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Zhou S, Long N, Swanstrom R. Evolution Driven By A Varying Host Environment Selects For Distinct HIV-1 Entry Phenotypes and Other Informative Variants. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2023; 3:1291996. [PMID: 38239974 PMCID: PMC10795538 DOI: 10.3389/fviro.2023.1291996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
HIV-1 generates remarkable intra- and inter-host viral diversity during infection. In response to dynamic selective pressures of the host environment, HIV-1 will evolve distinct phenotypes - biological features that provide fitness advantages. The transmitted form of HIV-1 has been shown to require a high density of CD4 on the target cell surface (as found on CD4+ T cells) and typically uses CCR5 as a co-receptor during entry. This phenotype is referred to as R5 T cell-tropic (or R5 T-tropic); however, HIV-1 can switch to a secondary co-receptor, CXCR4, resulting in a X4 T cell-tropic phenotype. Macrophage-tropic (or M-tropic) HIV-1 can evolve to efficiently enter cells expressing low densities of CD4 on their surface (such as macrophages/microglia). So far only CCR5-using M-tropic viruses have been found. M-tropic HIV-1 is most frequently found within the central nervous system, and infection of the CNS has been associated with neurological impairment. It has been shown that interferon resistance phenotypes have a selective advantage during transmission, but the underlying mechanism of this is still unclear. During untreated infection, HIV-1 evolves under selective pressure from both the humoral/antibody response and CD8+ T cell killing. Sufficiently potent antiviral therapy will suppress viral replication, but if the antiviral drugs are not sufficiently potent to stop replication then the replicating virus will evolve drug resistance. HIV-1 phenotypes are highly relevant to treatment efforts, clinical outcomes, vaccine studies, and cure strategies. Therefore, it is critical to understand the dynamics of the host environment that drive these phenotypes and how they affect HIV-1 pathogenesis. This review will provide a comprehensive discussion of HIV-1 entry, transmission, and drug resistance phenotypes. Finally, we will assess the methods used in previous and current research to characterize these phenotypes.
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Affiliation(s)
- Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nathan Long
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Fiebig U, Altmann B, Hauser A, Koppe U, Hanke K, Gunsenheimer-Bartmeyer B, Bremer V, Baumgarten A, Bannert N. Transmitted drug resistance and subtype patterns of viruses from reported new HIV diagnoses in Germany, 2017-2020. BMC Infect Dis 2023; 23:673. [PMID: 37817087 PMCID: PMC10563336 DOI: 10.1186/s12879-023-08649-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The transmission of resistant HIV variants jeopardizes the effective use of antiretrovirals for therapy and prophylaxis. Molecular surveillance of new HIV diagnoses with a focus on prevalence and type of resistance associated mutations and the subtype of circulating viruses is mandatory. METHOD From 2017 to 2020, 11,527 new HIV diagnoses were reported in Germany to the Robert Koch Institute (RKI). Protease (PR) and reverse-transcriptase (RT) sequences were obtained from 4559 (39.6%) cases, and PR, RT and integrase (IN) sequences were obtained from 3097 (26.9%) cases. The sequences were analyzed with data from the national HIV reports. RESULTS Among all cases in the analysis, the proportion of primary resistance was 4.3% for nucleoside reverse-transcriptase inhibitors (NRTIs), 9.2% for non-NRTI (NNRTIs), 3.3% for protease inhibitors (PIs) and 1.4% for integrase inhibitors (INIs). Dual-class resistance was highest for NRTIs/NNRTIs with 1.2%. There was no trend in the proportion of viruses resistant to drug classes. Most individual key mutations associated with relevant resistance had a prevalence below 1% including K65R (0.1%) and M184V (0.6%). A notable exception was K103NS, with a prevalence of 2.9% and a significant increase (pTrend=0.024) during 2017-2020. In this period, diagnoses of infections with HIV-1 subtype B were the most common at 58.7%, but its prevalence was declining (pTrend=0.049) while the frequency of minority subtypes (each < 1%) increased (pTrend=0.007). Subtype B was highest (75.6%) in men who have sex with men (MSM) and lowest in reported heterosexual transmissions (HETs, 22.6%). CONCLUSION The percentage of primary resistance was high but at a stable level. A genotypic determination of resistance is therefore still required before the start of therapy. The subtype diversity of circulating HIV-1 is increasing.
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Affiliation(s)
- Uwe Fiebig
- Unit 18 "HIV and other Retroviruses, Sexually transmitted bacterial Pathogens (STI) and HIV", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Britta Altmann
- Unit 18 "HIV and other Retroviruses", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Andrea Hauser
- Unit 18 "HIV and other Retroviruses", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Uwe Koppe
- Unit 34 "HIV/AIDS, STI and Blood-borne Infections", Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Kirsten Hanke
- Unit 18 "HIV and other Retroviruses, Sexually transmitted bacterial Pathogens (STI) and HIV", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Barbara Gunsenheimer-Bartmeyer
- Unit 34 "HIV/AIDS, STI and Blood-borne Infections", Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Viviane Bremer
- Unit 34 "HIV/AIDS, STI and Blood-borne Infections", Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Axel Baumgarten
- Center for Infectiology Berlin-Prenzlauer Berg, Nordufer 20, 13353, Berlin, Germany
| | - Norbert Bannert
- Unit 18 "HIV and other Retroviruses, Sexually transmitted bacterial Pathogens (STI) and HIV", Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany.
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Xu Y, Shi H, Dong X, Ding C, Wu S, Li X, Zhang H, Qiao M, Li X, Zhu Z. Transmitted drug resistance and transmission clusters among ART-naïve HIV-1-infected individuals from 2019 to 2021 in Nanjing, China. Front Public Health 2023; 11:1179568. [PMID: 37674678 PMCID: PMC10478099 DOI: 10.3389/fpubh.2023.1179568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/11/2023] [Indexed: 09/08/2023] Open
Abstract
Background Transmitted drug resistance (TDR) is an increasingly prevalent problem worldwide, which will significantly compromise the effectiveness of HIV treatments. However, in Nanjing, China, there is still a dearth of research on the prevalence and transmission of TDR among ART-naïve HIV-1-infected individuals. This study aimed to understand the prevalence and transmission of TDR in Nanjing. Methods A total of 1,393 participants who were newly diagnosed with HIV-1 and had not received ART between January 2019 and December 2021 were enrolled in this study. HIV-1 pol gene sequence was obtained by viral RNA extraction and nested PCR amplification. Genotypes, TDR and transmission cluster analyses were conducted using phylogenetic tree, Stanford HIV database algorithm and HIV-TRACE, respectively. Univariate and multivariate logistic regression analyses were performed to identify the factors associated with TDR. Results A total of 1,161 sequences were successfully sequenced, of which CRF07_BC (40.6%), CRF01_AE (38.4%) and CRF105_0107 (6.3%) were the main HIV-1 genotypes. The overall prevalence of TDR was 7.8%, with 2.0% to PIs, 1.0% to NRTIs, and 4.8% to NNRTIs. No sequence showed double-class resistance. Multivariate logistic regression analysis revealed that compared with CRF01_AE, subtype B (OR = 2.869, 95%CI: 1.093-7.420) and female (OR = 2.359, 95%CI: 1.182-4.707) were risk factors for TDR. Q58E was the most prevalent detected protease inhibitor (PI) -associated mutation, and V179E was the most frequently detected non-nucleoside reverse transcriptase inhibitor (NNRTI) -associated mutation. A total of 613 (52.8%) sequences were segregated into 137 clusters, ranging from 2 to 74 sequences. Among 44 individuals with TDR (48.4%) within 21 clusters, K103N/KN was the most frequent TDR-associated mutation (31.8%), followed by Q58E/QE (20.5%) and G190A (15.9%). Individuals with the same TDR-associated mutations were usually cross-linked in transmission clusters. Moreover, we identified 9 clusters in which there was a transmission relationship between drug-resistant individuals, and 4 clusters in which drug-resistant cases increased during the study period. Conclusion The overall prevalence of TDR in Nanjing was at a moderate level during the past 3 years. However, nearly half of TDR individuals were included in the transmission clusters, and some drug-resistant individuals have transmitted in the clusters. Therefore, HIV drug-resistance prevention, monitoring and response efforts should be sustained and expanded to reduce the prevalence and transmission of TDR in Nanjing.
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Affiliation(s)
- Yuanyuan Xu
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Hongjie Shi
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Xiaoxiao Dong
- Department of Microbiology Laboratory, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Chengyuan Ding
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sushu Wu
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Xin Li
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Hongying Zhang
- Department of Microbiology Laboratory, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Mengkai Qiao
- Department of Microbiology Laboratory, Nanjing Center for Disease Control and Prevention, Nanjing, China
| | - Xiaoshan Li
- Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Zhengping Zhu
- Department of AIDS/STD Control and Prevention, Nanjing Center for Disease Control and Prevention, Nanjing, China
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Zhukova A, Dunn D, Gascuel O. Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK. Viruses 2023; 15:1244. [PMID: 37376544 DOI: 10.3390/v15061244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
A deeper understanding of HIV-1 transmission and drug resistance mechanisms can lead to improvements in current treatment policies. However, the rates at which HIV-1 drug resistance mutations (DRMs) are acquired and which transmitted DRMs persist are multi-factorial and vary considerably between different mutations. We develop a method for the estimation of drug resistance acquisition and transmission patterns. The method uses maximum likelihood ancestral character reconstruction informed by treatment roll-out dates and allows for the analysis of very large datasets. We apply our method to transmission trees reconstructed on the data obtained from the UK HIV Drug Resistance Database to make predictions for known DRMs. Our results show important differences between DRMs, in particular between polymorphic and non-polymorphic DRMs and between the B and C subtypes. Our estimates of reversion times, based on a very large number of sequences, are compatible but more accurate than those already available in the literature, with narrower confidence intervals. We consistently find that large resistance clusters are associated with polymorphic DRMs and DRMs with long loss times, which require special surveillance. As in other high-income countries (e.g., Switzerland), the prevalence of sequences with DRMs is decreasing, but among these, the fraction of transmitted resistance is clearly increasing compared to the fraction of acquired resistance mutations. All this indicates that efforts to monitor these mutations and the emergence of resistance clusters in the population must be maintained in the long term.
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Affiliation(s)
- Anna Zhukova
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - David Dunn
- UK MRC Clinical Trials Unit, University College London, London WC1V 6LJ, UK
| | - Olivier Gascuel
- Institut de Systématique, Evolution, Biodiversité (ISYEB)-URM 7205 CNRS, Muséum National d'Histoire Naturelle, SU, EPHE & UA, 75005 Paris, France
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Johnson MM, Jones CE, Clark DN. The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles. Viruses 2022; 15:107. [PMID: 36680147 PMCID: PMC9861436 DOI: 10.3390/v15010107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.
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Affiliation(s)
- Madison M. Johnson
- Department of Microbiology, Weber State University, Ogden, UT 84408, USA
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Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW. Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clin Microbiol Rev 2022; 35:e0005222. [PMID: 36102816 PMCID: PMC9769561 DOI: 10.1128/cmr.00052-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
HIV-1 DNA exists in nonintegrated linear and circular episomal forms and as integrated proviruses. In patients with plasma viremia, most peripheral blood mononuclear cell (PBMC) HIV-1 DNA consists of recently produced nonintegrated virus DNA while in patients with prolonged virological suppression (VS) on antiretroviral therapy (ART), most PBMC HIV-1 DNA consists of proviral DNA produced months to years earlier. Drug-resistance mutations (DRMs) in PBMCs are more likely to coexist with ancestral wild-type virus populations than they are in plasma, explaining why next-generation sequencing is particularly useful for the detection of PBMC-associated DRMs. In patients with ongoing high levels of active virus replication, the DRMs detected in PBMCs and in plasma are usually highly concordant. However, in patients with lower levels of virus replication, it may take several months for plasma virus DRMs to reach detectable levels in PBMCs. This time lag explains why, in patients with VS, PBMC genotypic resistance testing (GRT) is less sensitive than historical plasma virus GRT, if previous episodes of virological failure and emergent DRMs were either not prolonged or not associated with high levels of plasma viremia. Despite the increasing use of PBMC GRT in patients with VS, few studies have examined the predictive value of DRMs on the response to a simplified ART regimen. In this review, we summarize what is known about PBMC HIV-1 DNA dynamics, particularly in patients with suppressed plasma viremia, the methods used for PBMC HIV-1 GRT, and the scenarios in which PBMC GRT has been used clinically.
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Affiliation(s)
- Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, California, USA
| | - Daniele Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Charles Walworth
- LabCorp-Monogram Biosciences, South San Francisco, California, USA
| | - Maria M. Santoro
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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7
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Arimide DA, Amogne MD, Kebede Y, Balcha TT, Adugna F, Ramos A, DeVos J, Zeh C, Agardh A, Chang JCW, Björkman P, Medstrand P. High Level of HIV Drug Resistance and Virologic Nonsuppression Among Female Sex Workers in Ethiopia: A Nationwide Cross-Sectional Study. J Acquir Immune Defic Syndr 2022; 89:566-574. [PMID: 34966147 PMCID: PMC9058170 DOI: 10.1097/qai.0000000000002908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/20/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To determine viral load (VL) nonsuppression (VLN) rates, HIV drug resistance (HIVDR) prevalence, and associated factors among female sex workers (FSWs) in Ethiopia. METHODS A cross-sectional biobehavioral survey was conducted among FSWs in 11 cities in Ethiopia in 2014. Whole blood was collected, and HIVDR genotyping was performed. Logistic regression analysis was performed to identify factors associated with VLN and HIVDR. RESULTS Among 4900 participants, 1172 (23.9%) were HIV-positive and 1154 (98.5%) had a VL result. Participants were categorized into antiretroviral therapy (ART) (n = 239) and ART-naive (n = 915) groups based on self-report. From the 521 specimens (ART, 59; ART-naive, 462) with VL ≥1000 copies/mL, genotyping was successful for 420 (80.6%) and 92 (21.9%) had drug resistance mutations (DRMs). Pretreatment drug resistance (PDR) was detected in 16.5% (63/381) of the ART-naive participants. Nucleoside reverse transcriptase inhibitor (NRTI), non-NRTIs (NNRTIs), and dual-class DRMs were detected in 40 (10.5%), 55 (14.4%), and 35 (9.2%) of the participants, respectively. Among 239 participants on ART, 59 (24.7%) had VLN. Genotyping was successfully performed for 39 (66.1%). DRMs were detected in 29 (74.4%). All 29 had NNRTI, 23 (79.3%) had NRTI or dual-class DRMs. VLN was associated with age 35 years or older, CD4+ T-cell count <350 cells/mm3, and being forced into selling sex. PDR and acquired drug resistance were associated with CD4+ T-cell count <350 cells/mm3 (P < 0.001). CONCLUSIONS The high VLN and HIVDR rates among FSWs underscore the need for targeted interventions to improve ART access and virologic monitoring to maximize the benefit of ART and limit the spread of HIV and HIVDR.
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Affiliation(s)
- Dawit Assefa Arimide
- Department of Translational Medicine, Lund University, Malmo, Sweden
- TB/HIV Department, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Minilik Demissie Amogne
- TB/HIV Department, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Clinical Sciences, Lund University, Malmo, Sweden
| | - Yenew Kebede
- Africa Centre for Disease Prevention and Control, Africa Union Commission, Addis Ababa, Ethiopia
| | - Taye T. Balcha
- Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Fekadu Adugna
- NPO - HIV/AIDS, World Health Organization, Addis Ababa, Ethiopia
| | - Artur Ramos
- Division of Global HIV & TB, Center for Global Health, Center for Disease Control and Prevention, Atlanta, GA USA
| | - Joshua DeVos
- Division of Global HIV & TB, Center for Global Health, Center for Disease Control and Prevention, Atlanta, GA USA
| | - Clement Zeh
- Division of Global HIV & TB, Center for Global Health, Center for Disease Control and Prevention, Atlanta, GA USA
| | - Anette Agardh
- Department of Clinical Sciences, Lund University, Malmo, Sweden
| | - Joy Chih-Wei Chang
- Division of Global HIV & TB, Center for Global Health, Center for Disease Control and Prevention, Atlanta, GA USA
| | - Per Björkman
- Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmo, Sweden
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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: 11] [Impact Index Per Article: 3.7] [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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Xu X, Luo L, Song C, Li J, Chen H, Zhu Q, Lan G, Liang S, Shen Z, Cao Z, Feng Y, Liao L, Xing H, Shao Y, Ruan Y. Survey of pretreatment HIV drug resistance and the genetic transmission networks among HIV-positive individuals in southwestern China, 2014-2020. BMC Infect Dis 2021; 21:1153. [PMID: 34772365 PMCID: PMC8590229 DOI: 10.1186/s12879-021-06847-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Pretreatment drug resistance (PDR) can limit the effectiveness of HIV antiretroviral therapy (ART). The aim of this study was to assess the prevalence of PDR among HIV-positive individuals that initiated antiretroviral therapy in 2014–2020 in southwestern China. Methods Consecutive cross-sectional surveys were conducted in Qinzhou, Guangxi. We obtained blood samples from individuals who were newly diagnosed with HIV in 2014–2020. PDR and genetic networks analyses were performed by HIV-1 pol sequences using the Stanford HIV-database algorithm and HIV-TRACE, respectively. Univariate and multivariate logistic regression models were used to explore the potential factors associated with PDR. Results In total, 3236 eligible HIV-positive individuals were included. The overall prevalence of PDR was 6.0% (194/3236). The PDR frequency to NNRTI (3.3%) was much higher than that of NRTI (1.7%, p < 0.001) and PI (1.2%, p < 0.001). A multivariate logistic regression analysis revealed that PDR was significantly higher among individuals aged 18–29 (adjusted odds ratio (aOR): 1.79, 95% CI 1.28–2.50) or 30–49 (aOR: 2.82, 95% CI 1.73–4.82), and harboring CRF08_BC (aOR: 3.23, 95% CI 1.58–6.59). A total of 1429 (43.8%) sequences were linked forming transmission clusters ranging in size from 2 to 119 individuals. Twenty-two individuals in 10 clusters had the same drug resistant mutations (DRMs), mostly to NNRTIs (50%, 5/10). Conclusions The overall prevalence of PDR was medium, numerous cases of the same DRMs among genetically linked individuals in networks further illustrated the importance of surveillance studies for mitigating PDR. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06847-5.
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Affiliation(s)
- Xiaoshan Xu
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Liuhong Luo
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Chang Song
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jianjun Li
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Huanhuan Chen
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Qiuying Zhu
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Guanghua Lan
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Shujia Liang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Zhiyong Shen
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, 530028, China
| | - Zhiqiang Cao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yi Feng
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Lingjie Liao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hui Xing
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yiming Shao
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yuhua Ruan
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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10
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Yuan D, Yu B, Li Y, Wang Z, Liu M, Ye L, Huang Y, Su L, Zhang Y, Api L, Chen M, Zhou C, Liu L, Zhang L, Liang S, Jia P, Yang S. Prevalence and Molecular Epidemiology of Transmitted Drug Resistance and Genetic Transmission Networks Among Newly Diagnosed People Living With HIV/AIDS in a Minority Area, China. Front Public Health 2021; 9:731280. [PMID: 34708015 PMCID: PMC8542729 DOI: 10.3389/fpubh.2021.731280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: Transmitted drug resistance (TDR) can compromise antiretroviral therapy (ART) efficacy. We aimed to understand the molecular epidemiology of TDR and its genetic transmission networks among newly diagnosed people living with HIV/AIDS (PLWH). Methods: A total of 1,318 newly diagnosed PLWH, identified in all population-based HIV screening in an HIV-affected county of a minority area of China (i.e., Butuo county), were enrolled between January 1, 2018, and November 31, 2018. HIV-1 pol gene sequences were used for phylogenetic and genotypic drug resistance analyses. The genetic transmission networks were identified. Results: The prevalence of TDR among newly diagnosed PLWH was 8.12% (107/1,318). Patients in the stage of AIDS (adjusted odds ratio, OR: 2.32) and who had a history of sharing a needle ≥5 times (adjusted OR: 3.89) were more likely to have an increased risk of TDR. The prevalence of TDR for non-nucleoside reverse transcriptase inhibitors (NNRTIs) is higher than that of other inhibitors, with a relatively high prevalence of three mutations [V179D/E/DE (4.93%), K103N/KN (3.11%), and E138A/G (1.52%)]. A total of 577 (43.78%) pol sequences were involved in the genetic transmission network, with 171 clusters ranging in size from 2 to 91 pol sequences; 37.38% (40/107) of individuals carrying TDR were involved in the network, and individuals with the same TDR-associated mutations were usually cross-linked. Conclusions: Our data suggest a relatively high level of TDR and many transmission clusters among the newly diagnosed PLWH. Targeted intervention, early identification, and monitoring of resistance are warranted to reduce the TDR and prevent HIV-1 transmission in areas with a high rate of HIV-1.
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Affiliation(s)
- Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Bin Yu
- West China Second University Hospital of Sichuan University and Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Zixin Wang
- Centre for Health Behaviours Research, The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Meijing Liu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yuling Huang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Ling Su
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yan Zhang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Laze Api
- Butuo Center for Disease Control and Prevention, Liangshan, China
| | - Maogang Chen
- Liangshan Center for Disease Control and Prevention, Xichang, China
| | - Chang Zhou
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Li Liu
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Linglin Zhang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Peng Jia
- School of Resources and Environmental Science, Wuhan University, Wuhan, China.,International Institute of Spatial Lifecourse Epidemiology (ISLE), Wuhan University, Wuhan, China
| | - Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.,International Institute of Spatial Lifecourse Epidemiology (ISLE), Wuhan University, Wuhan, China
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11
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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. 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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12
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McClung RP, Oster AM, Ocfemia MCB, Saduvala N, Heneine W, Johnson JA, Hernandez AL. Transmitted Drug Resistance Among HIV-1 Diagnoses in the United States, 2014-2018. Clin Infect Dis 2021; 74:1055-1062. [PMID: 34175948 DOI: 10.1093/cid/ciab583] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Transmitted HIV drug resistance can threaten the efficacy of antiretroviral therapy (ART) and preexposure prophylaxis (PrEP). Drug resistance testing is recommended at entry to HIV care in the United States and provides valuable insight for clinical decision-making and population-level monitoring. METHODS We assessed transmitted drug resistance-associated mutation (TDRM) prevalence and predicted susceptibility to common HIV drugs among U.S. persons with HIV diagnosed during 2014-2018 who had a drug resistance test performed ≤3 months after HIV diagnosis and reported to the National HIV Surveillance System and who resided in 28 jurisdictions where ≥20% of HIV diagnoses had an eligible sequence during this period. RESULTS Of 50,747 persons in the analysis, 9,616 (18.9%) had ≥1 TDRM. TDRM prevalence was 0.8% for integrase strand transfer inhibitors (INSTI), 4.2% for protease inhibitors, 6.9% for nucleoside reverse transcriptase inhibitors, and 12.0% for non-nucleoside reverse transcriptase inhibitors. Most individual mutations had a prevalence <1.0% including M184V (0.9%) and K65R (0.1%); K103N was most prevalent (8.6%). TDRM prevalence did not increase or decrease significantly during 2014-2018 overall, for individual drug classes, or for key individual mutations except for M184V (12.9% increase per year, 95% CI=5.6-20.6). CONCLUSIONS TDRM prevalence overall and for individual drug classes remained stable during 2014-2018; transmitted INSTI resistance was uncommon. Continued population-level monitoring of INSTI and NRTI mutations, especially M184V and K65R, is warranted amidst expanding use of second-generation INSTI and PrEP.
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Affiliation(s)
- R Paul McClung
- United States Public Health Service Commissioned Corps, Atlanta, GA, USA.,Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, CDC, Atlanta, GA, USA
| | - Alexandra M Oster
- United States Public Health Service Commissioned Corps, Atlanta, GA, USA.,Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, CDC, Atlanta, GA, USA
| | - M Cheryl Bañez Ocfemia
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, CDC, Atlanta, GA, USA
| | | | - Walid Heneine
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, CDC, Atlanta, GA, USA
| | - Jeffrey A Johnson
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, CDC, Atlanta, GA, USA
| | - Angela L Hernandez
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, CDC, Atlanta, GA, USA
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13
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Rhee SY, Tzou PL, Shafer RW. Temporal Trends in HIV-1 Mutations Used for the Surveillance of Transmitted Drug Resistance. Viruses 2021; 13:v13050879. [PMID: 34064774 PMCID: PMC8150354 DOI: 10.3390/v13050879] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/05/2021] [Accepted: 05/08/2021] [Indexed: 12/12/2022] Open
Abstract
In 2009, a list of nonpolymorphic HIV-1 drug resistance mutations (DRMs), called surveillance DRMs (SDRMs), was created to monitor transmitted drug resistance (TDR). Since 2009, TDR increased and antiretroviral therapy (ART) practices changed. We examined the changing prevalence of SDRMs and identified candidate SDRMs defined as nonpolymorphic DRMs present on ≥ 1 expert DRM list and in ≥0.1% of ART-experienced persons. Candidate DRMs were further characterized according to their association with antiretrovirals and changing prevalence. Among NRTI-SDRMs, tenofovir-associated mutations increased in prevalence while thymidine analog mutations decreased in prevalence. Among candidate NRTI-SDRMs, there were six tenofovir-associated mutations including three which increased in prevalence (K65N, T69deletion, K70G/N/Q/T). Among candidate NNRTI-SDRMs, six that increased in prevalence were associated with rilpivirine (E138K/Q, V179L, H221Y) or doravirine (F227C/L) resistance. With the notable exceptions of I47A and I50L, most PI-SDRMs decreased in prevalence. Three candidate PI-SDRMs were accessory darunavir-resistance mutations (L10F, T74P, L89V). Adding the candidate SDRMs listed above was estimated to increase NRTI, NNRTI, and PI TDR prevalence by 0.1%, 0.3%, and 0.3%, respectively. We describe trends in the prevalence of nonpolymorphic HIV-1 DRMs in ART-experienced persons. These data should be considered in decisions regarding SDRM list updates and TDR monitoring.
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14
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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: 6] [Impact Index Per Article: 2.0] [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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15
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Switching to Bictegravir/Emtricitabine/Tenofovir Alafenamide (B/F/TAF) From Dolutegravir (DTG)+F/TAF or DTG+F/Tenofovir Disoproxil Fumarate (TDF) in the Presence of Pre-existing NRTI Resistance. J Acquir Immune Defic Syndr 2021; 85:363-371. [PMID: 32701823 DOI: 10.1097/qai.0000000000002454] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Study 4030 was a phase 3, randomized, double-blinded study of 565 HIV-1 RNA-suppressed participants switching to bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF) or dolutegravir (DTG)+F/TAF. Nucleoside reverse transcriptase inhibitor (NRTI), non-NRTI, and protease inhibitor resistance (-R) was allowed, but integrase strand transfer inhibitor-R was excluded. Here, we describe the detailed resistance analysis. METHODS Historical plasma HIV-1 RNA genotypes and baseline proviral DNA genotypes were analyzed. Documented or investigator-suspected NRTI-R was grouped for stratification into 3 categories of level of resistance. Viral blips were assessed through week 48. Virologic failures had genotypic and phenotypic resistance analyses at week 48, confirmed failure, or last visit, if HIV-1 RNA did not resuppress to <50 copies/mL while on study drug. RESULTS In total, 83% (470/565) of participants had baseline genotypic data available with NRTI-R detected in 24% (138/565), including 5% (30/565) with K65R/E/N or ≥3 thymidine analog mutations and 19% (108/565) with other NRTI-R mutations. M184V/I was present in 14% (81/565). Pre-existing integrase strand transfer inhibitor-R mutations were found in 4% (20/565) of participants. Primary non-NRTI-R and protease inhibitor-R mutations were present in 21% (118/565) and 7% (38/565) of participants. High rates of viral suppression were maintained in all groups through week 48; blips were observed in only 15 participants (2.7%). Three participants met criteria for resistance analysis (all in DTG+F/TAF arm); none developed treatment-emergent resistance to study drugs. CONCLUSIONS Participants with baseline NRTI resistance, much of which was previously undocumented, maintained suppression 48 weeks after switching to B/F/TAF or DTG+F/TAF triple therapy. Blips and virologic failure were uncommon using either regimen, with no treatment-emergent resistance.
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16
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Liu L, Dong A, Liao L, Feng Y, Shao Y, Liang S, Ruan Y, Xing H. Survey of Pretreatment HIV Drug Resistance and Genetic Transmission Network Analysis Among HIV Patients in a High Drug-Use Area of Southwest China. Curr HIV Res 2021; 17:441-451. [PMID: 31778107 PMCID: PMC7497539 DOI: 10.2174/1570162x17666191128101426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/21/2019] [Accepted: 11/23/2019] [Indexed: 11/22/2022]
Abstract
Background: Pretreatment drug resistance (PDR) poses an increasing threat to the success of antiretroviral treatment (ART) programs in China. We aimed to conduct a survey of PDR among HIV patients in an area in Southwest China with extensive drug trafficking. Methods: Consecutive cross-sectional surveys were conducted in Liangshan Prefecture of Sichuan Province from 2009 to 2018 based on the WHO-recommended method. PDR was identified by testing pol region sequences with the Stanford HIVdb algorithm (version 7.0). PDR prevalence and related factors were assessed by multivariable logistic regression. The transmission of HIV drug resistance was analyzed using a genetic transmission network. Results: HIV-1 pol genes from 1889 patients were successfully amplified. The distribution of HIV-1 genotypes was as follows: CRF07_BC (94.0%), CRF08_BC (2.3%), CRF01_AE (2.0%) and others (1.4%). Of the participants, 6.9% (95% CI: 4.1-8.1%) had pretreatment resistance to 12 antiretroviral drugs recommended by the WHO, and nucleoside reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI) and protease inhibitors (PI) resistance were identified among 1.4% (95% CI: 0.7-3.4%), 5.8% (95% CI: 1.2-8.7%) and 0.4% (95% CI: 0.1-3.0%) of the patients, respectively. In the multivariate logistic model, the prevalence of PDR was 1.52-fold higher among intravenous drug users (IDUs) than among patients infected by heterosexual transmission (95% CI: 1.07-2.38; P=0.049), and the prevalence of PDR among patients diagnosed from 2017-2018 was 2.03-fold higher than that among patients diagnosed from 2009-2016 (95% CI: 1.18-5.76; P=0.018). A total of 26 clusters containing PDR and a rapidly growing drug resistance-related cluster containing the E138Q and V179D mutations were identified by genetic transmission network analysis. Conclusion: The results show a moderate overall level of PDR prevalence and rapidly growing drug resistance over time. Preventive intervention should be focused on controlling the HIV epidemic among drug users, and surveillance is urgently needed to monitor the trend of PDR.
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Affiliation(s)
- Lei Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Aobo Dong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Shu Liang
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, Sichuan, China
| | - Yuhua Ruan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
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17
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Mbisa JL, Kirwan P, Tostevin A, Ledesma J, Bibby DF, Brown A, Myers R, Hassan AS, Murphy G, Asboe D, Pozniak A, Kirk S, Gill ON, Sabin C, Delpech V, Dunn DT. Determining the Origins of Human Immunodeficiency Virus Type 1 Drug-resistant Minority Variants in People Who Are Recently Infected Using Phylogenetic Reconstruction. Clin Infect Dis 2020; 69:1136-1143. [PMID: 30534981 PMCID: PMC6743824 DOI: 10.1093/cid/ciy1048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Drug-resistant minority variants (DRMinVs) detected in patients who recently acquired human immunodeficiency virus type 1 (HIV-1) can be transmitted, generated de novo through virus replication, or technical errors. The first form is likely to persist and result in treatment failure, while the latter two could be stochastic and transient. METHODS Ultradeep sequencing of plasma samples from 835 individuals with recent HIV-1 infection in the United Kingdom was performed to detect DRMinVs at a mutation frequency between 2% and 20%. Sequence alignments including >110 000 HIV-1 partial pol consensus sequences from the UK HIV Drug Resistance Database (UK-HDRD), linked to epidemiological and clinical data from the HIV and AIDS Reporting System, were used for transmission cluster analysis. Transmission clusters were identified using Cluster Picker with a clade support of >90% and maximum genetic distances of 4.5% or 1.5%, the latter to limit detection to likely direct transmission events. RESULTS Drug-resistant majority variants (DRMajVs) were detected in 66 (7.9%) and DRMinVs in 84 (10.1%) of the recently infected individuals. High levels of clustering to sequences in UK-HDRD were observed for both DRMajV (n = 48; 72.7%) and DRMinV (n = 63; 75.0%) sequences. Of these, 43 (65.2%) with DRMajVs were in a transmission cluster with sequences that harbored the same DR mutation compared to only 3 (3.6%) sequences with DRMinVs (P < .00001, Fisher exact test). Evidence of likely direct transmission of DRMajVs was observed for 25/66 (37.9%), whereas none were observed for the DRMinVs (P < .00001). CONCLUSIONS Using a densely sampled HIV-infected population, we show no evidence of DRMinV transmission among recently infected individuals.
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Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Peter Kirwan
- National Infection Service, Public Health England, London, United Kingdom
| | - Anna Tostevin
- Institute for Global Health, University College London, London, United Kingdom
| | - Juan Ledesma
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David F Bibby
- National Infection Service, Public Health England, London, United Kingdom
| | - Alison Brown
- National Infection Service, Public Health England, London, United Kingdom
| | - Richard Myers
- National Infection Service, Public Health England, London, United Kingdom
| | - Amin S Hassan
- HIV/STI Group, Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Gary Murphy
- National Infection Service, Public Health England, London, United Kingdom
| | - David Asboe
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Anton Pozniak
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Stuart Kirk
- University College London Hospital, London, United Kingdom
| | - O Noel Gill
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Caroline Sabin
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom.,Institute for Global Health, University College London, London, United Kingdom
| | - Valerie Delpech
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David T Dunn
- Institute for Global Health, University College London, London, United Kingdom
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Tchiakpe E, Keke RK, Vidal N, Ahoussinou C, Sekpe O, Dagba HG, Gbaguidi E, Tonoukouen C, Afangnihoun A, Bachabi M, Gangbo FA, Diop-Ndiaye H, Toure-Kane C. Moderate rate of transmitted resistance mutations to antiretrovirals and genetic diversity in newly HIV-1 patients diagnosed in Benin. BMC Res Notes 2020; 13:314. [PMID: 32616057 PMCID: PMC7330984 DOI: 10.1186/s13104-020-05151-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/24/2020] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Seventeen years after the start of the IBAARV (Beninese initiative for access to antiretrovirals), transmitted drug resistance mutations in ARV-naïve patients and HIV-1 genetic diversity were investigated in Benin. RESULTS Drug resistance mutations were detected in (27/248; 10.9%) according to the WHO SDRM 2009 list, with a predominance of mutations directed against NNRTIs drugs (24/248; 10%). Phylogenetic and recombination analyses showed a predominance of CRF02_AG strains (165/248; 66.5%) and a high genetic diversity with five other variants and 39 URFs (15.7%) which contained portions of strains that co-circulate in Benin. Eight recent transmission chains revealed active ongoing transmission of HIV-1 strains among ARV-naïve patients. Our study showed a moderate primary drug resistance mutations rate and also provided recent data on the HIV-1 variants that circulate in Benin. Regular monitoring of primary drug resistance is required to adapt HIV-1 treatment strategies and adoption of new WHO recommendations in Benin.
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Affiliation(s)
- Edmond Tchiakpe
- National Reference Laboratory of Health Program Fighting Against AIDS in Benin (LNR/PSLS), Health Ministry of Benin, BP 1258, Cotonou, Benin
- Laboratory of Cell Biology and Physiology, Department of Biochemistry and Cellular Biology, Faculty of Sciences and Technology (FAST) and Institute of Applied Biomedical Sciences (ISBA), University of Abomey-Calavi, 01, BP 918 Cotonou, Benin
| | - Rene K. Keke
- National Reference Laboratory of Health Program Fighting Against AIDS in Benin (LNR/PSLS), Health Ministry of Benin, BP 1258, Cotonou, Benin
| | - Nicole Vidal
- UMI233-TransVIHMI, IRD (Institut de Recherche pour le développement), U1175 (INSERM) et Université de Montpellier, Montpellier, France
| | | | - Olga Sekpe
- National Reference Laboratory of Health Program Fighting Against AIDS in Benin (LNR/PSLS), Health Ministry of Benin, BP 1258, Cotonou, Benin
| | - Hermione G. Dagba
- National Reference Laboratory of Health Program Fighting Against AIDS in Benin (LNR/PSLS), Health Ministry of Benin, BP 1258, Cotonou, Benin
| | - Eric Gbaguidi
- Health Program Fighting Against AIDS in Benin (PSLS), Health Ministry of Benin, Cotonou, Benin
| | - Conrad Tonoukouen
- Health Program Fighting Against AIDS in Benin (PSLS), Health Ministry of Benin, Cotonou, Benin
| | - Aldric Afangnihoun
- Centre de Traitement Ambulatoire de l’Hôpital de zone de Suru Léré, Cotonou, Benin
| | - Moussa Bachabi
- Health Program Fighting Against AIDS in Benin (PSLS), Health Ministry of Benin, Cotonou, Benin
| | - Flore A. Gangbo
- Health Program Fighting Against AIDS in Benin (PSLS), Health Ministry of Benin, Cotonou, Benin
| | - Halimatou Diop-Ndiaye
- Institute for Health Research, Epidemiological Surveillance and Training of Senegal, Dakar, Senegal
| | - Coumba Toure-Kane
- Institute for Health Research, Epidemiological Surveillance and Training of Senegal, Dakar, Senegal
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Pan-resistant HIV-1 emergence in the era of integrase strand-transfer inhibitors: a case report. THE LANCET MICROBE 2020; 1:e130-e135. [DOI: 10.1016/s2666-5247(20)30006-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/17/2020] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
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Yuan D, Liu M, Jia P, Li Y, Huang Y, Ye L, Api L, Chen M, Yao L, Wang Z, Liu H, Liang S, Yang S. Prevalence and determinants of virological failure, genetic diversity and drug resistance among people living with HIV in a minority area in China: a population-based study. BMC Infect Dis 2020; 20:443. [PMID: 32576136 PMCID: PMC7310496 DOI: 10.1186/s12879-020-05124-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/27/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Liangshan Yi Autonomous Prefecture is one of the areas that most severely affected by human immunodeficiency virus (HIV) in China, and virological failure on antiretroviral therapy (ART) is serious in this area. Analyses of prevalence and determinants of ART failure, the genetic diversity and drug resistance among people living with HIV (PLWH) helps improve HIV treatment efficiency and prevent HIV transmission. METHODS A total of 5157 PLWH were recruited from 2016 to 2017. The venous blood samples were subjected to RT-PCR, followed by sequencing of the HIV-1 pol gene, targeting the protease and reverse transcriptase fragments. HIV-1 diversity was analyzed using the DNAStar software and drug resistance mutations were analyzed using the Stanford University HIV Drug Resistance Database. RESULTS A total of 2156 (41.81%) PLWH showed virological failure on ART. Males (ORm = 1.25), heterosexual behaviors and drug injection (ORm = 1.44) and mother to child transmission routes (ORm = 1.58), the clinical stage of AIDS (ORm = 1.35), having used illicit drugs and shared the needles (1-4 times: ORm = 1.34; more than 5 times: ORm = 1.52), having ever replaced ART regimen (ORm = 1.48) increased the risk of virological failure among PLWH, while higher education lever (ORm = 0.77) and ≥ 12 months on ART (12 ~ 36 months: ORm = 0.72; ≥36 months: ORm = 0.66) was associated with lower likelihood of virological failure. The data revealed that CRF07_BC (1508, 95.62%) were the most common strains, and the drug-resistant rate was 32.10% among PLWH with virological failure in this area. The high frequencies of drug resistance were found in EFV and NVP of NNRTIs, ABC, FTC and 3TC of NRTIs, and TPV/r in PIs. The most common mutations in NNRTIs, NRTIs and PIs were K103N/KN (64.69%), M184V/MV/I (36.29%) and Q58E/QE (4.93%), respectively. CONCLUSION We concluded that surveillance of virological failure, HIV-1 subtypes, and drug resistance to understand HIV-1 epidemiology and guide modification of ART guidelines, and target prevention and control strategies should be formatted to reduce the virological failure and drug resistance to promote viral suppression and prevent HIV-1 transmission.
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Affiliation(s)
- Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Meijing Liu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Peng Jia
- Department of Land Surveying and Geo-Informatics, The Hong Kong Polytechnic University, Hong Kong, China
- International Initiative on Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yuling Huang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Laze Api
- Butuo Center for Disease Control and Prevention, Butuo, China
| | - Maogang Chen
- Liangshan Center for Disease Control and Prevention, Xichang, China
| | - Liang Yao
- Butuo County People's Hospital, Butuo, China
| | - Zixin Wang
- Centre for Health Behaviours Research, The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Honglu Liu
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China.
| | - Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China.
- International Initiative on Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China.
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Geretti AM, White E, Orkin C, Tostevin A, Tilston P, Chadwick D, Leen C, Sabin C, Dunn DT. Virological outcomes of boosted protease inhibitor-based first-line ART in subjects harbouring thymidine analogue-associated mutations as the sole form of transmitted drug resistance. J Antimicrob Chemother 2020; 74:746-753. [PMID: 30544247 PMCID: PMC6376847 DOI: 10.1093/jac/dky468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/06/2018] [Accepted: 10/13/2018] [Indexed: 12/13/2022] Open
Abstract
Objectives In subjects with transmitted thymidine analogue mutations (TAMs), boosted PIs (PI/b) are often chosen to overcome possible resistance to the NRTI backbone. However, data to guide treatment selection are limited. Our aim was to obtain firmer guidance for clinical practice using real-world cohort data. Methods We analysed 1710 subjects who started a PI/b in combination with tenofovir or abacavir plus emtricitabine or lamivudine, and compared their virological outcomes with those of 4889 patients who started an NNRTI (predominantly efavirenz), according to the presence of ≥1 TAM as the sole form of transmitted drug resistance. Results Participants with ≥1 TAM comprised predominantly MSM (213 of 269, 79.2%), subjects of white ethnicity (206 of 269, 76.6%) and HIV-1 subtype B infections (234 of 269, 87.0%). Most (203 of 269, 75.5%) had singleton TAMs, commonly a revertant of T215Y or T215F (112 of 269, 41.6%). Over a median of 2.5 years of follow-up, 834 of 6599 (12.6%) subjects experienced viraemia (HIV-1 RNA >50 copies/mL). The adjusted HR for viraemia was 2.17 with PI/b versus NNRTI-based therapy (95% CI 1.88–2.51; P < 0.001). Other independent predictors of viraemia included injecting drug use, black ethnicity, higher viral load and lower CD4 cell count at baseline, and receiving abacavir instead of tenofovir. Resistance showed no overall impact (adjusted HR 0.77 with ≥1 TAM versus no resistance; 95% CI 0.54–1.10; P = 0.15). Conclusions In this cohort, patients harbouring ≥1 TAM as the sole form of transmitted drug resistance gained no apparent virological advantage from starting first-line ART with a PI/b.
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Affiliation(s)
- Anna Maria Geretti
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Ellen White
- MRC Clinical Trials Unit at University College London, London, UK
| | - Chloe Orkin
- Department of Infection & Immunity, Barts Health NHS Trust, London, UK
| | - Anna Tostevin
- Institute for Global Health, University College London, London, UK
| | - Peter Tilston
- Department of Clinical Virology, Manchester Royal Infirmary, Manchester, UK
| | - David Chadwick
- Department of Infectious Diseases, South Tees Hospitals NHS Trust, Middlesbrough, UK
| | - Clifford Leen
- Regional Infectious Diseases Unit, NHS Lothian, Edinburgh, UK
| | - Caroline Sabin
- Institute for Global Health, University College London, London, UK
| | - David T Dunn
- Institute for Global Health, University College London, London, UK
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Rhee SY, Clutter D, Fessel WJ, Klein D, Slome S, Pinsky BA, Marcus JL, Hurley L, Silverberg MJ, Kosakovsky Pond SL, Shafer RW. Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population. Clin Infect Dis 2020; 68:213-221. [PMID: 29846534 PMCID: PMC6321854 DOI: 10.1093/cid/ciy453] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/25/2018] [Indexed: 12/20/2022] Open
Abstract
Background There are few large studies of transmitted drug resistance (TDR) prevalence and the drug resistance mutations (DRMs) responsible for TDR in the United States. Methods Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and protease sequences were obtained from 4253 antiretroviral therapy (ART)–naive individuals in a California clinic population from 2003 to 2016. Phylogenetic analyses were performed to study linkages between TDR strains and selection pressure on TDR-associated DRMs. Results From 2003 to 2016, there was a significant increase in overall (odds ratio [OR], 1.05 per year [95% confidence interval {CI}, 1.03–1.08]; P < .001) and nonnucleoside RT inhibitor (NNRTI)–associated TDR (OR, 1.11 per year [95% CI, 1.08–1.15]; P < .001). Between 2012 and 2016, TDR rates to any drug class ranged from 15.7% to 19.2%, and class-specific rates ranged from 10.0% to 12.8% for NNRTIs, 4.1% to 8.1% for nucleoside RT inhibitors (NRTIs), and 3.6% to 5.2% for protease inhibitors. The thymidine analogue mutations, M184V/I and the tenofovir-associated DRMs K65R and K70E/Q/G/N/T accounted for 82.9%, 7.3%, and 1.4% of NRTI-associated TDR, respectively. Thirty-seven percent of TDR strains clustered with other TDR strains sharing the same DRMs. Conclusions Although TDR has increased significantly in this large cohort, many TDR strains are unlikely to influence the activity of currently preferred first-line ART regimens. The high proportion of DRMs associated with infrequently used regimens combined with the clustering of TDR strains suggest that some TDR strains are being transmitted between ART-naive individuals.
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Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University
| | - Dana Clutter
- Division of Infectious Diseases, Department of Medicine, Stanford University
| | - W Jeffrey Fessel
- Department of Internal Medicine, Kaiser Permanente Northern California, San Francisco
| | - Daniel Klein
- Department of Infectious Diseases, Kaiser Permanente Northern California, San Leandro
| | - Sally Slome
- Department of Infectious Diseases, Kaiser Permanente Northern California, Oakland
| | | | - Julia L Marcus
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Leo Hurley
- Division of Research, Kaiser Permanente Northern California, Oakland
| | | | | | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University
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Bavaro DF, Di Carlo D, Rossetti B, Bruzzone B, Vicenti I, Pontali E, Zoncada A, Lombardi F, Di Giambenedetto S, Borghi V, Pecorari M, Milini P, Meraviglia P, Monno L, Saracino A. Pretreatment HIV drug resistance and treatment failure in non-Italian HIV-1-infected patients enrolled in ARCA. Antivir Ther 2020; 25:61-71. [PMID: 32118584 DOI: 10.3851/imp3349] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND An increase in pretreatment drug resistance (PDR) to first-line antiretroviral therapy (ART) in low-income countries has been recently described. Herein we analyse the prevalence of PDR and risk of virological failure (VF) over time among migrants to Italy enrolled in ARCA. METHODS HIV-1 sequences from ART-naive patients of non-Italian nationality were retrieved from ARCA database from 1998 to 2017. PDR was defined by at least one mutation from the reference 2009 WHO surveillance list. RESULTS Protease/reverse transcriptase sequences from 1,155 patients, mainly migrants from sub-Saharan Africa (SSA; 42%), followed by Latin America (LA; 25%) and Western countries (WE; 21%), were included. PDR was detected in 8.6% of sequences (13.1% versus 5.8% for B and non-B strains, respectively; P<0.001). 2.1% of patients carried a PDR for protease inhibitors (PIs; 2.1% versus 2.3%; P=0.893), 3.9% for nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs; 6.8% versus 2.1%; P<0.001) and 4.3% for non-nucleoside/nucleotide reverse transcriptase inhibitors (NNRTIs; 6.3% versus 3.1%; P=0.013). Overall, prevalence of PDR over the years remained stable, while it decreased for PIs in LA (P=0.021) and for NRTIs (P=0.020) among migrants from WE. Having more than one class of PDR (P=0.015 versus absence of PDR), higher viral load at diagnosis (P=0.008) and being migrants from SSA (P=0.001 versus WE) were predictive of VF, while a recent calendar year of diagnosis (P<0.001) was protective for VF. CONCLUSIONS PDR appeared to be stable over the years in migrants to Italy enrolled in ARCA; however, it still remains an important cause of VF together with viral load at diagnosis.
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Affiliation(s)
- Davide Fiore Bavaro
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari Medical School, Bari, Italy.,These authors equally contributed to this work
| | - Domenico Di Carlo
- Pediatric Clinical Research Center 'Romeo and Enrica Invernizzi', University of Milan, Milan, Italy.,These authors equally contributed to this work
| | - Barbara Rossetti
- Infectious Diseases Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università di Siena, Siena, Italy
| | | | | | - Francesca Lombardi
- Università Cattolica del Sacro Cuore, Roma Italia, Istituto di Clinica Malattie Infettive, Rome, Italy
| | - Simona Di Giambenedetto
- Università Cattolica del Sacro Cuore, Roma Italia, Istituto di Clinica Malattie Infettive, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma Italia, UOC malattie infettive, Rome, Italy
| | - Vanni Borghi
- Clinica Malattie infettive, Azienda Ospedaliero Universitaria di Modena, Modena, Italy
| | - Monica Pecorari
- SSD Virologia, Azienda Ospedaliero-Univeristaria Policlinico Modena, Modena, Italy
| | - Paola Milini
- Infectious Diseases Unit, Macerata Hospital, Macerata, Italy
| | - Paola Meraviglia
- 1st Division of Infectious Diseases, ASST Fatebenefratelli-Sacco, Milan, Italy
| | - Laura Monno
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari Medical School, Bari, Italy
| | - Annalisa Saracino
- Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari Medical School, Bari, Italy
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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: 2.4] [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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Yuan D, Du Z, Zhou J, Ye L, Su L, Yang H, Yuan F, Li Y, Liu H, Zhai W, Liang S, Yang S. HIV-1 subtype diversity, drug resistance, and genetic transmission networks in men who have sex with men with virologic failure in antiretroviral therapy in Sichuan, China, 2011 to 2017. Medicine (Baltimore) 2019; 98:e17585. [PMID: 31651864 PMCID: PMC6824707 DOI: 10.1097/md.0000000000017585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study sought to examine the human immunodeficiency virus type 1 (HIV-1) genetic diversity on drug resistance among men who have sex with men (MSM) with virologic failure in antiretroviral therapy (ART), and investigate linking-associated factors for genetic transmission networks.Seven hundred and thirty-four HIV-positive MSM with virologic failure in ART were recruited into our study from 2011 to 2017. HIV-1 pol gene sequences were used for phylogenetic and genotypic drug resistance analyses. The drug resistance mutations were determined using the Stanford University HIV Drug Resistance Database. The genetic transmission networks were analyzed for CRF01_AE and CRF07_BC sequences by the genetic distance-based method.Of 734 subjects, 372 (50.68%) showed drug resistance, in which CRF01_AE and CRF07_BC were the predominating subtypes. Drug resistance more frequently occurred in non-nucleoside reverse transcriptase inhibitors (NNRTIs) treatment (48.64%), and followed by nucleoside reverse transcriptase inhibitors (NRTIs) (36.51%) and PIs (4.03%). The most common drug resistance-associated mutations in protease inhibitors (PIs), NRTIs and NNRTIs were K20I/R, M184V/I and K103N/KN, respectively. For 283CRF01_AE sequences, 64 (22.61%) fell into clusters at a genetic distance of 0.011, resulting in 17 clusters ranging in size from 2 to 16 individuals. For 230 CRF07_BC sequences, 66 (28.69%) were connected to at least one other sequence with 0.005 genetic distances, resulting in 8 clusters ranging in size from 2 to 52 individuals. Individuals who showed drug resistance to ART were less likely to fall into clusters than those who did not. The genetic linkage was robust by the exclusion of sites associated with drug resistance.CRF01_AE and CRF07_BC were the main strains among MSM with virologic failure in ART, and the drug resistance more frequently occurred in NNRTIs, followed by NRTIs and PIs. Genetic transmission networks revealed a complexity of transmission pattern, suggesting early-diagnosis and in-time intervention among MSM.
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Affiliation(s)
- Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Zonglun Du
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China,
| | - Junmin Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Ling Su
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Hong Yang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Fengshun Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Honglu Liu
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Wenwen Zhai
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention,
| | - Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Ishikawa SA, Zhukova A, Iwasaki W, Gascuel O. A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios. Mol Biol Evol 2019; 36:2069-2085. [PMID: 31127303 PMCID: PMC6735705 DOI: 10.1093/molbev/msz131] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences. We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server. The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
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Affiliation(s)
- Sohta A Ishikawa
- Unité Bioinformatique Evolutive, Institut Pasteur, C3BI USR 3756 IP & CNRS, Paris, France
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Evolutionary Genomics of RNA Viruses, Virology Department, Institut Pasteur, Paris, France
| | - Anna Zhukova
- Unité Bioinformatique Evolutive, Institut Pasteur, C3BI USR 3756 IP & CNRS, Paris, France
| | - Wataru Iwasaki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Olivier Gascuel
- Unité Bioinformatique Evolutive, Institut Pasteur, C3BI USR 3756 IP & CNRS, Paris, France
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An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors. Antimicrob Agents Chemother 2019; 63:AAC.00539-19. [PMID: 31109980 DOI: 10.1128/aac.00539-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/15/2019] [Indexed: 12/19/2022] Open
Abstract
Viral pathogens causing global disease burdens are often characterized by high rates of evolutionary changes. The extensive viral diversity at baseline can shorten the time to escape from therapeutic or immune selective pressure and alter mutational pathways. The impact of genotypic background on the barrier to resistance can be difficult to capture, particularly for agents in experimental stages or that are recently approved or expanded into new patient populations. We developed an evolutionary model-based counting method to quickly quantify the population genetic potential to resistance and assess population differences. We demonstrate its applicability to HIV-1 integrase inhibitors, as their increasing use globally contrasts with limited availability of non-B subtype resistant sequence data and corresponding knowledge gap. A large sequence data set encompassing most prevailing HIV-1 subtypes and resistance-associated mutations of currently approved integrase inhibitors was investigated. A complex interplay between codon predominance, polymorphisms, and associated evolutionary costs resulted in a subtype-dependent varied genetic potential for 15 resistance mutations against integrase inhibitors. While we confirm the lower genetic barrier of subtype B for G140S, we convincingly discard a similar effect previously suggested for G140C. A supplementary analysis for HIV-1 reverse transcriptase inhibitors identified a lower genetic barrier for K65R in subtype C through differential codon usage not reported before. To aid evolutionary interpretations of genomic differences for antiviral strategies, we advanced existing counting methods with increased sensitivity to identify subtype dependencies of resistance emergence. Future applications include novel HIV-1 drug classes or vaccines, as well as other viral pathogens.
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Abbas UL, Glaubius RL, Ding Y, Hood G. Drug resistance from preferred antiretroviral regimens for HIV infection in South Africa: A modeling study. PLoS One 2019; 14:e0218649. [PMID: 31269034 PMCID: PMC6609148 DOI: 10.1371/journal.pone.0218649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 06/06/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Tenofovir-containing regimens comprise the preferred first-line antiretroviral therapy (ART) in many countries including South Africa, where utilization of second-line regimens is limited. Considerable HIV drug resistance has occurred among persons failing tenofovir-containing first-line ART. We evaluated drug resistance at the population level using mathematical modeling. SETTING Heterosexual HIV epidemic in KwaZulu-Natal, South Africa. METHODS We constructed a stochastic individual-based model and simulated scenarios of ART implementation, either CD4-based (threshold < 500 cells/mL) or Fast-track (81% coverage by 2020), with consideration of major drug-associated mutations (M184V, K65R and non-nucleoside reverse transcriptase inhibitor (NNRTI)). Using base case and uncertainty analyses, we assessed (majority) drug resistance levels. RESULTS By 2030, the median total resistance (proportion of HIV-infected persons with drug resistance) is predicted to reach 31.4% (interquartile range (IQR): 16.5%-50.2%) with CD4-based ART, decreasing to 14.5% (IQR: 7.7%-25.8%) with Fast-track implementation. In both scenarios, we find comparably high prevalence (~80%) of acquired NNRTI-associated, M184V and K65R mutations. Over 48% of individuals with acquired resistance harbor dual, 44% triple and 7% just single drug mutations. Drug-resistant HIV is predicted to comprise 40% (IQR: 27%-50%) of incident infections, while 70% of prevalent transmitted resistance is NNRTI-associated. At 2018, the projected total resistance is 15% (IQR: 7.5%-25%), with 18% (IQR: 13%-24%) of incident infections from transmitted drug-resistant HIV. CONCLUSIONS WHO-recommended preferred first-line ART could lead to substantial drug resistance. Effective surveillance of HIV drug resistance and utilization of second-line as well as alternative first-line regimens is crucial.
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Affiliation(s)
- Ume L. Abbas
- Department of Medicine, Section of Infectious Diseases and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Quantitative Health Sciences and Infectious Disease, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Robert L. Glaubius
- Departments of Quantitative Health Sciences and Infectious Disease, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Yajun Ding
- Department of Medicine, Section of Infectious Diseases and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Gregory Hood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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Solomon DA. HIV Initial Assessment and Routine Follow-up: What Tests to Order and Why. Infect Dis Clin North Am 2019; 33:647-662. [PMID: 31239091 DOI: 10.1016/j.idc.2019.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Laboratory tests are an important tool in the care of patients with human immunodeficiency virus. An organized approach to laboratory ordering helps clinicians to understand the utility of each test, ensure a comprehensive evaluation, and decrease use of unnecessary tests. Tests are organized around the following goals of care: confirm the diagnosis, assess for immune suppression, guide antiretroviral therapy, screen for coinfections and latent infections, monitor response to therapy, and provide preventative care. This article reviews appropriate testing for patients with human immunodeficiency virus to accomplish these goals with a focus on how each test is useful in clinical practice.
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Affiliation(s)
- Daniel A Solomon
- Division of Infectious Disease, Brigham and Women's Hospital, 75 Francis Street, PBB 4A, Boston, MA 02115, USA.
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Chimukangara B, Lessells RJ, Rhee SY, Giandhari J, Kharsany AB, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, Gordon M, Makadzange T, Kiepiela P, Ramjee G, Ledwaba J, Kalimashe M, Morris L, Parikh UM, Mellors JW, Shafer RW, Katzenstein D, Moodley P, Gupta RK, Pillay D, Abdool Karim SS, de Oliveira T. Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis. EClinicalMedicine 2019; 9:26-34. [PMID: 31143879 PMCID: PMC6510720 DOI: 10.1016/j.eclinm.2019.03.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND South Africa has the largest public antiretroviral therapy (ART) programme in the world. We assessed temporal trends in pretreatment HIV-1 drug resistance (PDR) in ART-naïve adults from South Africa. METHODS We included datasets from studies conducted between 2000 and 2016, with HIV-1 pol sequences from more than ten ART-naïve adults. We analysed sequences for the presence of 101 drug resistance mutations. We pooled sequences by sampling year and performed a sequence-level analysis using a generalized linear mixed model, including the dataset as a random effect. FINDINGS We identified 38 datasets, and retrieved 6880 HIV-1 pol sequences for analysis. The pooled annual prevalence of PDR remained below 5% until 2009, then increased to a peak of 11·9% (95% confidence interval (CI) 9·2-15·0) in 2015. The pooled annual prevalence of non-nucleoside reverse-transcriptase inhibitor (NNRTI) PDR remained below 5% until 2011, then increased to 10.0% (95% CI 8.4-11.8) by 2014. Between 2000 and 2016, there was a 1.18-fold (95% CI 1.13-1.23) annual increase in NNRTI PDR (p < 0.001), and a 1.10-fold (95% CI 1.05-1.16) annual increase in nucleoside reverse-transcriptase inhibitor PDR (p = 0.001). INTERPRETATION Increasing PDR in South Africa presents a threat to the efforts to end the HIV/AIDS epidemic. These findings support the recent decision to modify the standard first-line ART regimen, but also highlights the need for broader public health action to prevent the further emergence and transmission of drug-resistant HIV. SOURCE OF FUNDING This research project was funded by the South African Medical Research Council (MRC) with funds from National Treasury under its Economic Competitiveness and Support Package. DISCLAIMER The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of CDC.
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Affiliation(s)
- Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
- Corresponding authors at: KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Science, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa.
| | - Richard J. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha B.M. Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC)-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cherie Cawood
- Epicentre AIDS Risk Management (Pty) Limited, PO Box 3484, Paarl, Cape Town, South Africa
| | - David Khanyile
- Epicentre AIDS Risk Management (Pty) Limited, PO Box 3484, Paarl, Cape Town, South Africa
| | | | - Karidia Diallo
- Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Reshmi Samuel
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alain Vandormael
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Babill Stray-Pedersen
- Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Michelle Gordon
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tariro Makadzange
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States of America
| | - Photini Kiepiela
- HIV Prevention Research Unit, Medical Research Council, Durban, South Africa
| | - Gita Ramjee
- HIV Prevention Research Unit, Medical Research Council, Durban, South Africa
| | - Johanna Ledwaba
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Monalisa Kalimashe
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Lynn Morris
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Urvi M. Parikh
- Department of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - John W. Mellors
- Department of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - David Katzenstein
- Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - Pravi Moodley
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Ravindra K. Gupta
- Department of Infection, University College London, United Kingdom of Great Britain and Northern Ireland
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Deenan Pillay
- Department of Infection, University College London, United Kingdom of Great Britain and Northern Ireland
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Corresponding authors at: KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Science, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa.
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Hassan AS, Bibby DF, Mwaringa SM, Agutu CA, Ndirangu KK, Sanders EJ, Cane PA, Mbisa JL, Berkley JA. Presence, persistence and effects of pre-treatment HIV-1 drug resistance variants detected using next generation sequencing: A Retrospective longitudinal study from rural coastal Kenya. PLoS One 2019; 14:e0210559. [PMID: 30759103 PMCID: PMC6373901 DOI: 10.1371/journal.pone.0210559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 12/27/2018] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The epidemiology of HIV-1 drug resistance (HIVDR) determined by Sanger capillary sequencing, has been widely studied. However, much less is known about HIVDR detected using next generation sequencing (NGS) methods. We aimed to determine the presence, persistence and effect of pre-treatment HIVDR variants detected using NGS in HIV-1 infected antiretroviral treatment (ART) naïve participants from rural Coastal Kenya. METHODS In a retrospective longitudinal study, samples from HIV-1 infected participants collected prior [n = 2 time-points] and after [n = 1 time-point] ART initiation were considered. An ultra-deep amplicon-based NGS assay, calling for nucleotide variants at >2.0% frequency of viral population, was used. Suspected virologic failure (sVF) was defined as a one-off HIV-1 viral load of >1000 copies/ml whilst on ART. RESULTS Of the 50 eligible participants, 12 (24.0% [95% CI: 13.1-38.2]) had at least one detectable pre-treatment HIVDR variant against Protease Inhibitors (PIs, n = 6 [12%]), Nucleoside Reverse Transcriptase Inhibitors (NRTIs, n = 4 [8.0%]) and Non-NRTIs (n = 3 [6.0%]). Overall, 15 pre-treatment resistance variants were detected (frequency, range: 2.3-92.0%). A positive correlation was observed between mutation frequency and absolute load for NRTI and/or NNRTI variants (r = 0.761 [p = 0.028]), but not for PI variants (r = -0.117 [p = 0.803]). Participants with pre-treatment NRTI and/or NNRTI resistance had increased odds of sVF (OR = 6.0; 95% CI = 1.0-36.9; p = 0.054). CONCLUSIONS Using NGS, pre-treatment resistance variants were common, though observed PI variants were unlikely transmitted, but rather probably generated de novo. Even when detected from a low frequency, pre-treatment NRTI and/or NNRTI resistance variants may adversely affect treatment outcomes.
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Affiliation(s)
| | - David F. Bibby
- Virus Reference Department, Public Health England, London, United Kingdom
| | | | | | | | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, United Kingdom
| | - Patricia A. Cane
- Virus Reference Department, Public Health England, London, United Kingdom
| | - Jean L. Mbisa
- Virus Reference Department, Public Health England, London, United Kingdom
| | - James A. Berkley
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, United Kingdom
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Luo XL, Mo LD, Su GS, Huang JP, Wu JY, Su HZ, Huang WH, Luo SD, Ni ZY. Incidence and types of HIV-1 drug resistance mutation among patients failing first-line antiretroviral therapy. J Pharmacol Sci 2019; 139:275-279. [PMID: 30928089 DOI: 10.1016/j.jphs.2018.11.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVE This study aims to investigate the prevalence and types of drug resistance mutations among patients failing first-line antiretroviral therapy (ART). METHODS Plasma samples from 112 patients with human immunodeficiency virus-1 (HIV-1) were collected for virus RNA extract and gene amplification. The mutations related to drug resistance were detected and the incidence was statistically analyzed, and the drug resistance rate against common drugs was also evaluated. RESULTS 103 cases were successfully amplified, and the main drug resistance mutations in the reverse transcriptase (RT) region were M184V (50.49%), K103N (28.16%), Y181C (25.24%), and K65R (27.18%), while no drug main resistance mutation was found in the protease (PR) region. The incidence of drug resistance mutations was significantly different among patients with different ages, routes of infection, duration of treatment, initial ART regimens and viral load. The drug resistance rate to the common drugs was assessed, including Efavirenz (EFV, 71.84%), Nevirapine (NVP, 74.76%), Lamivudine (3TC, 66.02%), Zidovudine (AZT, 4.85%), Stavudine (D4T, 16.51%), and Tenofovir (TDF, 21.36%). CONCLUSION The drug resistance mutations to NRTIs and NNRTIs are complex and highly prevalent, which was the leading cause of first-line ART failure. This study provides significant theoretical support for developing the second-line and third-line therapeutic schemes.
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Affiliation(s)
- Xiao-Lu Luo
- The 4th People's Hospital of Nanning, The Infectious Disease Hospital of Nanning Affiliated to Guangxi Medical University, and the AIDS Clinical Treatment Center of Guangxi (Nanning), Nanning, 530023, China
| | - Li-da Mo
- The 4th People's Hospital of Nanning, The Infectious Disease Hospital of Nanning Affiliated to Guangxi Medical University, and the AIDS Clinical Treatment Center of Guangxi (Nanning), Nanning, 530023, China.
| | - Guo-Sheng Su
- The 4th People's Hospital of Nanning, The Infectious Disease Hospital of Nanning Affiliated to Guangxi Medical University, and the AIDS Clinical Treatment Center of Guangxi (Nanning), Nanning, 530023, China
| | - Jin-Ping Huang
- The 4th People's Hospital of Nanning, The Infectious Disease Hospital of Nanning Affiliated to Guangxi Medical University, and the AIDS Clinical Treatment Center of Guangxi (Nanning), Nanning, 530023, China
| | - Jing-Yu Wu
- The Disease Control and Prevention Center of Xingning District of Nanning, Nanning 530023, Guangxi, China
| | - Han-Zhen Su
- The 4th People's Hospital of Nanning, The Infectious Disease Hospital of Nanning Affiliated to Guangxi Medical University, and the AIDS Clinical Treatment Center of Guangxi (Nanning), Nanning, 530023, China
| | - Wan-Hong Huang
- The 4th People's Hospital of Nanning, The Infectious Disease Hospital of Nanning Affiliated to Guangxi Medical University, and the AIDS Clinical Treatment Center of Guangxi (Nanning), Nanning, 530023, China
| | - Shun-da Luo
- The 4th People's Hospital of Nanning, The Infectious Disease Hospital of Nanning Affiliated to Guangxi Medical University, and the AIDS Clinical Treatment Center of Guangxi (Nanning), Nanning, 530023, China
| | - Zu-Yan Ni
- The 4th People's Hospital of Nanning, The Infectious Disease Hospital of Nanning Affiliated to Guangxi Medical University, and the AIDS Clinical Treatment Center of Guangxi (Nanning), Nanning, 530023, China
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Machnowska P, Meixenberger K, Schmidt D, Jessen H, Hillenbrand H, Gunsenheimer-Bartmeyer B, Hamouda O, Kücherer C, Bannert N. Prevalence and persistence of transmitted drug resistance mutations in the German HIV-1 Seroconverter Study Cohort. PLoS One 2019; 14:e0209605. [PMID: 30650082 PMCID: PMC6334938 DOI: 10.1371/journal.pone.0209605] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/07/2018] [Indexed: 02/03/2023] Open
Abstract
The prevalence of transmitted drug resistance (TDR) in antiretroviral therapy (ART)-naïve individuals remains stable in most developed countries despite a decrease in the prevalence of acquired drug resistance. This suggests that persistence and further transmission of HIV-1 that encodes transmitted drug resistance mutations (TDRMs) is occurring in ART-naïve individuals. In this study, we analysed the prevalence and persistence of TDRMs in the protease and reverse transcriptase-sequences of ART-naïve patients within the German HIV-1 Seroconverter Study Cohort who were infected between 1996 and 2017. The prevalence of TDRMs and baseline susceptibility to antiretroviral drugs were assessed using the Stanford HIVdb list and algorithm. Mean survival times of TDRMs were calculated by Kaplan-Meier analysis. The overall prevalence of TDR was 17.2% (95% CI 15.7–18.6, N = 466/2715). Transmitted NNRTI resistance was observed most frequently with 7.8% (95% CI 6.8–8.8), followed by NRTI resistance (5.0%, 95% CI 4.2–5.9) and PI resistance (2.8%, 95% CI 2.2–3.4). Total TDR (OR = 0.89, p = 0.034) and transmitted NRTI resistance (OR = 0.65, p = 0.000) decreased between 1996 and 2017 but has remained stable during the last decade. Viral susceptibility to NNRTIs (6.5%-6.9% for individual drugs) was mainly reduced, while <3% of the recommended NRTIs and PIs were affected. The longest mean survival times were calculated for the NNRTI mutations K103N (5.3 years, 95% CI 4.2–5.6) and E138A/G/K (8.0 years, 95% CI 5.8–10.2 / 7.9 years, 95% CI 5.4–10.3 / 6.7 years, 95% CI 6.7–6.7) and for the NRTI mutation M41L (6.4 years, 95% CI 6.0–6.7).The long persistence of single TDRMs indicates that onward transmission from ART-naïve individuals is the main cause for TDR in Germany. Transmitted NNRTI resistance was the most frequent TDR, showing simultaneously the highest impact on baseline ART susceptibility and on TDRMs with prolonged persistence. These results give cause for concern regarding the use of NNRTI in first-line regimens.
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Affiliation(s)
- Patrycja Machnowska
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (NB); (PM)
| | | | - Daniel Schmidt
- Division of HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | | | | | | | - Osamah Hamouda
- Division of HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | - Claudia Kücherer
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- * E-mail: (NB); (PM)
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De La Cruz J, Vardhanbhuti S, Sahoo MK, Rovner R, Bosch RJ, Manasa J, Katzenstein DA, Pinsky BA. Persistence of Human Immunodeficiency Virus-1 Drug Resistance Mutations in Proviral Deoxyribonucleic Acid After Virologic Failure of Efavirenz-Containing Antiretroviral Regimens. Open Forum Infect Dis 2019; 6:ofz034. [PMID: 30863788 PMCID: PMC6405934 DOI: 10.1093/ofid/ofz034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/09/2019] [Accepted: 01/15/2019] [Indexed: 01/23/2023] Open
Abstract
Background Efavirenz (EFV)-based regimens select broad drug resistance to nonnucleoside reverse-transcriptase inhibitors (NNRTIs), limiting the effectiveness of EFV and other NNRTIs. The duration, persistence, and decay of drug resistance mutations (DRMs) in the proviral reservoir is not well defined. Methods Participants with virologic failure of EFV-based regimens and drug-resistant viremia with the K103N mutation in plasma ribonucleic acid (RNA) were identified from AIDS Clinical Trials Group (ACTG) studies A364 and A5095. These individuals received a second-line, boosted protease inhibitor-based regimen with suppression of viremia for up to10 years during long-term follow-up (median = 3.6 years; interquartile range, 2.1-6.9 years). Proviral deoxyribonucleic acid (DNA) from cryopreserved peripheral blood mononuclear cells was sequenced to identify the persistence of DRM. Results Twenty-eight participants from ACTG 364 and ACTG 5095 were evaluated. Sanger sequencing of proviral DNA detected K103N as well as additional reverse-transcriptase inhibitor (RTI) mutations. Ultradeep sequencing confirmed persistence of K103N in 71% of participants with minimal decay over time. In an adjusted model including years since suppression, persistent proviral K103N was 2.6 times more likely (95% confidence interval, 1.0-6.4) per log10 higher human immunodeficiency virus RNA at EFV failure. Conclusions Persistence of RTI mutations in proviral DNA after virologic failure has implications for the effectiveness of future drug regimens and the recycling of RTI drugs.
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Affiliation(s)
- Justin De La Cruz
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine
| | | | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, California
| | - Robert Rovner
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine
| | - Ronald J Bosch
- Harvard TH Chan School of Public Health, Boston, Massachusetts
| | - Justen Manasa
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine
| | - David A Katzenstein
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine.,Department of Pathology, Stanford University School of Medicine, California
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Hassan AS, Esbjörnsson J, Wahome E, Thiong’o A, Makau GN, Price MA, Sanders EJ. HIV-1 subtype diversity, transmission networks and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya. PLoS One 2018; 13:e0206177. [PMID: 30562356 PMCID: PMC6298690 DOI: 10.1371/journal.pone.0206177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/08/2018] [Indexed: 11/21/2022] Open
Abstract
Background HIV-1 molecular epidemiology amongst men who have sex with men (MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR) in acute and early infected MSM from Coastal Kenya. Methods Analysis of HIV-1 partial pol sequences from MSM recruited 2005–2017 and sampled within six months of the estimated date of infection. Volunteers were classified as men who have sex with men exclusively (MSME) or with both men and women (MSMW). HIV-1 subtype and transmission clusters were determined by maximum-likelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug resistance database. Results Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters, with substantial mixing between MSME and MSMW. Majority of volunteer sequences were either not linked to any reference sequence (56%) or clustered exclusively with sequences of Kenyan origin (19%). Eight (8% [95% CI: 4–16]) had at least one TDR mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with sequences forming transmission clusters of two and three taxa each. There were no significant differences in HIV-1 subtype distribution and TDR between MSME and MSMW. Conclusions This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan origin, with many transmission clusters and having intermediate level of TDR. Targeted HIV-1 prevention, early identification and care interventions are warranted to break the transmission cycle amongst MSM from Coastal Kenya.
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Affiliation(s)
- Amin S. Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
- * E-mail:
| | | | | | | | - George N. Makau
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
| | - Mathew A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Oxford University, Oxford, United Kingdom
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Mbange AE, Kaba D, Diouara AAM, Diop-Ndiaye H, Ngom-Ngueye NF, Dieng A, Lo S, Toure KN, Fall M, Mbacham WF, Diallo MS, Cisse M, Mboup S, Kane CT. Surveillance of transmitted HIV-1 antiretroviral drug resistance in the context of decentralized HIV care in Senegal and the Ebola outbreak in Guinea. BMC Res Notes 2018; 11:723. [PMID: 30309385 PMCID: PMC6182815 DOI: 10.1186/s13104-018-3804-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/27/2018] [Indexed: 02/08/2023] Open
Abstract
Objectives Disruption in HIV care provision may enhance the development and spread of drug resistance due to inadequate antiretroviral therapy. This study thus determined the prevalence of HIV-1 transmitted drug resistance (TDR) in settings of decentralized therapy and care in Senegal and, the Ebola outbreak in Guinea. Antiretroviral-naïve patients were enrolled following a modified WHO TDR Threshold Survey method, implemented in Senegal (January–March 2015) and Guinea (August–September 2015). Plasma and dried blood spots specimens, respectively from Senegalese (n = 69) and Guinean (n = 50) patients, were collected for direct sequencing of HIV-1 pol genes. The Stanford Calibrated Population Resistance program v6.0 was used for Surveillance Drug Resistance Mutations (SDRMs). Results Genotyping was successful from 54/69 (78.2%) and 31/50 (62.0%) isolates. In Senegal, TDR prevalence was 0% (mean duration since HIV diagnosis 4.08 ± 3.53 years). In Guinea, two patients exhibited SDRMs M184V (NRTI), T215F (TAM) and, G190A (NNRTI), respectively. TDR prevalence at this second site, however, could not be ascertained because of low sample size. Phylogenetic inference confirmed CRF02_AG predominance in Senegal (62.96%) and Guinea (77.42%). TDR prevalence in Senegal remains extremely low suggesting improved control measures. Continuous surveillance in both settings is mandatory and, should be done closest to diagnosis/transmission time and with larger sample size.
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Affiliation(s)
- Aristid Ekollo Mbange
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal.,The Biotechnology center, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon.,Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Djiba Kaba
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal.,Laboratoire de Biologie Moléculaire Nestor Bangoura/Hélène Labrousse, Hôpital National Donka, Conakry, Guinée.,Service de Dermatologie-Vénéréologie Hôpital National Donka/UGAN, Conakry, Guinée
| | - Abou Abdallah Malick Diouara
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal.,Département de Génie chimique et de Biologie Appliquée, Ecole Supérieure Polytechnique/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal.,Laboratoire de Bio-informatique, Université du Québec à Montréal, Montréal, Canada
| | - Halimatou Diop-Ndiaye
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal.,Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | | | - Ahmed Dieng
- Hôpital régional de Saint-Louis, Saint-Louis, Sénégal
| | - Seynabou Lo
- Hôpital régional de Saint-Louis, Saint-Louis, Sénégal
| | - Kine Ndiaye Toure
- Centre de Traitement Ambulatoire, Fann, Centre Hospitalier Universitaire, Dakar, Sénégal
| | - Mamadou Fall
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Wilfred Fon Mbacham
- The Biotechnology center, Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Mariama Sadjo Diallo
- Laboratoire de Biologie Moléculaire Nestor Bangoura/Hélène Labrousse, Hôpital National Donka, Conakry, Guinée
| | - Mohamed Cisse
- Laboratoire de Biologie Moléculaire Nestor Bangoura/Hélène Labrousse, Hôpital National Donka, Conakry, Guinée
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal
| | - Coumba Toure Kane
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation (IRESSEF), Diamniadio, Sénégal. .,Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire, Aristide Le Dantec/Université Cheikh Anta Diop de Dakar, Dakar, Sénégal. .,Laboratoire de Bactériologie-Virologie CHNU Dalal Jam, Dakar, Sénégal.
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HIV-genetic diversity and drug resistance transmission clusters in Gondar, Northern Ethiopia, 2003-2013. PLoS One 2018; 13:e0205446. [PMID: 30304061 PMCID: PMC6179264 DOI: 10.1371/journal.pone.0205446] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The HIV-1 epidemic in Ethiopia has been shown to be dominated by two phylogenetically distinct subtype C clades, the Ethiopian (C'-ET) and East African (C-EA) clades, however, little is known about the temporal dynamics of the HIV epidemic with respect to subtypes and distinct clades. Moreover, there is only limited information concerning transmission of HIV-1 drug resistance (TDR) in the country. METHODS A cross-sectional survey was conducted among young antiretroviral therapy (ART)-naïve individuals recently diagnosed with HIV infection, in Gondar, Ethiopia, 2011-2013 using the WHO recommended threshold survey. A total of 84 study participants with a median age of 22 years were enrolled. HIV-1 genotyping was performed and investigated for drug resistance in 67 individuals. Phylogenetic analyses were performed on all available HIV sequences obtained from Gondar (n = 301) which were used to define subtype C clades, temporal trends and local transmission clusters. Dating of transmission clusters was performed using BEAST. RESULT Four of 67 individuals (6.0%) carried a HIV drug resistance mutation strain, all associated with non-nucleoside reverse transcriptase inhibitors (NNRTI). Strains of the C-EA clade were most prevalent as we found no evidence of temporal changes during this time period. However, strains of the C-SA clade, prevalent in Southern Africa, have been introduced in Ethiopia, and became more abundant during the study period. The oldest Gondar transmission clusters dated back to 1980 (C-EA), 1983 (C-SA) and 1990 (C'-ET) indicating the presence of strains of different subtype C clades at about the same time point in Gondar. Moreover, some of the larger clusters dated back to the 1980s but transmissions within clusters have been ongoing up till end of the study period. Besides being associated with more sequences and larger clusters, the C-EA clade sequences were also associated with clustering of HIVDR sequences. One cluster was associated with the G190A mutation and showed onward transmissions at high rate. CONCLUSION TDR was detected in 6.0% of the sequenced samples and confirmed pervious reports that the two subtype C clades, C-EA and C'-ET, are common in Ethiopia. Moreover, the findings indicated an increased diversity in the epidemic as well as differences in transmission clusters sizes of the different clades and association with resistance mutations. These findings provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.
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Abstract
The evolution of viral pathogens is shaped by strong selective forces that are exerted during jumps to new hosts, confrontations with host immune responses and antiviral drugs, and numerous other processes. However, while undeniably strong and frequent, adaptive evolution is largely confined to small parts of information-packed viral genomes, and the majority of observed variation is effectively neutral. The predictions and implications of the neutral theory have proven immensely useful in this context, with applications spanning understanding within-host population structure, tracing the origins and spread of viral pathogens, predicting evolutionary dynamics, and modeling the emergence of drug resistance. We highlight the multiple ways in which the neutral theory has had an impact, which has been accelerated in the age of high-throughput, high-resolution genomics.
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Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge,
United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Brittany Rife Magalis
- Institute for Genomics and Evolutionary Medicine, Temple University,
Philadelphia, PA
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Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing. J Clin Microbiol 2018; 56:JCM.00105-18. [PMID: 29618499 DOI: 10.1128/jcm.00105-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/20/2018] [Indexed: 11/20/2022] Open
Abstract
The ability of next-generation sequencing (NGS) technologies to detect low frequency HIV-1 drug resistance mutations (DRMs) not detected by dideoxynucleotide Sanger sequencing has potential advantages for improved patient outcomes. We compared the performance of an in vitro diagnostic (IVD) NGS assay, the Sentosa SQ HIV genotyping assay for HIV-1 genotypic resistance testing, with Sanger sequencing on 138 protease/reverse transcriptase (RT) and 39 integrase sequences. The NGS assay used a 5% threshold for reporting low-frequency variants. The level of complete plus partial nucleotide sequence concordance between Sanger sequencing and NGS was 99.9%. Among the 138 protease/RT sequences, a mean of 6.4 DRMs was identified by both Sanger and NGS, a mean of 0.5 DRM was detected by NGS alone, and a mean of 0.1 DRM was detected by Sanger sequencing alone. Among the 39 integrase sequences, a mean of 1.6 DRMs was detected by both Sanger sequencing and NGS and a mean of 0.15 DRM was detected by NGS alone. Compared with Sanger sequencing, NGS estimated higher levels of resistance to one or more antiretroviral drugs for 18.2% of protease/RT sequences and 5.1% of integrase sequences. There was little evidence for technical artifacts in the NGS sequences, but the G-to-A hypermutation was detected in three samples. In conclusion, the IVD NGS assay evaluated in this study was highly concordant with Sanger sequencing. At the 5% threshold for reporting minority variants, NGS appeared to attain a modestly increased sensitivity for detecting low-frequency DRMs without compromising sequence accuracy.
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40
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Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics. PLoS Pathog 2018; 14:e1006895. [PMID: 29462208 PMCID: PMC5877888 DOI: 10.1371/journal.ppat.1006895] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/30/2018] [Accepted: 01/23/2018] [Indexed: 11/23/2022] Open
Abstract
Drug resistant HIV is a major threat to the long-term efficacy of antiretroviral treatment. Around 10% of ART-naïve patients in Europe are infected with drug-resistant HIV type 1. Hence it is important to understand the dynamics of transmitted drug resistance evolution. Thanks to routinely performed drug resistance tests, HIV sequence data is increasingly available and can be used to reconstruct the phylogenetic relationship among viral lineages. In this study we employ a phylodynamic approach to quantify the fitness costs of major resistance mutations in the Swiss HIV cohort. The viral phylogeny reflects the transmission tree, which we model using stochastic birth–death-sampling processes with two types: hosts infected by a sensitive or resistant strain. This allows quantification of fitness cost as the ratio between transmission rates of hosts infected by drug resistant strains and transmission rates of hosts infected by drug sensitive strains. The resistance mutations 41L, 67N, 70R, 184V, 210W, 215D, 215S and 219Q (nRTI-related) and 103N, 108I, 138A, 181C, 190A (NNRTI-related) in the reverse trancriptase and the 90M mutation in the protease gene are included in this study. Among the considered resistance mutations, only the 90M mutation in the protease gene was found to have significantly higher fitness than the drug sensitive strains. The following mutations associated with resistance to reverse transcriptase inhibitors were found to be less fit than the sensitive strains: 67N, 70R, 184V, 219Q. The highest posterior density intervals of the transmission ratios for the remaining resistance mutations included in this study all included 1, suggesting that these mutations do not have a significant effect on viral transmissibility within the Swiss HIV cohort. These patterns are consistent with alternative measures of the fitness cost of resistance mutations. Overall, we have developed and validated a novel phylodynamic approach to estimate the transmission fitness cost of drug resistance mutations. The introduction of antiretroviral therapy (ART) has decreased mortality and morbidity rates among HIV-infected people, and improved their quality of life. In fact, the WHO states that antiretroviral therapy programmes averted an estimated 7.8 million deaths worldwide between 2000 and 2014. However, the antiretroviral regimen prescribed to a patient may be unable to control HIV infection. Factors that can contribute to treatment failure include drug resistance, drug toxicity, or poor treatment adherence. In this study we aim to understand the dynamics of transmitted drug resistance by analysing the viral sequence data that was collected for resistance testing. We present a novel approach to quantify how drug resistance impacts virus lineage transmissibility, how fast resistance mutations evolve in sensitive strains and how fast they revert back to the sensitive type. We apply our approach to the Swiss HIV cohort study, and obtain patterns of viral transmission fitness that are consistent with alternative, harder to obtain measures of fitness.
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41
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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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42
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Fabrizio C, Lepore L, Lagioia A, Punzi G, Saracino A, Angarano G, Monno L. Comment on: Integrase strand-transfer inhibitor polymorphic and accessory resistance substitutions in patients with acute/recent HIV infection. J Antimicrob Chemother 2017; 72:1546-1547. [PMID: 28158344 DOI: 10.1093/jac/dkx014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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43
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Memarnejadian A, Gouklani H, Mohammadi S, Moosazadeh M, Choi J. Prevalence of HIV-1 pre-treatment drug resistance in a southern province of Iran, 2016-2017. Arch Virol 2017; 163:57-63. [PMID: 28983848 DOI: 10.1007/s00705-017-3572-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 09/02/2017] [Indexed: 10/18/2022]
Abstract
HIV-1 transmitted drug resistance (TDR) occurs when primary viruses bear drug resistance mutations (DRMs). TDR causes first-line antiretroviral (ARV) therapy (ART) failure and is becoming more pronounced due to the widespread use of ART. With the absence of routine individual-level drug resistance testing, the World Health Organization (WHO) recommends the tracking of TDR mutations and optimizing the first-line ART following pre-treatment drug resistance (PDR) surveys. Here, we report the PDR frequency for the first time in Hormozgan, a southern province of Iran. In this study, 41 blood samples from HIV-1-positive ART-candidate volunteers were collected across the province between April 2016 and March 2017. Phylogenetic analysis of the sequenced protease (PR) and reverse transcriptase (RT) regions showed that 39 out of 41 samples (95%) were CRF35_AD and the two remaining cases were subtype B (2.5%) and C (2.5%). D67G (2.4%), a mutation that reduces susceptibility to nucleoside reverse transcriptase inhibitors (NRTIs) was the only detectable TDR mutation in this population. Two other DRMs, including E138A (9.7%) and V179T (4.9%), which confer resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs), were also identified. Although no major protease inhibitor (PI) resistance mutations were detected, the minor mutations L10F and L33F (2.5% each) as well as several highly frequent polymorphic mutations were identified. Our results show a PDR frequency of 17% in infected individuals from Hormozgan, classified further as 2.4% NRTIs and 14.6% NNRTIs. These results suggest that first-line ART should be practiced carefully in Hormozgan province, and alternative regimens may become necessary for all starters.
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Affiliation(s)
- Arash Memarnejadian
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran.,Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Hamed Gouklani
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Samira Mohammadi
- Counseling and Behavioral Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Masoomeh Moosazadeh
- Health Laboratories, Vice Chancellery for Health, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Joshua Choi
- Department of Microbiology and Immunology, Western University, London, ON, Canada
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Allen RC, Engelstädter J, Bonhoeffer S, McDonald BA, Hall AR. Reversing resistance: different routes and common themes across pathogens. Proc Biol Sci 2017; 284:20171619. [PMID: 28954914 PMCID: PMC5627214 DOI: 10.1098/rspb.2017.1619] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/23/2017] [Indexed: 11/12/2022] Open
Abstract
Resistance spreads rapidly in pathogen or pest populations exposed to biocides, such as fungicides and antibiotics, and in many cases new biocides are in short supply. How can resistance be reversed in order to prolong the effectiveness of available treatments? Some key parameters affecting reversion of resistance are well known, such as the fitness cost of resistance. However, the population biological processes that actually cause resistance to persist or decline remain poorly characterized, and consequently our ability to manage reversion of resistance is limited. Where do susceptible genotypes that replace resistant lineages come from? What is the epidemiological scale of reversion? What information do we need to predict the mechanisms or likelihood of reversion? Here, we define some of the population biological processes that can drive reversion, using examples from a wide range of taxa and biocides. These processes differ primarily in the origin of revertant genotypes, but also in their sensitivity to factors such as coselection and compensatory evolution that can alter the rate of reversion, and the likelihood that resistance will re-emerge upon re-exposure to biocides. We therefore argue that discriminating among different types of reversion allows for better prediction of where resistance is most likely to persist.
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Affiliation(s)
- Richard C Allen
- Institute of Integrative Biology, ETH Zürich, CH-8092 Zurich, Switzerland
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Bruce A McDonald
- Institute of Integrative Biology, ETH Zürich, CH-8092 Zurich, Switzerland
| | - Alex R Hall
- Institute of Integrative Biology, ETH Zürich, CH-8092 Zurich, Switzerland
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Multimethod Longitudinal HIV Drug Resistance Analysis in Antiretroviral-Therapy-Naive Patients. J Clin Microbiol 2017; 55:2785-2800. [PMID: 28659324 DOI: 10.1128/jcm.00634-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022] Open
Abstract
The global intensification of antiretroviral therapy (ART) can lead to increased rates of HIV drug resistance (HIVDR) mutations in treated and also in ART-naive patients. ART-naive HIV-1-infected patients from Cameroon were subjected to a multimethod HIVDR analysis using amplification-refractory mutation system (ARMS)-PCR, Sanger sequencing, and longitudinal next-generation sequencing (NGS) to determine their profiles for the mutations K103N, Y181C, K65R, M184V, and T215F/Y. We processed 66 ART-naive HIV-1-positive patients with highly diverse subtypes that underlined the predominance of CRF02_AG and the increasing rate of F2 and other recombinant forms in Cameroon. We compared three resistance testing methods for 5 major mutation sites. Using Sanger sequencing, the overall prevalence of HIVDR mutations was 7.6% (5/66) and included all studied mutations except K65R. Comparing ARMS-PCR with Sanger sequencing as a reference, we obtained a sensitivity of 100% (5/5) and a specificity of 95% (58/61), caused by three false-positive calls with ARMS-PCR. For 32/66 samples, we obtained NGS data and we observed two additional mismatches made up of minority variants (7% and 18%) that might not be clinically relevant. Longitudinal NGS analyses revealed changes in HIVDR mutations in all five positive subjects that could not be attributed to treatment. In one of these cases, superinfection led to the temporary masking of a resistant virus. HIVDR mutations can be sensitively detected by ARMS-PCR and sequencing methods with comparable performances. Longitudinal changes in HIVDR mutations have to be considered even in the absence of treatment.
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Response to Therapy in Antiretroviral Therapy-Naive Patients With Isolated Nonnucleoside Reverse Transcriptase Inhibitor-Associated Transmitted Drug Resistance. J Acquir Immune Defic Syndr 2017; 72:171-6. [PMID: 26855248 PMCID: PMC4866916 DOI: 10.1097/qai.0000000000000942] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Nonnucleoside reverse transcriptase inhibitor (NNRTI)-associated transmitted drug resistance (TDR) is the most common type of TDR. Few data guide the selection of antiretroviral therapy (ART) for patients with such resistance. METHODS We reviewed treatment outcomes in a cohort of HIV-1-infected patients with isolated NNRTI TDR who initiated ART between April 2002 and May 2014. In an as-treated analysis, virological failure (VF) was defined as not reaching undetectable virus levels within 24 weeks, virological rebound, or switching regimens during viremia. In an intention-to-treat analysis, failure was defined more broadly as VF, loss to follow-up, and switching during virological suppression. RESULTS Of 3245 patients, 131 (4.0%) had isolated NNRTI TDR; 122 received a standard regimen comprising 2 NRTIs plus a boosted protease inhibitor (bPI; n = 54), an integrase strand transfer inhibitor (INSTI; n = 52), or an NNRTI (n = 16). The median follow-up was 100 weeks. In the as-treated analysis, VF occurred in 15% (n = 8), 2% (n = 1), and 25% (n = 4) of patients in the bPI, INSTI, and NNRTI groups, respectively. In multivariate regression, there was a trend toward a lower risk of VF with INSTIs than with bPIs (hazard ratio: 0.14; 95% confidence interval: 0.02 to 1.1; P = 0.07). In intention-to-treat multivariate regression, INSTIs had a lower risk of failure than bPIs (hazard ratio: 0.38; 95% confidence interval: 0.18 to 0.82; P = 0.01). CONCLUSIONS Patients with isolated NNRTI TDR experienced low VF rates with INSTIs and bPIs. INSTIs were noninferior to bPIs in an analysis of VF but superior to bPIs when frequency of switching and loss to follow-up were also considered.
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47
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Todesco E, Charpentier C, Bertine M, Wirden M, Storto A, Desire N, Grude M, Nguyen T, Sayon S, Yazdanpanah Y, Katlama C, Descamps D, Calvez V, Marcelin AG. Disparities in HIV-1 transmitted drug resistance detected by ultradeep sequencing between men who have sex with men and heterosexual populations. HIV Med 2017; 18:696-700. [PMID: 28444829 DOI: 10.1111/hiv.12508] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2017] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Transmitted drug resistance (TDR) can impair the response to first-line antiretroviral therapy. In treatment-naïve patients chronically infected with HIV type 1 (HIV-1), it was previously shown through Sanger sequencing that TDR was more common in men who have sex with men (MSM) than in other transmission risk groups. We aimed to compare two HIV-1 transmission groups in terms of the presence of TDR mutations. METHODS We investigated, through Sanger sequencing and ultradeep sequencing (UDS), the presence of resistance mutations, both in majority (> 20%) and in minority (1-20%) proportions, in 70 treatment-naïve MSM and 70 treatment-naïve heterosexual patients who recently screened positive for HIV-1. RESULTS The global prevalence of TDR was not significantly different between the two groups, either by Sanger or by UDS. Nevertheless, a higher frequency of nucleoside reverse transcriptase inhibitor TDR was observed among heterosexual patients (P = 0.04). There was also a trend for a higher frequency of TDR among MSM infected with HIV-1 subtype B compared with MSM infected with HIV-1 non-B subtypes (P = 0.06). CONCLUSIONS Ultradeep sequencing UDS allowed sensitive monitoring of TDR, and highlighted some disparities between transmission groups.
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Affiliation(s)
- E Todesco
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - C Charpentier
- INSERM, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Paris, France.,Department of Virology, AP-HP, Bichat-Claude Bernard Hospital, Paris, France
| | - M Bertine
- INSERM, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Paris, France.,Department of Virology, AP-HP, Bichat-Claude Bernard Hospital, Paris, France
| | - M Wirden
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - A Storto
- Department of Virology, AP-HP, Bichat-Claude Bernard Hospital, Paris, France
| | - N Desire
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - M Grude
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - T Nguyen
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - S Sayon
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Y Yazdanpanah
- INSERM, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Paris, France.,Department of Infectious Diseases, AP-HP, Bichat-Claude Bernard Hospital, Paris, France
| | - C Katlama
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Department of Infectious Diseases, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - D Descamps
- INSERM, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Paris, France.,Department of Virology, AP-HP, Bichat-Claude Bernard Hospital, Paris, France
| | - V Calvez
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - A G Marcelin
- Sorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Department of Virology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
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48
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Wertheim JO, Oster AM, Johnson JA, Switzer WM, Saduvala N, Hernandez AL, Hall HI, Heneine W. Transmission fitness of drug-resistant HIV revealed in a surveillance system transmission network. Virus Evol 2017; 3:vex008. [PMID: 28458918 DOI: 10.1093/ve/vex008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Test-and-treat programs are central to the global control of HIV, but transmitted drug resistance threatens the effectiveness of these programs. HIV mutations conferring resistance to antiretroviral drugs reduce replicative fitness in vitro, but their effect on propagation in vivo is less understood. Here, we estimate transmission fitness of these mutations in antiretroviral-naïve populations in the U.S. National HIV Surveillance System by comparing their frequency of clustering in a genetic transmission network relative with wild-type viruses. The large dataset (66,221 persons), comprising 30,196 antiretroviral-naïve persons, permitted the evaluation of sixty-nine resistance mutations. Decreased transmission fitness was demonstrated for twenty-three mutations, including M184V. In contrast, many high prevalence mutations (e.g. K103N, Y181C, and L90M) had transmission fitness that was indistinguishable from or exceeded wild-type fitness, permitting the establishment of large, self-sustaining drug resistance reservoirs. We highlight implications of these findings on strategies to preserve global treatment effectiveness.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, 92093, USA.,ICF International, Atlanta, GA, 30329, USA
| | - Alexandra M Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Jeffrey A Johnson
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - William M Switzer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | | | - Angela L Hernandez
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - H Irene Hall
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Walid Heneine
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
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49
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L. Machado S, Gonçalves GS, Dudley D, O'Connor D, Keiko Toma H, Fernandes JCC, Tanuri A. Development of a Qualitative Quantitative Polymerase Chain Reaction Test to Identify Patients Failing First-Line Therapy to Non-Nucleotide Reverse Transcriptase Inhibitor. AIDS Res Hum Retroviruses 2017; 33:386-394. [PMID: 27819156 DOI: 10.1089/aid.2016.0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antiretroviral therapy (ART) can be compromised by selection of drug resistance strains, which can be promoted by lack of adherence during therapy and drug tolerance, and some of these drug-resistant strains can persist for years as minority populations. The K103N drug resistance mutation is selected by the use of non-nucleotide reverse transcriptase inhibitors, including nevirapine or efavirenz (EFV), used in low-income countries. Here we describe the use of a less expensive qualitative point mutation polymerase chain reaction (PMqPCRK103N) targeting K103N mutation. To validate the use of this methodology, we tested previously sequenced samples from patients treated with highly active ART with viral loads above 2,000 copies/ml and compared the results of our assay with Illumina deep sequencing. Due to its low cost and high specificity, this test is particularly suitable for low-income countries to screen for pretreatment resistance in patients either initiating ART or failing first-line regimens containing EFV.
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Affiliation(s)
- Sergio L. Machado
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gabriel S. Gonçalves
- Laboratório de Virologia Molecular, Instituto de Biologia, Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Dawn Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - David O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Helena Keiko Toma
- Faculdade de Farmacia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia, Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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50
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Tostevin A, White E, Dunn D, Croxford S, Delpech V, Williams I, Asboe D, Pozniak A, Churchill D, Geretti AM, Pillay D, Sabin C, Leigh‐Brown A, Smit E. Recent trends and patterns in HIV-1 transmitted drug resistance in the United Kingdom. HIV Med 2017; 18:204-213. [PMID: 27476929 PMCID: PMC5297994 DOI: 10.1111/hiv.12414] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2016] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Transmission of drug-resistant HIV-1 has decreased in the UK since the early 2000s. This analysis reports recent trends and characteristics of transmitted drug resistance (TDR) in the UK from 2010 to 2013. METHODS Resistance tests conducted in antiretroviral treatment (ART)-naïve individuals between 2010 and 2013 were analysed for the presence of transmitted drug resistance mutations (TDRMs), defined as any mutations from a modified 2009 World Health Organization surveillance list, or a modified 2013 International Antiviral Society-USA list for integrase tests. Logistic regression was used to examine associations between demographics and the prevalence of TDRMs. RESULTS TDRMs were observed in 1223 (7.5%) of 16 425 individuals; prevalence declined from 8.1% in 2010 to 6.6% in 2013 (P = 0.02). The prevalence of TDRMs was higher among men who have sex with men (MSM) compared with heterosexual men and women (8.7% versus 6.4%, respectively) with a trend for decreasing TDRMs among MSM (P = 0.008) driven by a reduction in nucleoside reverse transcriptase inhibitor (NRTI)-related mutations. The most frequently detected TDRMs were K103N (2.2%), T215 revertants (1.6%), M41L (0.9%) and L90M (0.7%). Predicted phenotypic resistance to first-line ART was highest to the nonnucleoside reverse transcriptase inhibitors (NNRTIs) rilpivirine and efavirenz (6.2% and 3.4%, respectively) but minimal to NRTIs, including tenofovir, and protease inhibitors (PIs). No major integrase TDRMs were detected among 101 individuals tested while ART-naïve. CONCLUSIONS We observed a decrease in TDRMs in recent years. However, this was confined to the MSM population and rates remained stable in those with heterosexually acquired HIV infection. Resistance to currently recommended first-line ART, including integrase inhibitors, remained reassuringly low.
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Affiliation(s)
- A Tostevin
- MRC Clinical Trials Unit at UCLUniversity College LondonLondonUK
| | - E White
- MRC Clinical Trials Unit at UCLUniversity College LondonLondonUK
| | - D Dunn
- MRC Clinical Trials Unit at UCLUniversity College LondonLondonUK
| | - S Croxford
- Centre for Infectious Disease Surveillance and Control (CIDSC)Public Health EnglandLondonUK
| | - V Delpech
- Centre for Infectious Disease Surveillance and Control (CIDSC)Public Health EnglandLondonUK
| | - I Williams
- Mortimer Market CentreUniversity College London Hospitals NHS TrustLondonUK
| | - D Asboe
- Chelsea & Westminster HospitalLondonUK
| | - A Pozniak
- Chelsea & Westminster HospitalLondonUK
| | - D Churchill
- Brighton and Sussex University Hospitals NHS TrustBrightonUK
| | | | - D Pillay
- Division of Infection and ImmunityUniversity College LondonLondonUK
- Africa Centre for Health and Population StudiesUniversity of KwaZulu‐NatalMtubatubaSouth Africa
| | - C Sabin
- Research Department of Infection and Population HealthUniversity College LondonLondonUK
| | | | - E Smit
- Public Health EnglandBirmingham Heartlands HospitalBirminghamUK
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