% (24, 29) in 2016, respectively. In 2016, prevalence of integrase strand transfer inhibitor (INSTI) resistance was 2% (1, 3) and triple-class resistance 10% (9, 12). Over the study period, cumulative resistance was frequent among patients with detectable viremia, but uncommon among patients initiating ART post-2007. Among 1553 patients in care in 2016, ART initiation at an older age, with an INSTI, and with higher CD4 cell counts were associated with resistance to fewer or no classes. CONCLUSION Prevalence of resistance to older ART classes has decreased in the last 10 years in this clinical cohort, whereas INSTI resistance has increased but remained very low. Patients with viremia continue to have a high burden of resistance even if they initiated ART recently.
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17
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Huruy K, Mulu A, Liebert UG, Melanie M. HIV-1C proviral DNA for detection of drug resistance mutations. PLoS One 2018; 13:e0205119. [PMID: 30286160 PMCID: PMC6171930 DOI: 10.1371/journal.pone.0205119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/22/2018] [Indexed: 11/19/2022] Open
Abstract
Background Using HIV proviral DNA as a template may be suitable for initial detection of transmitted drug resistance mutations (TDRMs) as it is easy to handle and less expensive compared to RNA. However, existing literatures which are mainly focused on HIV-1B subtypes DNA extracted from PBMCs revealed controversial findings ranging from the detection of significantly lower or higher mutations in proviral DNA compared to historic viral RNA. Thus, to verify whether viral RNA or proviral DNA has improved sensitivity in detecting transmitted genotypic drug resistance mutations paired viral RNA and proviral DNA (which is directly extracted from stored whole blood) samples were tested from Ethiopian antiretroviral naive HIV-1C infected subjects. Methods In the present comparative study the frequency of TDR mutations was assessed in paired samples of viral RNA and proviral DNA (extracted directly from stored whole blood) of HIV-1C infected treatment naïve patients and interpreted using the 2009 WHO drug resistance surveillance mutation lists, Stanford University drug resistance data base and International Antiviral Society-USA mutation lists. Results High agreement in rate of TDR between the two compartments was observed using the WHO mutation lists. While mutations G190A and E138A were concurrently found in both compartments, others such as G73S on PR and A62V, M184I, M230I on RT were identified in proviral DNA only. All signature mutations seen in viral RNA were not missed in proviral DNA. Conclusions The concordance of major genotype drug resistance mutation between RNA and proviral DNA in treatment naïve patients suggests that proviral DNA might be an alternative approaches for an initial assessment of drug resistance prior to initiation of antiretroviral therapy using the WHO mutations lists in resource-limited countries. However, the clinical importance of TDRMs observed only in proviral DNA in terms of being a risk factor for virologic failure and whether they limit future treatment options needs additional investigation using more sensitive sequencing approaches such as Next Generation Sequencing (NGS).
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Affiliation(s)
- Kahsay Huruy
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
| | - Andargachew Mulu
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
- * E-mail:
| | | | - Maier Melanie
- Institute of Virology, Leipzig University, Leipzig, Germany
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Ross LL, Shortino D, Shaefer MS. Changes from 2000 to 2009 in the Prevalence of HIV-1 Containing Drug Resistance-Associated Mutations from Antiretroviral Therapy-Naive, HIV-1-Infected Patients in the United States. AIDS Res Hum Retroviruses 2018; 34:672-679. [PMID: 29732898 PMCID: PMC6080107 DOI: 10.1089/aid.2017.0295] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pre-existing HIV drug resistance can jeopardize first-line antiretroviral therapy (ART) success. Changes in the prevalence of drug resistance-associated mutations (DRMs) were analyzed from HIV-infected, ART-naive, U.S. individuals seeking ART treatment from 2000 to 2009. HIV DRM data from 3,829 ART-naive subjects were analyzed by year of sample collection using International Antiviral Society-United States (IAS-USA) and World Health Organization (WHO) “surveillance” DRM definitions; minor IAS-USA-defined DRMs were excluded. IAS-USA DRM prevalence between 2000 and 2009 was 14%, beginning with 8% in 2000 and 13% in 2009. The greatest incidence was observed in 2007 (17%). Overall, IAS-USA-defined non-nucleoside reverse transcriptase inhibitor (NNRTI) DRMs were 9.5%; nucleoside reverse transcriptase inhibitor (NRTI): 4%, and major protease inhibitor (PI): 3%. The most frequently detected IAS-USA-defined DRMs by class were NNRTI: K103N/S (4%), NRTI: M41L (1.5%), and PI: L90M (1%). Overall, WHO-defined DRM prevalence was 13% (5% in 2000; 13% in 2009). By class, NNRTI prevalence was 6%, NRTI: 6%, and PI: 3.2%. The most frequent WHO-defined DRMs were NRTI: codon T215 (3.0%), NNRTI: K103N/S (4%), and PI: L90 (1%). WHO-defined NNRTI DRMs declined significantly (p = .0412) from 2007 to 2009. The overall prevalence of HIV-1 containing major IAS-USA or WHO-defined DRMs to ≥2 or ≥3 classes was 2% and <1%, respectively. The prevalence of HIV-1 with WHO-defined dual- or triple-class resistance significantly declined (p = .0461) from 2008 (4%) to 2009 (<1%). In this U.S. cohort, the prevalence of HIV-1 DRMs increased from 2000 onward, peaked between 2005 and 2007, and then declined between 2008 and 2009; the detection of WHO-defined dual- or triple-class DRM similarly decreased from 2008 to 2009.
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Affiliation(s)
- Lisa L. Ross
- ViiV Healthcare, Research Triangle Park, North Carolina
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19
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Alidjinou EK, Deldalle J, Hallaert C, Robineau O, Ajana F, Choisy P, Hober D, Bocket L. RNA and DNA Sanger sequencing versus next-generation sequencing for HIV-1 drug resistance testing in treatment-naive patients. J Antimicrob Chemother 2018; 72:2823-2830. [PMID: 29091197 DOI: 10.1093/jac/dkx232] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/09/2017] [Indexed: 11/12/2022] Open
Abstract
Background Sanger sequencing of plasma RNA is the standard method for HIV-1 drug resistance testing in treatment-naive patients, but is limited by the non-detection of resistance-associated mutations (RAMs) with prevalence below approximately 20%. Objectives We compared RNA and DNA Sanger sequencing (RSS and DSS) with RNA next-generation sequencing (NGS) for RAM detection in HIV-1 reverse transcriptase (RT), protease (PR) and integrase (IN) genes. Methods Sanger sequencing was performed on RNA and DNA, following the recommendations of the French Agency for AIDS Research (ANRS). NGS was performed on RNA using the HIV-1 Drug Resistance Assay, v. 3.0 (Roche) on the 454 GS Junior sequencer. The IAS-USA list was used to identify RAMs. ANRS, Rega and Stanford algorithms were used for drug resistance interpretation. Results The study included 48 ART-naive patients. The number of patients with at least one major RAM was 3, 3, 4 and 8 when using RSS, DSS, NGS 20% and NGS 5%, respectively. Numerous minor mutations were detected in patients, especially in the protease gene. None of the methods detected any major mutation in the integrase gene. Overall, the mutation detection rate was similar between RSS and DSS, and higher with NGS 20%. Differences in drug resistance interpretation were found between algorithms. No impact of the minority RAMs detected by NGS was found on the short-term treatment outcome. Conclusions DSS does not clearly improve the detection of RAMs in ART-naive patients, as compared with RSS. NGS allows detection of additional minority RAMs; however, their clinical relevance requires further investigation.
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Affiliation(s)
- E K Alidjinou
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - J Deldalle
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - C Hallaert
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - O Robineau
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - F Ajana
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - P Choisy
- Service Universitaire des Maladies Infectieuses, CH Dron, Tourcoing, France
| | - D Hober
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - L Bocket
- Univ Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
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20
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Socías ME, Nosova E, Kerr T, Hayashi K, Harrigan PR, Shoveller J, Montaner J, Milloy MJ. Patterns of Transmitted Drug Resistance and Virological Response to First-line Antiretroviral Treatment Among Human Immunodeficiency Virus-Infected People Who Use Illicit Drugs in a Canadian Setting. Clin Infect Dis 2018; 65:796-802. [PMID: 28482025 DOI: 10.1093/cid/cix428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/03/2017] [Indexed: 11/14/2022] Open
Abstract
Background Transmitted drug resistance (TDR) may compromise response to antiretroviral therapy (ART). However, there are limited data on TDR patterns and impacts among people who use illicit drugs (PWUD). Methods Data were drawn from 2 prospective cohorts of PWUD in Vancouver, Canada. We characterized patterns of TDR among human immunodeficiency virus (HIV)-infected PWUD, and assessed its impacts on first-line ART virological outcomes. Results Between 1996 and 2015, among 573 ART-naive PWUD (18% with recent HIV infection), the overall TDR prevalence was 9.8% (95% confidence interval [CI], 7.3%-12.2%), with an increasing trend over time, from 8.5% in 1996-1999 to 21.1% in 2010-2015 (P = .003), mainly driven by resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs). TDR-associated mutations were more common for NNRTIs (5.4%), followed by nucleoside reverse transcriptase inhibitors (3.0%) and protease inhibitors (1.9%). TDR prevalence was lower among recently infected PWUD (adjusted odds ratio, 0.39 [95% CI, .15-.87]). Participants with TDR had higher risk of virological failure than those without TDR (log-rank P = .037) in the first year of ART. Conclusions Between 1996 and 2015, TDR prevalence increased significantly among PWUD in Vancouver. Higher risk of virological failure among PWUD with TDR may be explained by some inappropriate ART prescribing, as well as undetected minority resistant variants in participants with chronic HIV infection. Our findings support baseline resistance testing early in the course of HIV infection to guide ART selection among PWUD in our setting.
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Affiliation(s)
- M Eugenia Socías
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
| | | | - Thomas Kerr
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
| | - Kanna Hayashi
- British Columbia Centre for Excellence in HIV/AIDS.,Faculty of Health Sciences, Simon Fraser University, Burnaby
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
| | - Jeannie Shoveller
- British Columbia Centre for Excellence in HIV/AIDS.,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Julio Montaner
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
| | - M-J Milloy
- British Columbia Centre for Excellence in HIV/AIDS.,Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver
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21
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Abstract
BACKGROUND The rate of transmitted drug resistance (TDR) may increase with wider use of antiretroviral therapy and can contribute to therapeutic failure. We analysed time trends in TDR among HIV seroconverters. METHODS Using CASCADE data of individuals with well estimated dates of HIV seroconversion, we examined HIV nucleotide sequences collected prior to antiretroviral therapy use from 1996-2012. All samples were taken within 12 months of testing HIV positive. Using logistic regression, we examined the association between TDR and year of seroconversion, adjusting for confounders. RESULTS Of 4717 individuals seroconverting between 1996 and 2012, median (IQR) age at seroconversion was 33 (27, 39) years. The majority (3839; 92%) were male, mainly exposed through MSM (3767; 80%), and infected with subtype B (3464; 73%). Overall, 515 (11%) individuals had at least one drug resistance-related mutation; 280 individuals with nucleoside reverse transcriptase, 185 with nonnucleoside reverse transcriptase, and 144 with protease inhibitor mutations. Estimated TDR prevalence was 19.4% (8.2, 36.0) in 1996, significantly decreasing to 8.5% (5.9, 11.9) in 2012 [odds ratio (OR; 95% confidence interval (CI)) = 0.92 (0.90, 0.95) per year increase]. Individuals exposed through sex between men and women were significantly less likely to have been infected with a drug-resistant strain [OR (95% CI) = 0.59 (0.41, 0.87) compared with MSM], and there was marginal evidence that sampling during acute infection was associated with higher odds of resistance [OR (95% CI) = 1.20 (0.97, 1.7), P = 0.093] compared with later sampling. CONCLUSION TDR has decreased over calendar time although a significant proportion of new infections still carry resistance-related mutations.
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22
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Dasgupta S, Hall HI, Hernandez AL, Ocfemia MCB, Saduvala N, Oster AM. Receipt and timing of HIV drug resistance testing in six U.S. jurisdictions. AIDS Care 2017; 29:1567-1575. [PMID: 28464705 PMCID: PMC5685490 DOI: 10.1080/09540121.2017.1316356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The Department of Health and Human Services recommends drug resistance testing at linkage to HIV care. Because receipt and timing of testing are not well characterized, we examined testing patterns among persons with diagnosed HIV who are linked to care. Using surveillance data in six jurisdictions for persons aged ≥13 years with HIV infection diagnosed in 2013, we assessed the proportion receiving testing, and among these, the proportion receiving testing at linkage. Multivariable log-binomial regression modeling estimated associations between selected characteristics and receipt of testing (1) overall, and (2) at linkage among those tested. Of 9,408 persons linked to care, 66% received resistance testing, among whom 68% received testing at linkage. Less testing was observed among male persons who inject drugs (PWID), compared with men who have sex with men (adjusted prevalence ratio [aPR]: 0.88; 95% confidence interval [CI]: 0.81-0.97) and persons living in areas with population <500,000 compared with those in areas with population ≥2,500,000 (aPR: 0.88; CI: 0.84-0.93). In certain jurisdictions, testing was lower for persons with initial CD4 counts ≥500 cells/mm3, compared with those with CD4 counts <200 cells/mm3 (aPR range: 0.80-0.85). Of those tested, testing at linkage was lower among male PWID (aPR: 0.85; CI: 0.75-0.95) and, in some jurisdictions, persons with CD4 counts ≥500 cells/mm3 (aPR range: 0.63-0.73). Two-thirds of persons with diagnosed HIV who were linked to care received resistance testing, and most received testing at linkage as recommended. Improving receipt and timing of testing among male PWID, persons in less populous settings, and in all jurisdictions, regardless of CD4 count, may improve care outcomes.
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Affiliation(s)
- Sharoda Dasgupta
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | - H. Irene Hall
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | - Angela L. Hernandez
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
| | | | | | - Alexandra M. Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA
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23
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Pessôa R, Sanabani SS. High prevalence of HIV-1 transmitted drug-resistance mutations from proviral DNA massively parallel sequencing data of therapy-naïve chronically infected Brazilian blood donors. PLoS One 2017; 12:e0185559. [PMID: 28953964 PMCID: PMC5617215 DOI: 10.1371/journal.pone.0185559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/14/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND An improved understanding of the prevalence of low-abundance transmitted drug-resistance mutations (TDRM) in therapy-naïve HIV-1-infected patients may help determine which patients are the best candidates for therapy. In this study, we aimed to obtain a comprehensive picture of the evolving HIV-1 TDRM across the massive parallel sequences (MPS) of the viral entire proviral genome in a well-characterized Brazilian blood donor naïve to antiretroviral drugs. MATERIALS AND METHODS The MPS data from 128 samples used in the analysis were sourced from Brazilian blood donors and were previously classified by less-sensitive (LS) or "detuned" enzyme immunoassay as non-recent or longstanding HIV-1 infections. The Stanford HIV Resistance Database (HIVDBv 6.2) and IAS-USA mutation lists were used to interpret the pattern of drug resistance. The minority variants with TDRM were identified using a threshold of ≥ 1.0% and ≤ 20% of the reads sequenced. The rate of TDRM in the MPS data of the proviral genome were compared with the corresponding published consensus sequences of their plasma viruses. RESULTS No TDRM were detected in the integrase or envelope regions. The overall prevalence of TDRM in the protease (PR) and reverse transcriptase (RT) regions of the HIV-1 pol gene was 44.5% (57/128), including any mutations to the nucleoside analogue reverse transcriptase inhibitors (NRTI) and non-nucleoside analogue reverse transcriptase inhibitors (NNRTI). Of the 57 subjects, 43 (75.4%) harbored a minority variant containing at least one clinically relevant TDRM. Among the 43 subjects, 33 (76.7%) had detectable minority resistant variants to NRTIs, 6 (13.9%) to NNRTIs, and 16 (37.2%) to PR inhibitors. The comparison of viral sequences in both sources, plasma and cells, would have detected 48 DNA provirus disclosed TDRM by MPS previously missed by plasma bulk analysis. CONCLUSION Our findings revealed a high prevalence of TDRM found in this group, as the use of MPS drastically increased the detection of these mutations. Sequencing proviral DNA provided additional information about TDRM, which may impact treatment decisions. The overall results emphasize the importance of continuous monitoring.
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Affiliation(s)
- Rodrigo Pessôa
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Sabri S. Sanabani
- Laboratory of Dermatology and Immunodeficiencies, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil
- Clinical Laboratory, Department of Pathology, Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo, Brazil
- * E-mail:
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24
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Aldous AM, Castel AD, Parenti DM. Prevalence and trends in transmitted and acquired antiretroviral drug resistance, Washington, DC, 1999-2014. BMC Res Notes 2017; 10:474. [PMID: 28893321 PMCID: PMC5594524 DOI: 10.1186/s13104-017-2764-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 08/31/2017] [Indexed: 11/29/2022] Open
Abstract
Background Drug resistance limits options for antiretroviral therapy (ART) and results in poorer health outcomes among HIV-infected persons. We sought to characterize resistance patterns and to identify predictors of resistance in Washington, DC. Methods We analyzed resistance in the DC Cohort, a longitudinal study of HIV-infected persons in care in Washington, DC. We measured cumulative drug resistance (CDR) among participants with any genotype between 1999 and 2014 (n = 3411), transmitted drug resistance (TDR) in ART-naïve persons (n = 1503), and acquired drug resistance (ADR) in persons with genotypes before and after ART initiation (n = 309). Using logistic regression, we assessed associations between patient characteristics and transmitted resistance to any antiretroviral. Results Prevalence of TDR was 20.5%, of ADR 40.5%, and of CDR 45.1% in the respective analysis groups. From 2004 to 2013, TDR prevalence decreased for nucleoside and nucleotide analogue reverse transcriptase inhibitors (15.0 to 5.5%; p = 0.0003) and increased for integrase strand transfer inhibitors (INSTIs) (0.0–1.4%; p = 0.04). In multivariable analysis, TDR was not associated with age, race/ethnicity, HIV risk group, or years from HIV diagnosis. Conclusions In this urban cohort of HIV-infected persons, almost half of participants tested had evidence of CDR; and resistance to INSTIs was increasing. If this trend continues, inclusion of the integrase-encoding region in baseline genotype testing should be strongly considered.
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Affiliation(s)
- Annette M Aldous
- Department of Epidemiology and Biostatistics, The George Washington University, Milken Institute School of Public Health, Washington, DC, 20037, USA
| | - Amanda D Castel
- Department of Epidemiology and Biostatistics, The George Washington University, Milken Institute School of Public Health, Washington, DC, 20037, USA
| | - David M Parenti
- Division of Infectious Diseases, The George Washington University School of Medicine, 2150 Pennsylvania Avenue, NW, Washington, DC, USA.
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Moscona R, Ram D, Wax M, Bucris E, Levy I, Mendelson E, Mor O. Comparison between next-generation and Sanger-based sequencing for the detection of transmitted drug-resistance mutations among recently infected HIV-1 patients in Israel, 2000-2014. J Int AIDS Soc 2017; 20:21846. [PMID: 28799325 PMCID: PMC5577736 DOI: 10.7448/ias.20.1.21846] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/22/2017] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Transmitted drug-resistance mutations (TDRM) may hamper successful anti-HIV-1 therapy and impact future control of the HIV-1 epidemic. Recently infected, therapy-naïve individuals are best suited for surveillance of such TDRM. In this study, TDRM, detected by next-generation sequencing (NGS) were compared to those identified by Sanger-based population sequencing (SBS) in recently infected HIV-1 patients. METHODS Historical samples from 80 recently infected HIV-1 patients, diagnosed between 2000 and 2014, were analysed by MiSeq (NGS) and ABI (SBS). DeepChek-HIV (ABL) was used for interpretation of the results. RESULTS Most patients were males (80%); Men who have sex with men (MSM) was the major transmission group (58.8%). Overall, TDRM were detected in 31.3% of patients by NGS and 8.8% by SBS, with SBS TDRM restricted to persons infected with subtype B. All SBS-detected TDRM were identified by NGS. The prevalence of TDRM impacting protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) was 11.3, 26.2 7.5%, respectively, in NGS analyses and 0, 3.8 and 5%, respectively, in SBS analyses. More patients with NGS and SBS TDRM were identified in 2008-2014 (37.2% or 13.9%, respectively) compared to 2000-2007 (24.3% or 2.7%, respectively), and a significantly greater number of these patients had multiple NGS TDRM. The most abundant, albeit, minor-frequency RT TDRM, were the K65R and D67N, while K103N, M184V and T215S were high-frequency mutations. Minor TDRM did not become a major variant in later samples and did not hinder successful treatment. CONCLUSIONS NGS can replace SBS for mutation detection and allows for the detection of low-frequency TDRM not identified by SBS. Although rates of TDRM in Israel continued to increase from 2000 to 2014, minor TDRM did not become major species. The need for ongoing surveillance of low-frequency TDRM should be revisited in a larger study.
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Affiliation(s)
- Roy Moscona
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Daniela Ram
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Marina Wax
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Itzchak Levy
- Infectious Disease Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
- School of Public Health, Tel Aviv University, Ramat-Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
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26
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Drug resistance in B and non-B subtypes amongst subjects recently diagnosed as primary/recent or chronic HIV-infected over the period 2013-2016: Impact on susceptibility to first-line strategies including integrase strand-transfer inhibitors. J Glob Antimicrob Resist 2017; 10:106-112. [PMID: 28732792 DOI: 10.1016/j.jgar.2017.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/30/2017] [Accepted: 05/03/2017] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES To characterize the prevalence of transmitted drug resistance mutations (TDRMs) by plasma analysis of 750 patients at the time of HIV diagnosis from January 1, 2013 to November 16, 2016 in the Veneto region (Italy), where all drugs included in the recommended first line therapies were prescribed, included integrase strand transfer inhibitors (InNSTI). METHODS TDRMs were defined according to the Stanford HIV database algorithm. RESULTS Subtype B was the most prevalent HIV clade (67.3%). A total of 92 patients (12.3%) were expected to be resistant to one drug at least, most with a single class mutation (60/68-88.2% in subtype B infected subjectsand 23/24-95.8% in non-B subjects) and affecting mainly NNRTIs. No significant differences were observed between the prevalence rates of TDRMs involving one or more drugs, except for the presence of E138A quite only in patients with B subtype and other NNRTI in subjects with non-B infection. The diagnosis of primary/recent infection was made in 73 patients (9.7%): they had almost only TDRMs involving a single class. Resistance to InSTI was studied in 484 subjects (53 with primary-recent infection), one patient had 143C in 2016, a total of thirteen 157Q mutations were detected (only one in primary/recent infection). CONCLUSIONS Only one major InSTI-TDRM was identified but monitoring of TDRMs should continue in the light of continuing presence of NNRTI-related mutation amongst newly diagnosed subjects, sometime impacting also to modern NNRTI drugs recommended in first-line therapy.
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Onywera H, Maman D, Inzaule S, Auma E, Were K, Fredrick H, Owiti P, Opollo V, Etard JF, Mukui I, Kim AA, Zeh C. Surveillance of HIV-1 pol transmitted drug resistance in acutely and recently infected antiretroviral drug-naïve persons in rural western Kenya. PLoS One 2017; 12:e0171124. [PMID: 28178281 PMCID: PMC5298248 DOI: 10.1371/journal.pone.0171124] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/16/2017] [Indexed: 11/21/2022] Open
Abstract
HIV-1 transmitted drug resistance (TDR) is of increasing public health concern in sub-Saharan Africa with the rollout of antiretroviral (ARV) therapy. Such data are, however, limited in Kenya, where HIV-1 drug resistance testing is not routinely performed. From a population-based household survey conducted between September and November 2012 in rural western Kenya, we retrospectively assessed HIV-1 TDR baseline rates, its determinants, and genetic diversity among drug-naïve persons aged 15–59 years with acute HIV-1 infections (AHI) and recent HIV-1 infections (RHI) as determined by nucleic acid amplification test and both Limiting Antigen and BioRad avidity immunoassays, respectively. HIV-1 pol sequences were scored for drug resistance mutations using Stanford HIVdb and WHO 2009 mutation guidelines. HIV-1 subtyping was computed in MEGA6. Eighty seven (93.5%) of the eligible samples were successfully sequenced. Of these, 8 had at least one TDR mutation, resulting in a TDR prevalence of 9.2% (95% CI 4.7–17.1). No TDR was observed among persons with AHI (n = 7). TDR prevalence was 4.6% (95% CI 1.8–11.2) for nucleoside reverse transcriptase inhibitors (NRTIs), 6.9% (95% CI 3.2–14.2) for non- nucleoside reverse transcriptase inhibitors (NNRTIs), and 1.2% (95% CI 0.2–6.2) for protease inhibitors. Three (3.4% 95% CI 0.8–10.1) persons had dual-class NRTI/NNRTI resistance. Predominant TDR mutations in the reverse transcriptase included K103N/S (4.6%) and M184V (2.3%); only M46I/L (1.1%) occurred in the protease. All the eight persons were predicted to have different grades of resistance to the ARV regimens, ranging from potential low-level to high-level resistance. HIV-1 subtype distribution was heterogeneous: A (57.5%), C (6.9%), D (21.8%), G (2.3%), and circulating recombinant forms (11.5%). Only low CD4 count was associated with TDR (p = 0.0145). Our findings warrant the need for enhanced HIV-1 TDR monitoring in order to inform on population-based therapeutic guidelines and public health interventions.
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Affiliation(s)
- Harris Onywera
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
- * E-mail: (CZ); (HO)
| | - David Maman
- Epicentre, Médecins Sans Frontières (MSF), Paris, France
| | - Seth Inzaule
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Erick Auma
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Kennedy Were
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Harrison Fredrick
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Prestone Owiti
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Valarie Opollo
- Center for Global Health Research (CGHR), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Jean-François Etard
- TransVIHMI IRD UMI 233 –INSERM U 1175 –Université de Montpellier, Montpellier, France
| | - Irene Mukui
- National AIDS and STI Control Programme (NASCOP), Ministry of Health, Nairobi, Kenya
| | - Andrea A. Kim
- US Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Clement Zeh
- US Centers for Disease Control and Prevention (CDC), Kisumu, Kenya
- * E-mail: (CZ); (HO)
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Fixed-dose combination emtricitabine/tenofovir/efavirenz initiated during acute HIV infection; 96-week efficacy and durability. AIDS 2016; 30:2815-2822. [PMID: 27662549 DOI: 10.1097/qad.0000000000001255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Updated guidelines recommend immediate antiretroviral treatment (ART) during acute HIV infection (AHI), but efficacy data on regimens during AHI are limited. METHODS We provide final data on a prospective, single-arm 96-week open-label study of once-daily emtricitabine/tenofovir/efavirenz initiated during AHI. The primary endpoint was the proportion of responders with HIV RNA less than 200 copies/ml by week 24. We examined time to viral suppression, retention, and CD8 cell activation through week 96 in relation to baseline characteristics. RESULTS Between January 2005 and December 2011, 92 AHI participants enrolled. Most participants (78%) were men who have sex with men (MSM), and 42% were young MSM (18-25 years of age). Two participants withdrew leaving 90 patients for analysis. Eighty-one (90%) remained on therapy and achieved viral suppression to less than 200 copies/ml by week 24, and 71 (79%) to less than 50 copies/ml at week 48. The median time from ART initiation to suppression less than 200 copies/ml was 65 days (range 7-523) and to less than 50 copies/ml was 105 days (range 14-523). The frequency of immune activation declined from a median of 67% to 16% through week 96. Retention on study was maintained in 92% of participants at week 48 and in 83% through week 96. Among 75 participants retained through week 96, 92% were suppressed to less than 50 copies/ml. Among 39 young MSM, 79% completed a week 96 visit and 67% were suppressed at week 96. CONCLUSION ART during AHI resulted in rapid and sustained viral suppression with high rates of retention in care and on ART in this cohort including a large proportion of young MSM.
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Declining trend in transmitted drug resistance detected in a prospective cohort study of acute HIV infection in Bangkok, Thailand. J Int AIDS Soc 2016; 19:20966. [PMID: 27802846 PMCID: PMC5090107 DOI: 10.7448/ias.19.1.20966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/18/2016] [Accepted: 08/22/2016] [Indexed: 12/14/2022] Open
Abstract
Introduction As availability of antiretroviral therapy expands in developing countries, the risk for transmission of drug-resistant HIV also increases. Patients with acute HIV infection (AHI) provide an opportunity for real-time monitoring of transmitted drug resistance (TDR). SEARCH 010/RV 254 study is a prospective, longitudinal study of AHI. This analysis was performed to characterize changes in TDR over time in persons enrolled in the AHI cohort. Methods Genotype testing for TDR mutations was performed on 229 subjects enrolled from 2009 to 2014. Results The cohort was predominantly male (95%) and men who have sex with men (92%). TDR prevalence was 7.0%, declining from 12.5% in 2009–2010 to 4.8% in 2013–2014 (p=0.08). By drug class, resistance prevalence was 3.6% for proteases inhibitors, 2.6% for nucleoside/nucleotide reverse transcriptase inhibitors and 2.2% for non-nucleoside reverse transcriptase inhibitors. The greatest decline in prevalence was seen in the non-nucleoside reverses transcriptase inhibitors, from 9.4% in 2009–2010 to 0.7% in 2013–2014 (p=0.005). Conclusions TDR appears to be declining among individuals with AHI in Bangkok and in 2013 to 2014 met the World Health Organization definition for low prevalence. Continued surveillance is necessary to determine if this trend persists.
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Understanding Local Spatial Variation Along the Care Continuum: The Potential Impact of Transportation Vulnerability on HIV Linkage to Care and Viral Suppression in High-Poverty Areas, Atlanta, Georgia. J Acquir Immune Defic Syndr 2016; 72:65-72. [PMID: 26630673 DOI: 10.1097/qai.0000000000000914] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Engagement in care is central to reducing mortality for HIV-infected persons and achieving the White House National AIDS Strategy of 80% viral suppression in the US by 2020. Where an HIV-infected person lives impacts his or her ability to achieve viral suppression. Reliable transportation access for healthcare may be a key determinant of this place-suppression relationship. METHODS ZIP code tabulation areas (ZCTAs) were the units of analysis. We used geospatial and ecologic analyses to examine spatial distributions of neighborhood-level variables (eg, transportation accessibility) and associations with: (1) community linkage to care, and (2) community viral suppression. Among Atlanta ZCTAs with data for newly diagnosed HIV cases (2006-2010), we used Moran I to evaluate spatial clustering and linear regression models to evaluate associations between neighborhood variables and outcomes. RESULTS In 100 ZCTAs with 8413 newly diagnosed HIV-positive residents, a median of 60 HIV cases were diagnosed per ZCTA during the 5-year period. We found significant clustering of ZCTAs with low linkage to care and viral suppression (Moran I = 0.218, P < 0.05). In high-poverty ZCTAs, a 10% point increase in ZCTA-level household vehicle ownership was associated with a 4% point increase in linkage to care (P = 0.02, R = 0.16). In low-poverty ZCTAs, a 10% point increase in ZCTA-level household vehicle ownership was associated with a 30% point increase in ZCTA-level viral suppression (P = 0.01, R = 0.08). CONCLUSIONS Correlations between transportation variables and community-level care linkage and viral suppression vary by area poverty level and provide opportunities for interventions beyond individual-level factors.
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Cho MC, Park CW, Park BG, Oh HB, Choi SH, Choi SE, Cho NS. Detecting primary drug-resistant mutations in Korean HIV patients using ultradeep pyrosequencing. J Virol Methods 2016; 234:115-22. [PMID: 27109046 DOI: 10.1016/j.jviromet.2016.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/24/2016] [Accepted: 04/10/2016] [Indexed: 12/13/2022]
Abstract
HIV primary resistance, drug resistance in treatment-naïve patients, is an emerging public health issue. The prevalence of HIV primary resistance mutations down to the level of 1% minor variants was investigated using ultradeep pyrosequencing (UDPS) in HIV-positive Korean blood donors and in treatment naïve chronic patients for the comparison. The entire pol region was sequenced from 25 HIV-positive blood donors, and 18 treatment-naïve chronic HIV patients. UDPS was successful in 19 blood donors and 18 chronic patients. In total, 1,011,338 sequence reads were aligned, and 28,093 sequence reads were aligned on average per sample. The prevalence of HIV primary resistance mutations in the HIV-positive blood donors and chronic HIV patients were 63.2% and 44.4% according to UDPS, respectively. Protease inhibitor (PI) drugs demonstrated different patterns in HIV-positive blood donors and chronic HIV patients, whereas non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors (NRTI), and integrase inhibitor (INI) drugs showed similar patterns between the two groups. Higher level of primary resistance prevalence was observed mainly because UDPS method could detect mutations in minor variants with 1-10% frequency. The higher resistance prevalence was observed in HIV-positive blood donors than in chronic patients. Considering that treatments for HIV-infected patients were recently amended to start at an earlier stage, information about degree of drug resistance to each drug between the two groups would help to establish future policies, design additional clinical trials, assess HIV patient care in Korea.
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Affiliation(s)
- Min-Chul Cho
- Department of Laboratory Medicine, Gyeongsang National University Hospital and Gyeongsang National University School of Medicine, Jinju, Korea, South Korea
| | - Chang-Wook Park
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Borae G Park
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Heung-Bum Oh
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea.
| | - Sang-Ho Choi
- Department of Infectious Diseases, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Sung-Eun Choi
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
| | - Nam-Sun Cho
- Korea Red Cross Blood Service, Korean Red Cross, Seoul, South Korea
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Baxter JD, Dunn D, White E, Sharma S, Geretti AM, Kozal MJ, Johnson MA, Jacoby S, Llibre JM, Lundgren J. Global HIV-1 transmitted drug resistance in the INSIGHT Strategic Timing of AntiRetroviral Treatment (START) trial. HIV Med 2015; 16 Suppl 1:77-87. [PMID: 25711326 DOI: 10.1111/hiv.12236] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2014] [Indexed: 01/21/2023]
Abstract
OBJECTIVES HIV-1 transmitted drug resistance (TDR) in treatment-naïve individuals is a well-described phenomenon. Baseline genotypic resistance testing is considered standard of care in most developed areas of the world. The aim of this analysis was to characterize HIV-1 TDR and the use of resistance testing in START trial participants. METHODS In the Strategic Timing of AntiRetroviral Treatment (START) trial, baseline genotypic resistance testing results were collected at study entry and analysed centrally to determine the prevalence of TDR in the study population. Resistance was based on a modified 2009 World Health Organization definition to reflect newer resistance mutations. RESULTS Baseline resistance testing was available in 1946 study participants. Higher rates of testing occurred in Europe (86.7%), the USA (81.3%) and Australia (89.9%) as compared with Asia (22.2%), South America (1.8%) and Africa (0.1%). The overall prevalence of TDR was 10.1%, more commonly to nonnucleoside reverse transcriptase inhibitors (4.5%) and nucleoside reverse transcriptase inhibitors (4%) compared with protease inhibitors (2.8%). The most frequent TDR mutations observed were M41L, D67N/G/E, T215F/Y/I/S/C/D/E/V/N, 219Q/E/N/R, K103N/S, and G190A/S/E in reverse transcriptase, and M46I/L and L90M in protease. By country, the prevalence of TDR was highest in Australia (17.5%), France (16.7%), the USA (12.6%) and Spain (12.6%). No participant characteristics were identified as predictors of the presence of TDR. CONCLUSIONS START participants enrolled in resource-rich areas of the world were more likely to have baseline resistance testing. In Europe, the USA and Australia, TDR prevalence rates varied by country.
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Affiliation(s)
- J D Baxter
- Cooper University Hospital/Cooper Medical School of Rowan University, Camden, NJ, USA
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Lai CC, Liu WC, Fang CT, Yang JY, Chang LH, Wu PY, Luo YZ, Chang SF, Su YC, Chang SY, Hung CC. Transmitted drug resistance of HIV-1 strains among individuals attending voluntary counselling and testing in Taiwan. J Antimicrob Chemother 2015; 71:226-34. [PMID: 26404079 DOI: 10.1093/jac/dkv284] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 08/13/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Genotypic drug resistance testing for HIV-1 has been integrated into voluntary counselling and testing (VCT) programmes to investigate the trends of transmitted drug resistance (TDR), including integrase mutations, among individuals with recent or chronic HIV infections in Taiwan. METHODS Between 2006 and 2014, 745 of 21 886 subjects (3.4%) tested HIV positive in the VCT service. The BED assay was used to identify recent HIV infections. Genotypic resistance mutations were interpreted using the WHO 2009 list. Integrase resistance mutations were analysed using the Stanford HIV Drug Resistance Database. RESULTS Three-hundred-and-sixty (48.3%) patients were recently infected with HIV-1. Of 440 patients linked to HIV care with analysable reverse transcriptase and protease genes, 49 (11.1%) were infected with HIV-1 harbouring at least one resistance-associated mutation (RAM). The prevalence of TDR to NRTIs, NNRTIs and PIs was 4.1%, 6.4% and 2.3%, respectively. TDR prevalence did not change significantly during the study period. CD4 counts ≤500 cells/mm(3) and hepatitis B surface antigen positivity were independent factors associated with acquiring drug-resistant HIV. The prevalence of integrase mutations was 3.2%. Among the seven major integrase mutations (T66I, E92Q, G140S, Y143C/H/R, S147G, Q148H/K/R and N155H), only one strain harbouring the Q148R mutation was detected. We found no statistically significant difference between patients with chronic infection and those with recent infection in the prevalence of drug-resistant mutations to any of the four classes of antiretroviral agents. CONCLUSIONS The prevalence of TDR of HIV-1 strains to available antiretroviral agents is moderately high, but transmission of HIV-1 with drug-resistant mutations remains stable in Taiwan.
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Affiliation(s)
- Chung-Chih Lai
- Department of Internal Medicine, Kaohsiung Medical University Hospital and College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Chun Liu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chi-Tai Fang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health, Taipei, Taiwan
| | - Jyh-Yuan Yang
- Center for Research, Diagnostics, and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Lan-Hsin Chang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Ying Wu
- Center of Infection Control, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Zhen Luo
- Center of Infection Control, National Taiwan University Hospital, Taipei, Taiwan
| | - Shu-Fang Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Ching Su
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chien-Ching Hung
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan Department of Medical Research, China Medical University Hospital, Taichung, Taiwan Department of Medical Research, China Medical University Hospital and China Medical University, Taichung, Taiwan
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Richterman A, Sawinski D, Reese PP, Lee DH, Clauss H, Hasz RD, Thomasson A, Goldberg DS, Abt PL, Forde KA, Bloom RD, Doll SL, Brady KA, Blumberg EA. An Assessment of HIV-Infected Patients Dying in Care for Deceased Organ Donation in a United States Urban Center. Am J Transplant 2015; 15:2105-16. [PMID: 25976241 DOI: 10.1111/ajt.13308] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/05/2015] [Accepted: 03/05/2015] [Indexed: 01/25/2023]
Abstract
Organ transplantation is an acceptable option for human immunodeficiency virus (HIV)-infected patients with end-stage kidney or liver disease. With worse outcomes on the waitlist, HIV-infected patients may actually be disproportionately affected by the organ shortage in the United States. One potential solution is the use of HIV-infected deceased donors (HIVDD), recently legalized by the HIV Organ Policy Equity (HOPE) Act. This is the first analysis of patient-specific data from potential HIVDD, retrospectively examining charts of HIV-infected patients dying in care at six HIV clinics in Philadelphia, Pennsylvania from January 1, 2009 to June 30, 2014. Our data suggest that there are four to five potential HIVDD dying in Philadelphia annually who might yield two to three kidneys and three to five livers for transplant. Extrapolated nationally, this would approximate 356 potential HIVDD yielding 192 kidneys and 247 livers annually. However, several donor risk indices raise concerns about the quality of kidneys that could be recovered from HIVDD as a result of older donor age and comorbidities. On the other hand, livers from these potential HIVDD are of similar quality to HIV-negative donors dying locally, although there is a high prevalence of positive hepatitis C antibody.
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Affiliation(s)
- A Richterman
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - D Sawinski
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - P P Reese
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - D H Lee
- Department of Medicine, Drexel University, Philadelphia, PA
| | - H Clauss
- Department of Medicine, Temple University, Philadelphia, PA
| | - R D Hasz
- Gift of Life Donor Program, Philadelphia, PA
| | - A Thomasson
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - D S Goldberg
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - P L Abt
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - K A Forde
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - R D Bloom
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - S L Doll
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - K A Brady
- Philadelphia Department of Public Health, Philadelphia, PA
| | - E A Blumberg
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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Matthew JS, Virginia LK, David MP. Human immunodeficiency virus (HIV) in Washington, D.C.: Prevalence of antiretroviral resistance in treatment nave patients from 2007 to 2010. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/jahr2015.0327] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Buchacz K, Young B, Palella FJ, Armon C, Brooks JT. Trends in use of genotypic resistance testing and frequency of major drug resistance among antiretroviral-naive persons in the HIV Outpatient Study, 1999-2011. J Antimicrob Chemother 2015; 70:2337-46. [PMID: 25979729 DOI: 10.1093/jac/dkv120] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/09/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Monitoring antiretroviral drug resistance can inform treatment recommendations; however, there are few such data from US patients before they initiate ART. METHODS We analysed data from HIV Outpatient Study (HOPS) participants from nine US HIV clinics who were diagnosed with HIV infection during 1999-2011. Using the IAS-USA December 2010 guidelines, we assessed the frequency of major drug resistance mutations (mDRMs) related to antiretroviral agents in viral isolates from patients who underwent commercial genotypic testing (GT) for resistance before initiating ART. We employed general linear regression models to assess factors associated with having undergone GT, and then factors associated with having mDRM. RESULTS Among 1531 eligible patients, 758 (49.5%) underwent GT before first ART, increasing from 15.5% in 1999-2002 to 75.9% in 2009-11 (P < 0.001). GT was carried out a median of 1.2 months after the diagnosis of HIV. In adjusted regression analyses, patients with pre-ART CD4+ T lymphocyte counts ≥200 cells/mm(3) or with HIV RNA levels >5.0 log10 copies/mL and those with a first HOPS visit in 2006 or later were significantly (P < 0.05) more likely to have undergone GT. Of the 758 patients, 114 (15.0%) had mDRMs; mutations relating to NRTIs, NNRTIs and PIs were present in 8.0%, 7.1% and 2.6%, respectively. There was no temporal change in the frequency of mDRM, and mDRMs were associated with an HIV RNA level <4.0 log10 copies/mL. CONCLUSIONS During 1999-2011, GT use among antiretroviral-naive patients became more common, but a quarter of patients in recent years remained untested. The frequency of mDRMs remained stable over time at about 15%.
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Affiliation(s)
- Kate Buchacz
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin Young
- APEX Family Medicine, Denver, CO, USA International Association of Providers of AIDS Care, Washington, DC, USA
| | | | | | - John T Brooks
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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High prevalence of transmitted drug resistance in acute HIV-infected Thai men who have sex with men. J Acquir Immune Defic Syndr 2015; 68:481-5. [PMID: 25559593 DOI: 10.1097/qai.0000000000000502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
: As use of antiretroviral therapy in Thailand increases, so does the potential for transmission of drug-resistant HIV. We describe the prevalence of WHO surveillance drug resistance mutations among 120 subjects who underwent genotypic testing during acute HIV infection in Bangkok, Thailand. In this cohort of predominantly men who have sex with men, we observed an overall transmitted drug resistance prevalence of 9.2%, including nucleoside/nucleotide analog reverse transcriptase inhibitor 5.0%, nonnucleoside analog reverse transcriptase inhibitor 3.4%, and protease inhibitor 3.4%. These prevalence estimates are higher than previous reports of transmitted drug resistance in Thailand. Baseline drug resistance testing may be warranted, particularly among men who have sex with men.
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Zhang J, Guo Z, Yang J, Pan X, Jiang J, Ding X, Zhang W, Xia Y, Xu Y, Huang J. Genetic diversity of HIV-1 and transmitted drug resistance among newly diagnosed individuals with HIV infection in Hangzhou, China. J Med Virol 2015; 87:1668-76. [PMID: 25899877 DOI: 10.1002/jmv.24223] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2015] [Indexed: 11/06/2022]
Abstract
HIV transmitted drug resistance (TDR) can compromise antiretroviral therapy (ART) in resource-limited countries like China where ART has been scaled up and thus leads to an important public health concern. The aim of the study was to elucidate the HIV-1 genetic characteristics and TDR in Hangzhou, China. Two-hundred eleven ART-naive, newly diagnosed individuals were enrolled during January and August 2013. Specimens were classified as recent or chronic infections using the BED capture enzyme immunoassay (BED-CEIA). The pol fragment covering the entire protease and the first 300 codons of the reverse transcriptase gene was amplified by RT-PCR and nested PCR. Genotypic drug resistance (DR) and phylogenetic analysis were performed on the 200 obtained sequences. Multiple genotypes were identified, including CRF01_AE (62.0%), CRF07_BC (31.0%), subtype B (2.0%), CRF08_BC (1.5%), CRF55_01B (1.0%), CRF18_cpx (0.5%), and unique recombinant forms (URFs, 2.0%). All the four URFs were found in men who have sex with men, consisting of a recombination of CRF01_AE with subtype B or CRF07_BC. The prevalence of primary DR in newly diagnosed individuals in Hangzhou was low (4.0%). The proportion of DR mutation to protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) was 1.5%, 1.5%, and 1.0%, respectively. BED-CEIA revealed that 21.8% (45/211) of the specimens were associated with recent infections. The prevalence of TDR in recent infections was moderate (6.5%). High HIV diversity and relatively high prevalence of TDR in new infections has been found in Hangzhou, indicating an increasing challenge for future HIV prevention and treatment.
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Affiliation(s)
- Jiafeng Zhang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhihong Guo
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jiezhe Yang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaohong Pan
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jun Jiang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaobei Ding
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Wenjun Zhang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yan Xia
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yun Xu
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jingjing Huang
- Department of HIV/AIDS & STD control and prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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HIV diversity and drug resistance from plasma and non-plasma analytes in a large treatment programme in western Kenya. J Int AIDS Soc 2014; 17:19262. [PMID: 25413893 PMCID: PMC4238965 DOI: 10.7448/ias.17.1.19262] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Antiretroviral resistance leads to treatment failure and resistance transmission. Resistance data in western Kenya are limited. Collection of non-plasma analytes may provide additional resistance information. METHODS We assessed HIV diversity using the REGA tool, transmitted resistance by the WHO mutation list and acquired resistance upon first-line failure by the IAS-USA mutation list, at the Academic Model Providing Access to Healthcare (AMPATH), a major treatment programme in western Kenya. Plasma and four non-plasma analytes, dried blood-spots (DBS), dried plasma-spots (DPS), ViveST(TM)-plasma (STP) and ViveST-blood (STB), were compared to identify diversity and evaluate sequence concordance. RESULTS Among 122 patients, 62 were treatment-naïve and 60 treatment-experienced; 61% were female, median age 35 years, median CD4 182 cells/µL, median viral-load 4.6 log10 copies/mL. One hundred and ninety-six sequences were available for 107/122 (88%) patients, 58/62 (94%) treatment-naïve and 49/60 (82%) treated; 100/122 (82%) plasma, 37/78 (47%) attempted DBS, 16/45 (36%) attempted DPS, 14/44 (32%) attempted STP from fresh plasma and 23/34 (68%) from frozen plasma, and 5/42 (12%) attempted STB. Plasma and DBS genotyping success increased at higher VL and shorter shipment-to-genotyping time. Main subtypes were A (62%), D (15%) and C (6%). Transmitted resistance was found in 1.8% of plasma sequences, and 7% combining analytes. Plasma resistance mutations were identified in 91% of treated patients, 76% NRTI, 91% NNRTI; 76% dual-class; 60% with intermediate-high predicted resistance to future treatment options; with novel mutation co-occurrence patterns. Nearly 88% of plasma mutations were identified in DBS, 89% in DPS and 94% in STP. Of 23 discordant mutations, 92% in plasma and 60% in non-plasma analytes were mixtures. Mean whole-sequence discordance from frozen plasma reference was 1.1% for plasma-DBS, 1.2% plasma-DPS, 2.0% plasma-STP and 2.3% plasma-STB. Of 23 plasma-STP discordances, one mutation was identified in plasma and 22 in STP (p<0.05). Discordance was inversely significantly related to VL for DBS. CONCLUSIONS In a large treatment programme in western Kenya, we report high HIV-1 subtype diversity; low plasma transmitted resistance, increasing when multiple analytes were combined; and high-acquired resistance with unique mutation patterns. Resistance surveillance may be augmented by using non-plasma analytes for lower-cost genotyping in resource-limited settings.
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Charest H, Doualla-Bell F, Cantin R, Murphy DG, Lemieux L, Brenner B, Hardy I, Moisi D, Lo E, Baril JG, Wainberg MA, Roger M, Tremblay C. A significant reduction in the frequency of HIV-1 drug resistance in Québec from 2001 to 2011 is associated with a decrease in the monitored viral load. PLoS One 2014; 9:e109420. [PMID: 25295725 PMCID: PMC4190276 DOI: 10.1371/journal.pone.0109420] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
Background HIV drug resistance represents a major threat for effective treatment. We assessed the trends in the frequency of drug resistance mutations and the monitored viral load (VL) in treatment-naïve (TN) and treatment-experienced (TE) individuals infected with HIV-1 in Québec, Canada, between 2001 and 2011. Methods and Findings Resistance data were obtained from 4,105 and 5,086 genotypic tests performed on TN and TE patients, respectively. Concomitantly, 274,161 VL tests were carried out in the Province. Changes over time in drug resistance frequency and in different categories of VL were assessed using univariate logistic regression. Multiple logistic regression was used to evaluate associations between the rates of certain mutations and antiretroviral prescriptions. From 2001 to 2011, the proportion of undetectable VL test results continually increased, from 42.1% to 75.9%, while a significant decrease in the frequency of resistance mutations associated with protease inhibitors [PI (from 54% to 16%)], nucleoside [NRTI (from 78% to 37%) and non-nucleoside reverse transcriptase inhibitors [NNRTI (from 44% to 31%)] was observed in TE patients. In TN individuals, the overall frequency of transmitted drug resistance was 13.1%. A multiple logistic regression analysis indicated that the introduction of co-formulated emtricitabine/tenofovir or emtricitabine/tenofovir/efavirenz was positively associated with the decrease of the frequency of the M184I/V mutations observed overtime (p = 0.0004). Conclusions We observed a significant decrease in the frequency of drug resistance mutations in TE patients, concomitant with a decrease in the proportion of patients with detectable viremia. These findings may be related to both the increased potencies and adherence to therapy associated with newer antiretroviral regimens. Nevertheless, our data demonstrate that broad use of antiretrovirals does not increase the level of circulating drug resistant variants.
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Affiliation(s)
- Hugues Charest
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
| | - Florence Doualla-Bell
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Régis Cantin
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Donald G. Murphy
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Linda Lemieux
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Bluma Brenner
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Isabelle Hardy
- Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Daniela Moisi
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Ernest Lo
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | | | - Mark A. Wainberg
- McGill AIDS Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Michel Roger
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
- Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Cécile Tremblay
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
- Centre hospitalier de l’Université de Montréal (CHUM), Montréal, Québec, Canada
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Lee GQ, Bangsberg DR, Muzoora C, Boum Y, Oyugi JH, Emenyonu N, Bennett J, Hunt PW, Knapp D, Brumme CJ, Harrigan PR, Martin JN. Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda. AIDS Res Hum Retroviruses 2014; 30:896-906. [PMID: 24960249 DOI: 10.1089/aid.2014.0043] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Few reports have examined the impact of HIV-1 transmitted drug resistance (TDR) in resource-limited settings where there are fewer regimen choices and limited pretherapy/posttherapy resistance testing. In this study, we examined TDR prevalence in Kampala and Mbarara, Uganda and assessed its virologic consequences after antiretroviral therapy initiation. We sequenced the HIV-1 protease/reverse transcriptase from n=81 and n=491 treatment-naive participants of the Uganda AIDS Rural Treatment Outcomes (UARTO) pilot study in Kampala (AMU 2002-2004) and main cohort in Mbarara (MBA 2005-2010). TDR-associated mutations were defined by the WHO 2009 surveillance mutation list. Posttreatment viral load data were available for both populations. Overall TDR prevalence was 7% (Kampala) and 3% (Mbarara) with no significant time trend. There was a slight but statistically nonsignificant trend indicating that the presence of TDR was associated with a worse treatment outcome. Virologic suppression (≤400 copies/ml within 6 months posttherapy initiation) was achieved in 87% and 96% of participants with wildtype viruses versus 67% and 83% of participants with TDR (AMU, MBA p=0.2 and 0.1); time to suppression (log-rank p=0.3 and p=0.05). Overall, 85% and 96% of study participants achieved suppression regardless of TDR status. Surprisingly, among the TDR cases, approximately half still achieved suppression; the presence of pretherapy K103N while on nevirapine and fewer active drugs in the first regimen were most often observed with failures. The majority of patients benefited from the local HIV care system even without resistance monitoring. Overall, TDR prevalence was relatively low and its presence did not always imply treatment failure.
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Affiliation(s)
| | - David R. Bangsberg
- Mbarara University of Science of Technology, Mbarara, Uganda
- Harvard Medical School, Boston, Massachusetts
- Harvard School of Public Health, Boston, Massachusetts
- Massachusetts General Hospital, Boston, Massachusetts
| | - Conrad Muzoora
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - Yap Boum
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - Jessica H. Oyugi
- University of California, San Francisco, California
- Independent consultant
| | - Nneka Emenyonu
- Mbarara University of Science of Technology, Mbarara, Uganda
| | - John Bennett
- University of California, San Francisco, California
| | | | - David Knapp
- B.C. Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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Dai L, Li N, Wei F, Li J, Liu Y, Xia W, Zhang T, Guo C, Wang W, Schwartz SA, Mahajan SD, Hsiao CB, Wu H. Transmitted antiretroviral drug resistance in the men who have sex with men HIV patient cohort, Beijing, China, 2008-2011. Viral Immunol 2014; 27:392-7. [PMID: 25084305 DOI: 10.1089/vim.2014.0025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transmitted drug resistance (TDR) is an ongoing public health problem in HIV disease treatment. However, little is known about TDR among men who have sex with men (MSM) patients in China. In addition, TDR prevalence among patients with acute HIV infection (AHI) or early HIV infection (EHI) was believed higher than that of patients with chronic HIV infection (CHI), but as AHI is typically either unidentified or crudely defined in large populations, very few direct comparisons have been made. We did a retrospective analysis of TDR in 536 antiretroviral-naive MSM patients from our immunodeficiency clinics at You'an Hospital, Capital Medical University (CMU), in Beijing, China, 2008-2011. The cohort included 266 patients with AHI/EHI and 270 patients with CHI. We analyzed the subtype, estimated the TDR prevalence, and characterized the model of TDR and the predicted drug sensitivity. Additionally, we made a comparison of TDR between the patients with AHI/EHI and patients with CHI. Our results indicated that among the 536 patients, HIV-1 subtype CRF01_AE accounted for 52.1%, subtype B accounted for 24.8%, CRF07_BC/ CRF08_BC accounted for 21.6% (116/536), and 1.3% were denoted as unique recombinant forms (URFs). A total of 7.8% patients had one or more transmitted HIV-1 drug resistance mutations, representing 6.2% for PI-related mutations, 0.9% for NRTI-related mutations, and 1.7% for NNRTI-related mutations. Although patients with AHI/EHI had a higher TDR prevalence as compared to that of patients with CHI, the difference was not statistically significant. There was no significant difference in TDR model and predicted drug susceptibility between the two groups of patients either. This study provides important strategic information for public health planning by healthcare officials in China and warrants a comprehensive study with larger patient cohorts from various healthcare centers within China.
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Affiliation(s)
- Lili Dai
- 1 Center for Infectious Diseases, Beijing You'an Hospital, Capital Medical University , Beijing, China
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Transmitted drug resistance and antiretroviral treatment outcomes in non-subtype B HIV-1-infected patients in South East Asia. J Acquir Immune Defic Syndr 2014; 66:74-9. [PMID: 24413039 DOI: 10.1097/qai.0000000000000108] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND We compared treatment outcomes of transmitted drug resistance (TDR) in patients on fully or partially sensitive drug regimens. METHODS Factors associated with survival and failure were analyzed using Cox proportional hazards and discrete time conditional logistic models. RESULTS TDR, found in 60 (4.1%) of 1471 Asian treatment-naive patients, was one of the significant predictors of failure. Patients with TDR to >1 drug in their regimen were >3 times as likely to fail compared to no TDR. CONCLUSIONS TDR was associated with failure in the context of non-fully sensitive regimens. Efforts are needed to incorporate resistance testing into national treatment programs.
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Stekler JD, McKernan J, Milne R, Tapia KA, Mykhalchenko K, Holte S, Maenza J, Stevens CE, Buskin SE, Mullins JI, Frenkel LM, Collier AC. Lack of resistance to integrase inhibitors among antiretroviral-naive subjects with primary HIV-1 infection, 2007-2013. Antivir Ther 2014; 20:77-80. [PMID: 24831260 DOI: 10.3851/imp2780] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND US guidelines recommend genotyping for persons newly diagnosed with HIV infection to identify transmitted drug resistance mutations associated with decreased susceptibility to nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors and protease inhibitors. To date, testing for integrase strand transfer inhibitor (INSTI) mutations has not been routinely recommended. We aimed to evaluate the prevalence of transmitted INSTI mutations among persons with primary HIV-1 infection in Seattle, WA, USA. METHODS Persons with primary HIV-1 infection have enrolled in an observational cohort at the University of Washington Primary Infection Clinic since 1992. We performed a retrospective analysis of plasma specimens collected prospectively from the 82 antiretroviral-naive subjects who were enrolled from 2007-2013, after FDA-approval of the first INSTI. Resistance testing was performed by consensus sequencing. RESULTS Specimens for analysis had been obtained a median of 24 (IQR 18-41, range 8-108) days after the estimated date of HIV-1 infection. All subjects were infected with HIV-1 subtype B except for one subject infected with subtype C. Consensus sequencing identified no subjects with major INSTI mutations (T66I, E92Q, G140S, Y143C/H/R, S147G, Q148H/K/R, N155H). Using exact binomial CIs, the upper bound of the 95% CI was 4.4%. CONCLUSIONS Although our sample size was small, this study does not support the need at this time to evaluate integrase mutations as part of routine consensus sequencing among persons newly diagnosed with HIV-1 infection. However, it is likely that the prevalence of transmitted INSTI mutations may increase with the recent commercial introduction of additional INSTIs and presumably greater INSTI use among persons living with HIV-1.
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Affiliation(s)
- Joanne D Stekler
- Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA.
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Abstract
Human immunodeficiency virus (HIV) exhibits remarkable diversity in its genomic makeup and exists in any given individual as a complex distribution of closely related but nonidentical genomes called a viral quasispecies, which is subject to genetic variation, competition, and selection. This viral diversity clinically manifests as a selection of mutant variants based on viral fitness in treatment-naive individuals and based on drug-selective pressure in those on antiretroviral therapy (ART). The current standard-of-care ART consists of a combination of antiretroviral agents, which ensures maximal viral suppression while preventing the emergence of drug-resistant HIV variants. Unfortunately, transmission of drug-resistant HIV does occur, affecting 5% to >20% of newly infected individuals. To optimize therapy, clinicians rely on viral genotypic information obtained from conventional population sequencing-based assays, which cannot reliably detect viral variants that constitute <20% of the circulating viral quasispecies. These low-frequency variants can be detected by highly sensitive genotyping methods collectively grouped under the moniker of deep sequencing. Low-frequency variants have been correlated to treatment failures and HIV transmission, and detection of these variants is helping to inform strategies for vaccine development. Here, we discuss the molecular virology of HIV, viral heterogeneity, drug-resistance mutations, and the application of deep sequencing technologies in research and the clinical care of HIV-infected individuals.
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Affiliation(s)
- Shiven B Chabria
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut 06510; , ,
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Spatial epidemiology of recently acquired HIV infections across rural and urban areas of North Carolina. PLoS One 2014; 9:e88512. [PMID: 24520392 PMCID: PMC3919766 DOI: 10.1371/journal.pone.0088512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/06/2014] [Indexed: 01/25/2023] Open
Abstract
Transmission of HIV continues in the United States (US), despite prevention efforts aimed at education and treatment. Concurrently, drug resistance in HIV, particularly in patients being infected with HIV for the first time, poses a threat to the continued success of treatment for HIV positive individuals. In North Carolina, nearly one in five individuals with acute HIV infection (AHI) is infected with a drug-resistant strain, a phenomenon known as transmitted drug resistance (TDR). Few studies of AHI or TDR take into account both the spatial aspects of residence at time of infection and the genetic characteristics of the viruses, and questions remain about how viruses are transmitted across space and the rural-urban divide. Using AHI strains from North Carolina, we examined whether differences exist in the spatial patterns of AHI versus AHI with TDR, as well as whether the genetic characteristics of these HIV infections vary by rural-urban status and across Health Service Areas. The highest amounts of TDR were detected in persons under age 30, African Americans, and men who have sex with men (MSM) - similar to the populations where the highest numbers of AHI without TDR are observed. Nearly a quarter of patients reside in rural areas, and there are no significant differences between rural and urban residence among individuals infected with drug resistant or drug susceptible viruses. We observe similar levels of genetic distance between HIV found in rural and urban areas, indicating that viruses are shared across the rural-urban divide. Genetic differences are observed, however, across Health Service Areas, suggesting that local areas are sites of genetic differentiation in viruses being transmitted to newly infected individuals. These results indicate that future efforts to prevent HIV transmission need to be spatially targeted, focusing on local-level transmission in risky populations, in addition to statewide anti- HIV efforts.
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Geretti AM, Conibear T, Hill A, Johnson JA, Tambuyzer L, Thys K, Vingerhoets J, Van Delft Y, Rieger A, Vetter N, Greil R, Pedersen C, Storgaard M, Morlat P, Katlama C, Durant J, Cotte L, Duvivier C, Rey D, Esser S, Stellbrink C, Schmidt W, Stoll M, Stephan C, Fatkenheuer G, Stoehr A, Rockstroh J, Banhegyi D, Itzchak L, Shahar E, Maayan S, Turner D, Lazzarin A, Antinori A, Carosi G, Minoli L, di Perri G, Filice G, Andreoni M, Duiculescu D, Rugina S, Erscoiu S, Streinu A, Pronin A, Pokrovsky V, Gruzdev B, Yakovlev A, Voronin E, Clotet B, Gatell J, Arribas J, Podzamczer D, Domingo P, Alvarez CM, Quero JH, Furrer H, Feher J, Johnson M, Fox J, Nelson M, Fisher M, Orkin C. Sensitive testing of plasma HIV-1 RNA and Sanger sequencing of cellular HIV-1 DNA for the detection of drug resistance prior to starting first-line antiretroviral therapy with etravirine or efavirenz. J Antimicrob Chemother 2013; 69:1090-7. [DOI: 10.1093/jac/dkt474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Affiliation(s)
- Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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Transmitted antiretroviral drug resistance in New York City, 2006-2010: the first five years of routine genotype surveillance. J Acquir Immune Defic Syndr 2013; 63:e119-22. [PMID: 23760097 DOI: 10.1097/qai.0b013e31828d2fc1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Technologic advances in human immunodeficiency virus type 1 (HIV-1) sequencing have revolutionized the study of antiretroviral drug resistance and are increasingly moving from the laboratory to clinical practice. These techniques are able to detect HIV-1 drug resistance mutations present at low frequencies not detectable by current HIV-1 genotyping assays. For a number of commonly used antiretroviral medications, such as nonnucleoside reverse transcriptase inhibitors, the detection of these drug-resistant minority variants significantly increases the risk of treatment failure. The level of evidence, however, is insufficient to determine the impact of HIV-1 minority variants for several other classes of antiretroviral medications. Clinicians should be aware of the novel technologies that are moving into routine clinical use and the clinical implications of HIV-1 minority variants. Additional studies are needed to determine the optimal platform for clinical application of these new technologies and to provide guidance to clinicians on the type and frequency of clinically important HIV-1 minority variants.
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Affiliation(s)
- Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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