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Kiros M, Biset S, Gebremariam B, Yalew GT, Abegaz WE, Geteneh A. Trends in HIV-1 pretreatment drug resistance and HIV-1 variant dynamics among antiretroviral therapy-naive Ethiopians from 2003 to 2018: a pooled sequence analysis. Virol J 2023; 20:243. [PMID: 37880705 PMCID: PMC10601210 DOI: 10.1186/s12985-023-02205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Ethiopia is among the highly HIV-affected countries, with reported 12,000 and 12,000 AIDS-related deaths and incidents as per reports from 2021. Although the country has made a promising progress in antiretroviral therapy, recent studies have indicated that pretreatment drug resistance (PDR) is alarmingly increasing, which has become a challenge for the effectiveness of HIV treatment. Epidemiologic data on PDR is necessary to help establish ART regimens with good efficacy. Thus, this systematic review aimed to determine the trend analysis of PDR among ART-naïve individuals along with HIV variant dynamics in Ethiopia. METHOD HIV-1 pol sequences from studies conducted between 2003 and 2018 among ART-naïve Ethiopian individuals were retrieved from GenBank and analyzed for the presence of PDR mutations (PDRM) along with the analysis of HIV-1 variant dynamics. The Calibrated Population Resistance (CPR) tool Version 8.1 and the REGA HIV-1 Subtyping Tool Version 3 were used to determine the PDRM and HIV-1 genetic diversity, respectively. RESULT We identified nine studies and analyzed 1070 retrieved HIV-1 pol sequences in this systematic review. The pooled prevalence of PDR was 4.8% (51/1070), including 1.4% (15/1070), 2.8% (30/1070), and 0.8% (9/1070) for nucleoside reverse transcriptase inhibitor (NRTI), non-NRTI (NNRTI), and protease inhibitor (PI) resistance, respectively. NRTI and NNRTI concurrent PDRM were observed among 0.2% (2/799) of the analyzed sequences. The overall PDR prevalence has been increasing over the years. Though the prevalence of the NNRTI, NRTI, and PI PDR also increased over the years, the NNRTI increment was more pronounced than the others, reaching 7.84% in 2018 from 2.19% in 2003. The majority (97%; 1038/1070) of the genetic diversity was HIV-1 subtype C virus, followed by subtype C' (2%; 20/1038) and other subtypes (1%; 10/1038). CONCLUSIONS According to this systematic review, the overall pooled prevalence of PDR is low. Despite the low prevalence, there has been an increasing trend of PDR over the years, which implies the need for routine surveillance of PDRMs along with preventive measures. Hence, this supports the recently endorsed transition of ART regimens from NNRTI to integrase strand transfer inhibitor-based regimens recommended by the WHO. In addition, this finding underscores the need for routine baseline genotypic drug resistance testing for all newly diagnosed HIV-infected patients before initiating treatment to halt the upward trend of PDR.
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Affiliation(s)
- Mulugeta Kiros
- Department of Medical Laboratory Science, CollegeofMedicineandHealth Sciences, Aksum University, Aksum, Ethiopia.
| | - Sirak Biset
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Birhane Gebremariam
- Department of Medical Laboratory Science, CollegeofMedicineandHealth Sciences, Aksum University, Aksum, Ethiopia
| | - Gebrehiwet Tesfay Yalew
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Adigrat University, Adigrat, Ethiopia
| | - Woldaregay Erku Abegaz
- Department of Microbiology, Parasitology, and Immunology, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alene Geteneh
- Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia
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Pang X, Liang S, Tang K, Huang J, He Q, Fang N, Xie B, Xie X, Wang H, Hu Y, Lan G. Disparity of HIV-1 Pretreatment Drug Resistance in Men Who Have Sex With Men and the Heterosexual Population in Guangxi, China. Open Forum Infect Dis 2023; 10:ofad016. [PMID: 36751650 PMCID: PMC9898876 DOI: 10.1093/ofid/ofad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Background The prevalence of human immunodeficiency type 1 (HIV-1) pretreatment drug resistance (PDR) in men who have sex with men (MSM) in Guangxi remains unclear, and its effect on antiretroviral therapy (ART) needs to be further studied. Methods Individuals newly diagnosed with HIV in Guangxi from 2016 to 2020, which mainly included MSM and the heterosexual (HES) population, were recruited in this study. Pol sequences were sequenced to analyze PDR and construct a genetic network. The risk factors for PDR and the effect on ART were respectively analyzed. Results The PDR of MSM in Guangxi was 4.7% (34/716), consisting of nonnucleoside reverse transcriptase inhibitors (3.5%), protease inhibitors (0.8%), integrase strand transfer inhibitors (0.7%), and nucleoside reverse transcriptase inhibitors (0.4%), and lower than that of HES (9.3% [77/827]). The subtype was associated with PDR, and MSM was lower than HES (CRF01_AE: 3.0% vs 8.0%; CRF07_BC: 4.1% vs 7.2%). CRF55_01B (adjusted odds ratio [aOR], 3.35) was a risk factor for PDR in MSM, while CRF08_BC (aOR, 2.34) and older (aOR, 2.75) were risk factors for PDR in HES. Six of 18 (33.3%) PDR of MSM in the network connected to each other, lower than that of HES (61.1% [22/36]). CRF55_01B (aOR, 5.69) was a risk factor for PDR transmission in MSM, while CRF08_BC (aOR, 4.08) was a risk factor in HES. Pretreatment CD4+ T-cell count, age, infection route, and subtype were associated with recovery of CD4+ count and suppression of viral load. Conclusions The prevalence of PDR was different between MSM and HES, which may be associated with subtype. Thus, the monitoring of subtype and PDR should be strengthened.
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Affiliation(s)
| | | | - Kailing Tang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Jinghua Huang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Qin He
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Ningye Fang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Center for Disease Control and Prevention, Nanning, Guangxi, China
| | - Bo Xie
- School of Information and Management, Guangxi Medical University, Nanning, Guangxi, China
| | - Xing Xie
- Clinical Laboratory Center of The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Huifeng Wang
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Yanling Hu
- Correspondence: Yanling Hu, MD, PhD, Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, 22 Shuangyong Road, Qingxiu District, 530028, Nanning, Guangxi, China (); Guanghua Lan, MD, PhD, Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Center for Disease Control and Prevention, 18 Jinzhou Road, Qingxiu District, 530021, Nanning, Guangxi, China ()
| | - Guanghua Lan
- Correspondence: Yanling Hu, MD, PhD, Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, 22 Shuangyong Road, Qingxiu District, 530028, Nanning, Guangxi, China (); Guanghua Lan, MD, PhD, Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Key Laboratory of AIDS Prevention Control and Translation, Guangxi Center for Disease Control and Prevention, 18 Jinzhou Road, Qingxiu District, 530021, Nanning, Guangxi, China ()
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Miranda MNS, Pingarilho M, Pimentel V, Martins MDRO, Kaiser R, Seguin-Devaux C, Paredes R, Zazzi M, Incardona F, Abecasis AB. Trends of Transmitted and Acquired Drug Resistance in Europe From 1981 to 2019: A Comparison Between the Populations of Late Presenters and Non-late Presenters. Front Microbiol 2022; 13:846943. [PMID: 35495657 PMCID: PMC9044068 DOI: 10.3389/fmicb.2022.846943] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background The increased use of antiretroviral therapy (ART) has decreased mortality and morbidity of HIV-1 infected people but increasing levels of HIV drug resistance threatens the success of ART regimens. Conversely, late presentation can impact treatment outcomes, health costs, and potential transmission of HIV. Objective To describe the patterns of transmitted drug resistance (TDR) and acquired drug resistance (ADR) in HIV-1 infected patients followed in Europe, to compare its patterns in late presenters (LP) vs non-late presenters (NLP), and to analyze the most prevalent drug resistance mutations among HIV-1 subtypes. Methods Our study included clinical, socio-demographic, and genotypic information from 26,973 HIV-1 infected patients from the EuResist Integrated Database (EIDB) between 1981 and 2019. Results Among the 26,973 HIV-1 infected patients in the analysis, 11,581 (42.9%) were ART-naïve patients and 15,392 (57.1%) were ART-experienced. The median age was 37 (IQR: 27.0-45.0) years old and 72.6% were males. The main transmission route was through heterosexual contact (34.9%) and 81.7% of patients originated from Western Europe. 71.9% of patients were infected by subtype B and 54.8% of patients were classified as LP. The overall prevalence of TDR was 12.8% and presented an overall decreasing trend (p for trend < 0.001), the ADR prevalence was 68.5% also with a decreasing trend (p for trend < 0.001). For LP and NLP, the TDR prevalence was 12.3 and 12.6%, respectively, while for ADR, 69.9 and 68.2%, respectively. The most prevalent TDR drug resistance mutations, in both LP and NLP, were K103N/S, T215rev, T215FY, M184I/V, M41I/L, M46I/L, and L90M. Conclusion Our study showed that the overall TDR (12.8%) and ADR (68.5%) presented decreasing trends during the study time period. For LP, the overall TDR was slightly lower than for NLP (12.3 vs 12.6%, respectively); while this pattern was opposite for ADR (LP slightly higher than NLP). We suggest that these differences, in the case of TDR, can be related to the dynamics of fixation of drug resistance mutations; and in the case of ADR with the more frequent therapeutic failure in LPs.
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Affiliation(s)
- Mafalda N S Miranda
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Maria do Rosário O Martins
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), Lisbon, Portugal
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Roger Paredes
- Infectious Diseases Department and IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Ana B Abecasis
- Global Health and Tropical Medicine (GHTM), Institute of Hygiene and Tropical Medicine, New University of Lisbon (IHMT/UNL), Lisbon, Portugal
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Mortier V, Debaisieux L, Dessilly G, Stoffels K, Vaira D, Vancutsem E, Van Laethem K, Vanroye F, Verhofstede C. Prevalence and evolution of transmitted HIV drug resistance in Belgium between 2013 and 2019. Open Forum Infect Dis 2022; 9:ofac195. [PMID: 35794938 PMCID: PMC9251670 DOI: 10.1093/ofid/ofac195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/08/2022] [Indexed: 11/27/2022] Open
Abstract
Background To assess the prevalence and evolution of transmitted drug resistance (TDR) in Belgium, a total of 3708 baseline human immunodeficiency virus (HIV)-1 polymerase sequences from patients diagnosed between 2013 and 2019 were analyzed. Methods Protease and reverse-transcriptase HIV-1 sequences were collected from the 7 national Aids Reference Laboratories. Subtype determination and drug resistance scoring were performed using the Stanford HIV Drug Resistance Database. Trends over time were assessed using linear regression, and the maximum likelihood approach was used for phylogenetic analysis. Results A total of 17.9% of the patients showed evidence of TDR resulting in at least low-level resistance to 1 drug (Stanford score ≥15). If only the high-level mutations (Stanford score ≥60) were considered, TDR prevalence dropped to 6.3%. The majority of observed resistance mutations impacted the sensitivity for nonnucleoside reverse-transcriptase inhibitors (NNRTIs) (11.4%), followed by nucleoside reverse-transcriptase inhibitors (6.2%) and protease inhibitors (2.4%). Multiclass resistance was observed in 2.4%. Clustered onward transmission was evidenced for 257 of 635 patients (40.5%), spread over 25 phylogenetic clusters. Conclusions The TDR prevalence remained stable between 2013 and 2019 and is comparable to the prevalence in other Western European countries. The high frequency of NNRTI mutations requires special attention and follow-up. Phylogenetic analysis provided evidence for local clustered onward transmission of some frequently detected mutations.
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Affiliation(s)
- Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Laurent Debaisieux
- Aids Reference Laboratory, Université Libre de Bruxelles, CUB Hôpital Erasme, 1070 Brussels, Belgium
| | - Géraldine Dessilly
- Aids Reference Laboratory, Medical Microbiology Unit, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Karolien Stoffels
- Aids Reference Laboratory, Centre Hospitalier Universitaire St. Pierre, 1000 Brussels, Belgium
| | - Dolores Vaira
- Aids Reference Laboratory, Centre Hospitalier Universitaire de Liège, 4000 Liège, Belgium
| | - Ellen Vancutsem
- Aids Reference Laboratory, Vrije Universiteit Brussel VUB, 1090 Brussels, Belgium
| | - Kristel Van Laethem
- Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, 3000 Leuven, Belgium Aids Reference Laboratory, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Fien Vanroye
- Aids Reference Laboratory, Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
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Pre-Treatment Integrase Inhibitor Resistance and Natural Polymorphisms among HIV-1 Subtype C Infected Patients in Ethiopia. Viruses 2022; 14:v14040729. [PMID: 35458459 PMCID: PMC9029575 DOI: 10.3390/v14040729] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Dolutegravir-based antiretroviral therapy (ART) has been scaled up in many developing countries, including Ethiopia. However, subtype-dependent polymorphic differences might influence the occurrence of HIV-drug-resistance mutations (HIVDRMs). We analyzed the prevalence of pre-treatment integrase strand transfer inhibitor (INSTI) HIVDRMs and naturally occurring polymorphisms (NOPs) of the integrase gene, using plasma samples collected as part of the national HIVDR survey in Ethiopia in 2017. We included a total of 460 HIV-1 integrase gene sequences from INSTI-naïve (n = 373 ART-naïve and n = 87 ART-experienced) patients. No dolutegravir-associated HIVDRMs were detected, regardless of previous exposure to ART. However, we found E92G in one ART-naïve patient specimen and accessory mutations in 20/460 (4.3%) of the specimens. Moreover, among the 288 integrase amino acid positions of the subtype C, 187/288 (64.9%) were conserved (<1.0% variability). Analysis of the genetic barrier showed that the Q148H/K/R dolutegravir resistance pathway was less selected in subtype C. Docking analysis of the dolutegravir showed that protease- and reverse-transcriptase-associated HIVDRMs did not affect the native structure of the HIV-1 integrase. Our results support the implementation of a wide scale-up of dolutegravir-based regimes. However, the detection of polymorphisms contributing to INSTI warrants the continuous surveillance of INSTI resistance.
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Stirrup O, Tostevin A, Ragonnet-Cronin M, Volz E, Burns F, Delpech V, Dunn D. Diagnosis delays in the UK according to pre or postmigration acquisition of HIV. AIDS 2022; 36:415-422. [PMID: 35084383 PMCID: PMC7612284 DOI: 10.1097/qad.0000000000003110] [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] [Indexed: 10/20/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate whether infection occurred pre or postmigration and the associated diagnosis delay in migrants diagnosed with HIV in the UK. DESIGN We analyzed a cohort of individuals diagnosed with HIV in the UK in 2014-2016 born in Africa or elsewhere in Europe. Inclusion criteria were arrival within 15 years before diagnosis, availability of HIV pol sequence, and viral subtype shared by at least 10 individuals. METHODS We examined phylogenies for evidence of infection after entry into the UK and incorporated this information into a Bayesian analysis of timing of infection using biomarkers of CD4+ cell count, avidity assays, proportion of ambiguous nucleotides in viral sequences, and last negative test dates where available. RESULTS One thousand, two hundred and fifty-six individuals were included. The final model indicated that HIV was acquired postmigration for most MSM born in Europe (posterior expectation 65%, 95% credibility interval 64-67%) or Africa (65%, 62-69%), whereas a minority (20-30%) of men and women with heterosexual transmission acquired HIV postmigration. Estimated diagnosis delays were lower for MSM than for those with heterosexual transmission, and were lower for those with postmigration infection across all subgroups. For MSM acquiring HIV postmigration, the estimated mean time to diagnosis was less than one year, but for those who acquired HIV premigration, the mean time from infection to diagnosis was more than five years for all subgroups. CONCLUSION Acquisition of HIV postmigration is common, particularly among MSM, calling for prevention efforts aimed at migrant communities. Delays in diagnosis reinforce the need for targeted testing initiatives.
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Affiliation(s)
- Oliver Stirrup
- Institute for Global Health, University College London, London, UK
| | - Anna Tostevin
- Institute for Global Health, University College London, London, UK
| | - Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Fiona Burns
- Institute for Global Health, University College London, London, UK
- Royal Free London NHS Foundation Trust, London, UK
| | - Valerie Delpech
- HIV and STI Department, National Infection Service, Public Health England, London, United Kingdom
| | - David Dunn
- Institute for Global Health, University College London, London, UK
- MRC Clinical Trials Unit, University College London, London, UK
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Novitsky V, Steingrimsson J, Gillani FS, Howison M, Aung S, Solomon M, Won CY, Brotherton A, Shah R, Dunn C, Fulton J, Bertrand T, Civitarese A, Howe K, Marak T, Chan P, Bandy U, Alexander-Scott N, Hogan J, Kantor R. Statewide Longitudinal Trends in Transmitted HIV-1 Drug Resistance in Rhode Island, USA. Open Forum Infect Dis 2022; 9:ofab587. [PMID: 34988256 PMCID: PMC8709897 DOI: 10.1093/ofid/ofab587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
Background HIV-1 transmitted drug resistance (TDR) remains a global challenge that can impact care, yet its comprehensive assessment is limited and heterogenous. We longitudinally characterized statewide TDR in Rhode Island. Methods Demographic and clinical data from treatment-naïve individuals were linked to protease, reverse transcriptase, and integrase sequences routinely obtained over 2004-2020. TDR extent, trends, impact on first-line regimens, and association with transmission networks were assessed using the Stanford Database, Mann-Kendall statistic, and phylogenetic tools. Results In 1123 individuals, TDR to any antiretroviral increased from 8% (2004) to 26% (2020), driven by non-nucleotide reverse transcriptase inhibitor (NNRTI; 5%-18%) and, to a lesser extent, nucleotide reverse transcriptase inhibitor (NRTI; 2%-8%) TDR. Dual- and triple-class TDR rates were low, and major integrase strand transfer inhibitor resistance was absent. Predicted intermediate to high resistance was in 77% of those with TDR, with differential suppression patterns. Among all individuals, 34% were in molecular clusters, some only with members with TDR who shared mutations. Among clustered individuals, people with TDR were more likely in small clusters. Conclusions In a unique (statewide) assessment over 2004-2020, TDR increased; this was primarily, but not solely, driven by NNRTIs, impacting antiretroviral regimens. Limited TDR to multiclass regimens and pre-exposure prophylaxis are encouraging; however, surveillance and its integration with molecular epidemiology should continue in order to potentially improve care and prevention interventions.
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Affiliation(s)
| | | | | | - Mark Howison
- Research Improving People's Life, Providence, Rhode Island, USA
| | - Su Aung
- Brown University, Providence, Rhode Island, USA
| | | | - Cindy Y Won
- Brown University, Providence, Rhode Island, USA
| | | | - Rajeev Shah
- Brown University, Providence, Rhode Island, USA
| | - Casey Dunn
- Yale University, New Haven, Connecticut, USA
| | - John Fulton
- Brown University, Providence, Rhode Island, USA
| | - Thomas Bertrand
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Anna Civitarese
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Katharine Howe
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Theodore Marak
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Philip Chan
- Brown University, Providence, Rhode Island, USA.,Rhode Island Department of Health, Providence, Rhode Island, USA
| | - Utpala Bandy
- Rhode Island Department of Health, Providence, Rhode Island, USA
| | | | | | - Rami Kantor
- Brown University, Providence, Rhode Island, USA
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Pinto A, Carrera A, Salem H, Thapa K, Shaik A, Petoumenos K, Cunningham P, Garsia R, Dwyer D, Cooper DA, Kelleher A. Evolution of HIV-1 Surveillance Drug Resistance Mutations Over 10 Years in New South Wales, Australia. AIDS Res Hum Retroviruses 2021; 37:897-902. [PMID: 28474534 DOI: 10.1089/aid.2016.0301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
New South Wales has the greatest burden of HIV in Australia, with 2012 and 2013 recording the highest rates of new diagnoses in 20 years. Concurrently, there has been significant changes in antiretroviral treatments and testing paradigms. We compiled a statewide resistance database to characterize changes in HIV-1 resistance mutations over time. Genotypic antiretroviral resistance testing (GART) was performed on request at three reference laboratories using commercial and in-house methods. In total, 7629 HIV-1 polymerase sequences obtained from GART from 2004 to 2013 were retrospectively collated, reformatted, de-identified, and analyzed using Stanford HIVdb program 7.0 and the 2009 World Health Organization (WHO) surveillance drug resistance mutations (SDRMs). Analyses were performed on subgroups of known treatment naives, treatment experienced, and seroconverters. There has been a decrease in overall rates of prevalent drug resistance mutations from 57.8% in 2004 to 21% in 2013. Dual and triple class resistance mutations have decreased from 32.7% in 2004 to 5.8% in 2013 and 16.4% to 1.2%, respectively. In treatment-naive individuals (n = 450), the frequency of protease inhibitor (PI) mutations remains low at 2.7%. In seroconverters, rates of transmitted drug resistance (TDR) are 6.6%, 3%, 3%, and 1.5% for overall, PI, non-nucleoside reverse transcription inhibitor (NNRTI), and NRTI, respectively. In treatment experienced, rates remain stable with 36.0%, 18.9%, 29.1%, and 6.4% for overall, NNRTI, NRTI, and PI mutations. The most common mutations in treatment experienced occurred at position M184, T215 (NRTI); K103 (NNRTI); I54 (PI). Apparent decreases in prevalent SDRMs can be attributed to changes in GART testing indications over time. In treatment-naive and -experienced subgroups, rates have been stable with low rates of TDR in seroconverters.
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Affiliation(s)
- Angie Pinto
- Immunovirology and Pathogenesis Program, The Kirby Institute, Randwick, New South Wales, Australia
| | - Alex Carrera
- Department of Immunology, HIV Reference Laboratory, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Hanan Salem
- Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Kiran Thapa
- Pathology West, Institute for Clinical Pathology and Medical Research, Sydney, New South Wales, Australia
| | - Ansari Shaik
- Immunovirology and Pathogenesis Program, The Kirby Institute, Randwick, New South Wales, Australia
| | - Kathy Petoumenos
- Immunovirology and Pathogenesis Program, The Kirby Institute, Randwick, New South Wales, Australia
| | - Philip Cunningham
- Virology Research Program, St Vincent's Centre for Applied Medical Research, Sydney, New South Wales, Australia
| | - Roger Garsia
- Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Dominic Dwyer
- Pathology West, Institute for Clinical Pathology and Medical Research, Sydney, New South Wales, Australia
| | - David A. Cooper
- Immunovirology and Pathogenesis Program, The Kirby Institute, Randwick, New South Wales, Australia
| | - Anthony Kelleher
- Immunovirology and Pathogenesis Program, The Kirby Institute, Randwick, New South Wales, Australia
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9
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Huang SW, Shen MC, Wang WH, Li WY, Wang JH, Tseng CY, Liu PY, Wang LS, Lee YL, Chen YMA, Lee CY, Lu PL, Wang SF. High prevalence of HIV-1 transmitted drug resistance and factors associated with time to virological failure and viral suppression in Taiwan. J Antimicrob Chemother 2021; 77:185-195. [PMID: 34648632 DOI: 10.1093/jac/dkab361] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/06/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Integrase strand transfer inhibitor (InSTI)-based regimens have become the major first-line treatment for HIV-1-infected patients in Taiwan. Transmitted drug resistance (TDR) and several clinical characteristics are associated with time to virological failure or viral suppression; however, these have not been investigated in Taiwan. OBJECTIVES To determine the impact of several factors on treatment outcomes in HIV-1-infected patients in Taiwan. METHODS The cohort included 164 HIV-1 treatment-naive patients in Taiwan from 2018 to 2020. Blood specimens were collected to determine the genotypic drug resistance using the Stanford University HIV drug resistance database. Cox proportional hazards models were used to identify factors associated with time to virological failure or viral suppression. RESULTS The prevalence of TDR in Taiwan was 27.4% and an increasing trend was seen from 2018 to 2020. TDR mutations related to NNRTIs were the most prevalent (21%) while TDR to InSTIs remained at a relatively low level (1.3%). A baseline HIV-1 viral load of ≥100 000 copies/mL was associated with a shorter time to virological failure [multivariate hazard ratio (mHR) 7.84; P = 0.018] and longer time to viral suppression (mHR 0.46; P < 0.001). Time to viral suppression was shorter in patients receiving InSTI-based regimens (mHR 2.18; P = 0.006). Different InSTI-based regimens as initial treatment did not affect the treatment outcomes. CONCLUSIONS This study found an increasing trend of HIV-1 TDR prevalence from 2018 to 2020 in Taiwan. Baseline HIV-1 viral load and receiving InSTI-based regimens are important factors associated with time to virological failure or viral suppression.
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Affiliation(s)
- Szu-Wei Huang
- Model Development Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Mei-Chen Shen
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Hung Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wei-You Li
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Jen-Hsien Wang
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Cheng-Yin Tseng
- Department of Internal Medicine, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Po-Yu Liu
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Lih-Shinn Wang
- Section of Infectious Disease, Department of Internal Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Yu-Lin Lee
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Ming Arthur Chen
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan.,Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Chun-Yuan Lee
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Internal Medicine, Kaohsiung Municipal Siaogang Hospital, Kaohsiung, Taiwan
| | - Po-Liang Lu
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
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10
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Rolle CP, Berhe M, Singh T, Ortiz R, Wurapa A, Ramgopal M, Leone PA, Matthews JE, Dalessandro M, Underwood MR, Angelis K, Wynne BR, Merrill D, Nguyen C, van Wyk J, Zolopa AR. Dolutegravir/lamivudine as a first-line regimen in a test-and-treat setting for newly diagnosed people living with HIV. AIDS 2021; 35:1957-1965. [PMID: 34115650 PMCID: PMC8462441 DOI: 10.1097/qad.0000000000002979] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Dolutegravir/lamivudine (DTG/3TC) is indicated for treatment-naive and experienced people with HIV; however, questions remain about its utility in a test-and-treat setting because of potential transmitted resistance and baseline hepatitis B virus (HBV) co-infection. We present feasibility and efficacy of DTG/3TC in newly diagnosed individuals in a test-and-treat setting. DESIGN The single-arm STAT study evaluated DTG/3TC in a US test-and-treat setting. METHODS Eligible adults initiated DTG/3TC 14 days or less after HIV-1 diagnosis without availability of baseline laboratory results. If baseline testing indicated DTG or 3TC resistance, HBV co-infection, or creatinine clearance less than 30 ml/min per 1.73 m2, participants remained on study with treatment modification. Efficacy endpoints included proportions of participants with HIV-1 RNA less than 50 copies/ml at Week 24, regardless of antiretroviral regimen, among all participants (intention-to-treat exposed) and those with available HIV-1 RNA data (observed). RESULTS Of 131 participants enrolled, 8% were female and 50% were non-white. Through Week 24, treatment was modified in eight participants [five with HBV co-infection, one with baseline M184V, one for adverse event (rash), one participant decision]. At Week 24, 78% (102/131) of all participants and 92% (102/111) of those with available data achieved HIV-1 RNA less than 50 copies/ml. Incidence of drug-related adverse events was low (7%); no drug-related serious adverse events occurred. CONCLUSION These data demonstrate the feasibility, efficacy, and safety of using DTG/3TC as a first-line regimen in a test-and-treat setting, with therapy adjustments for baseline resistance or HBV co-infection occurring safely via routine clinical care as needed [ClinicalTrials.gov, NCT03945981; see Supplemental Digital Content 1, video abstract (Video abstract summarizing the STAT study design and results), http://links.lww.com/QAD/C189].
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Affiliation(s)
| | | | | | | | - Anson Wurapa
- Infectious Disease Specialists of Atlanta, Decatur, GA
| | - Moti Ramgopal
- Midway Immunology and Research Center, Fort Pierce, FL
| | | | | | | | - Mark R. Underwood
- Clinical Virology, Translational Medical Research, ViiV Healthcare, Research Triangle Park, NC, USA
| | | | | | | | - Christopher Nguyen
- Regional Medical Department, ViiV Healthcare, Research Triangle Park, NC, USA
| | - Jean van Wyk
- Global Medical Department, ViiV Healthcare, Brentford, UK
| | - Andrew R. Zolopa
- Department of Medical Affairs, ViiV Healthcare, Research Triangle Park, NC
- Stanford University, Palo Alto, CA, USA
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11
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Yuan H, Liu Z, Wu X, Wu M, Fang Q, Zhang X, Shi T, Tully DC, Zhang T. Prevalence of transmitted HIV-1 drug resistance among treatment-naive individuals in China, 2000-2016. Arch Virol 2021; 166:2451-2460. [PMID: 34195923 DOI: 10.1007/s00705-021-05140-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/29/2021] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus (HIV) with transmitted drug-resistance (TDR) limits the therapeutic options available for treatment-naive HIV patients. This study aimed to further our understanding of the prevalence and transmission characteristics of HIV with TDR for the application of first-line antiretroviral regimens. A total of 6578 HIV-1 protease/reverse-transcriptase sequences from treatment-naive individuals in China between 2000 and 2016 were obtained from the Los Alamos HIV Sequence Database and were analyzed for TDR. Transmission networks were constructed to determine genetic relationships. The spreading routes of large TDR clusters were identified using a Bayesian phylogeographic framework. TDR mutations were detected in 274 (4.51%) individuals, with 1.40% associated with resistance to nucleoside reverse transcriptase inhibitors, 1.52% to non-nucleoside reverse transcriptase inhibitors, and 1.87% to protease inhibitors. The most frequent mutation was M46L (58, 0.89%), followed by K103N (36, 0.55%), M46I (36, 0.55%), and M184V (26, 0.40%). The prevalence of total TDR initially decreased between 2000 and 2010 (OR = 0.83, 95% CI 0.73-0.95) and then increased thereafter (OR = 1.50, 95% CI 1.13-1.97). The proportion of sequences in a cluster (clustering rate) among HIV isolates with TDR sequences was lower than that of sequences without TDR (40.5% vs. 48.8%, P = 0.023) and increased from 27.3% in 2005-2006 to 63.6% in 2015-2016 (P < 0.001). While most TDR mutations were associated with reduced relative transmission fitness, mutation M46I was associated with higher relative transmission fitness than the wild-type strain. This study identified a low-level prevalence of TDR HIV in China during the last two decades. However, the increasing TDR HIV rate since 2010, the persistent circulation of drug resistance mutations, and the expansion of self-sustaining drug resistance reservoirs may compromise the efficacy of antiretroviral therapy programs.
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Affiliation(s)
- Huangbo Yuan
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200237, China.,State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Zhenqiu Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Xuefu Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200237, China
| | - Mingshan Wu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200237, China
| | - Qiwen Fang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200237, China
| | - Xin Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200237, China
| | - Tingting Shi
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200237, China
| | - Damien C Tully
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200237, China.
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12
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Mbisa JL, Ledesma J, Kirwan P, Bibby DF, Manso C, Skingsley A, Murphy G, Brown A, Dunn DT, Delpech V, Geretti AM. Surveillance of HIV-1 transmitted integrase strand transfer inhibitor resistance in the UK. J Antimicrob Chemother 2021; 75:3311-3318. [PMID: 32728703 PMCID: PMC7566560 DOI: 10.1093/jac/dkaa309] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Background HIV treatment guidelines have traditionally recommended that all HIV-positive individuals are tested for evidence of drug resistance prior to starting ART. Testing for resistance to reverse transcriptase inhibitors and PIs is well established in routine care. However, testing for integrase strand transfer inhibitor (InSTI) resistance is less consistent. Objectives To inform treatment guidelines by determining the prevalence of InSTI resistance in a national cohort of recently infected individuals. Patients and methods Recent (within 4 months) HIV-1 infections were identified using a Recent Infection Testing Algorithm of new HIV-1 diagnoses in the UK. Resistance-associated mutations (RAMs) in integrase, protease and reverse transcriptase were detected by ultradeep sequencing, which allows for the sensitive estimation of the frequency of each resistant variant in a sample. Results The analysis included 655 randomly selected individuals (median age = 33 years, 95% male, 83% MSM, 78% white) sampled in the period 2014 to 2016 and determined to have a recent infection. These comprised 320, 138 and 197 samples from 2014, 2015 and 2016, respectively. None of the samples had major InSTI RAMs occurring at high variant frequency (≥20%). A subset (25/640, 3.9%) had major InSTI RAMs occurring only as low-frequency variants (2%–20%). In contrast, 47/588 (8.0%) had major reverse transcriptase inhibitor and PI RAMs at high frequency. Conclusions Between 2014 and 2016, major InSTI RAMs were uncommon in adults with recent HIV-1 infection, only occurring as low-frequency variants of doubtful clinical significance. Continued surveillance of newly diagnosed patients for evidence of transmitted InSTI resistance is recommended to inform clinical practice.
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Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Juan Ledesma
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Peter Kirwan
- National Infection Service, Public Health England, London, UK
| | - David F Bibby
- National Infection Service, Public Health England, London, UK
| | - Carmen Manso
- National Infection Service, Public Health England, London, UK
| | | | - Gary Murphy
- National Infection Service, Public Health England, London, UK
| | - Alison Brown
- National Infection Service, Public Health England, London, UK
| | - David T Dunn
- Institute for Global Health, University College London, London, UK
| | - Valerie Delpech
- National Infection Service, Public Health England, London, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, UK
| | - Anna Maria Geretti
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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13
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Casadellà M, Santos JR, Noguera-Julian M, Micán-Rivera R, Domingo P, Antela A, Portilla J, Sanz J, Montero-Alonso M, Navarro J, Masiá M, Valcarce-Pardeiro N, Ocampo A, Pérez-Martínez L, Pasquau J, Vivancos MJ, Imaz A, Carmona-Oyaga P, Muñoz-Medina L, Villar-García J, Barrufet P, Paredes R. Primary resistance to integrase strand transfer inhibitors in Spain using ultrasensitive HIV-1 genotyping. J Antimicrob Chemother 2021; 75:3517-3524. [PMID: 32929472 DOI: 10.1093/jac/dkaa349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/03/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Transmission of resistance mutations to integrase strand transfer inhibitors (INSTIs) in HIV-infected patients may compromise the efficacy of first-line antiretroviral regimens currently recommended worldwide. Continued surveillance of transmitted drug resistance (TDR) is thus warranted. OBJECTIVES We evaluated the rates and effects on virological outcomes of TDR in a 96 week prospective multicentre cohort study of ART-naive HIV-1-infected subjects initiating INSTI-based ART in Spain between April 2015 and December 2016. METHODS Pre-ART plasma samples were genotyped for integrase, protease and reverse transcriptase resistance using Sanger population sequencing or MiSeq™ using a ≥ 20% mutant sensitivity cut-off. Those present at 1%-19% of the virus population were considered to be low-frequency variants. RESULTS From a total of 214 available samples, 173 (80.8%), 210 (98.1%) and 214 (100.0%) were successfully amplified for integrase, reverse transcriptase and protease genes, respectively. Using a Sanger-like cut-off, the overall prevalence of any TDR, INSTI-, NRTI-, NNRTI- and protease inhibitor (PI)-associated mutations was 13.1%, 1.7%, 3.8%, 7.1% and 0.9%, respectively. Only three (1.7%) subjects had INSTI TDR (R263K, E138K and G163R), while minority variants with integrase TDR were detected in 9.6% of subjects. There were no virological failures during 96 weeks of follow-up in subjects harbouring TDR as majority variants. CONCLUSIONS Transmitted INSTI resistance remains rare in Spain and, to date, is not associated with virological failure to first-line INSTI-based regimens.
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Affiliation(s)
- M Casadellà
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
| | - J R Santos
- Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | | | - P Domingo
- Infectious Diseases Unit, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - A Antela
- Infectious Diseases Unit, Santiago de Compostela Clinical University Hospital, Santiago de Compostela, Spain
| | - J Portilla
- Hospital General Universitario de Alicante, Alicante, Spain
| | - J Sanz
- University Hospital de La Princesa, Madrid, Spain
| | - M Montero-Alonso
- Infectious Diseases Unit, La Fe University and Polytechnic Hospital, Valencia, Spain
| | - J Navarro
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - M Masiá
- Infectious Diseases Unit, Elche University General Hospital, Elche, Spain
| | | | - A Ocampo
- HIV Unit, Hospital Álvaro Cunqueiro, Vigo, Spain
| | - L Pérez-Martínez
- Infectious Diseases Area, Hospital San Pedro-CIBIR, Logroño, Spain
| | - J Pasquau
- University Hospital Virgen de las Nieves, Granada, Spain
| | - M J Vivancos
- Infectious Diseases Unit, Ramón y Cajal Hospital, Madrid, Spain
| | - A Imaz
- HIV and STI Unit, Infectious Diseases Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
| | - P Carmona-Oyaga
- Infectious Diseases Unit, Donostia University Hospital, San Sebastián, Spain
| | | | - J Villar-García
- Infectious Diseases Department, Hospital del Mar - IMIM, Barcelona, Spain
| | - P Barrufet
- Infectious Diseases Unit, Mataró Hospital, Mataró, Spain
| | - R Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain.,Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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14
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Dolutegravir Plus Lamivudine Two-Drug Regimen: Safety, Efficacy and Diagnostic Considerations for Its Use in Real-Life Clinical Practice-A Refined Approach in the COVID-19 Era. Diagnostics (Basel) 2021; 11:diagnostics11050809. [PMID: 33947009 PMCID: PMC8145545 DOI: 10.3390/diagnostics11050809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
The diagnostic and therapeutic management of the Coronavirus Disease 2019 (COVID-19) pandemic in the HIV population brought some known criticalities (and opportunities) to the forefront, for both those who are facing their first therapeutic line today, and for those already well viro-suppressed. The clinical, socioeconomic, and psychological impact of the COVID-19 pandemic should not affect the long-term care of people living with HIV, which creates an urgent need to optimize the diagnostic and treatment approach to the first-line or switch regimens. The use of dolutegravir plus a lamivudine two-drug regimen is one of the most promising solutions to ease the management of HIV treatment in this difficult period. In this review, we report the most salient features related to the use of this regimen from real-life cohorts, meta-analyses, randomized clinical trials, and studies presented at international conferences up to March 2021. We focused on the diagnostic and clinical-management implications of its use in real life, and how these comply with the contingent historical situation. The issue of the timing and type of diagnostic procedures and the relevance of classical diagnostic tests (such as genotype for resistance detection) is also discussed. According to the currently available results, dolutegravir plus a lamivudine two-drug regimen represents an outstanding tool, whose expected advantages fulfill the current requirements for optimal daily care of our HIV patients.
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15
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Young N, Hobbs M, Rahnama F, Shi J, Briggs S. An observational study of high- and low-abundance anti-retroviral resistance mutations among treatment-naïve people living with HIV in New Zealand between 2012 and 2017. Intern Med J 2021; 50:872-876. [PMID: 32656973 DOI: 10.1111/imj.14899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 11/29/2022]
Abstract
HIV resistance genotyping detects drug resistance mutations (DRMs) in ≥20% of circulating virus within an infected individual (high-abundance DRMs). Deep sequencing also detects DRMs in smaller viral subpopulations (low-abundance DRMs), although these are of uncertain importance. In this retrospective analysis of 292 treatment-naïve patients, high-abundance DRMs were present in 30/292 (10%) patients, but only one (0.3%) had resistance to first-line anti-retrovirals. Low-abundance DRMs were present in 36/247 (15%) patients, but none who received anti-retrovirals for which these were present had virologic failure. These findings demonstrate that starting first-line therapy in treatment-naïve patients need not be delayed while awaiting resistance testing.
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Affiliation(s)
- Nicholas Young
- Infectious Diseases Service, Auckland City Hospital, Auckland, New Zealand
| | - Mark Hobbs
- Infectious Diseases Service, Auckland City Hospital, Auckland, New Zealand
| | - Fahimeh Rahnama
- Virology Laboratory, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Jinyang Shi
- Virology Laboratory, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Simon Briggs
- Infectious Diseases Service, Auckland City Hospital, Auckland, New Zealand
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16
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Mikasi SG, Isaacs D, Chitongo R, Ikomey GM, Jacobs GB, Cloete R. Interaction analysis of statistically enriched mutations identified in Cameroon recombinant subtype CRF02_AG that can influence the development of Dolutegravir drug resistance mutations. BMC Infect Dis 2021; 21:379. [PMID: 33892628 PMCID: PMC8063366 DOI: 10.1186/s12879-021-06059-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/08/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The Integrase (IN) strand transfer inhibitor (INSTI), Dolutegravir (DTG), has been given the green light to form part of first-line combination antiretroviral therapy (cART) by the World Health Organization (WHO). DTG containing regimens have shown a high genetic barrier against HIV-1 isolates carrying specific resistance mutations when compared with other class of regimens. METHODS We evaluated the HIV-1 CRF02_AG IN gene sequences from Cameroon for the presence of resistance-associated mutations (RAMs) against INSTIs and naturally occurring polymorphisms (NOPs), using study sequences (n = 20) and (n = 287) sequences data derived from HIV Los Alamos National Laboratory database. The possible impact of NOPs on protein structure caused by HIV-1 CRF02_AG variations was addressed within the context of a 3D model of the HIV-1 IN complex and interaction analysis was performed using PyMol to validate DTG binding to the Wild type and seven mutant structures. RESULTS We observed 12.8% (37/287) sequences to contain RAMs, with only 1.0% (3/287) of the sequences having major INSTI RAMs: T66A, Q148H, R263K and N155H. Of these,11.8% (34/287) of the sequences contained five different IN accessory mutations; namely Q95K, T97A, G149A, E157Q and D232N. NOPs occurred at a frequency of 66% on the central core domain (CCD) position, 44% on the C-terminal domain (CTD) position and 35% of the N-terminal domain (NTD) position. The interaction analysis revealed that DTG bound to DNA, 2MG ions and DDE motif residues for T66A, T97A, Q148H, N155H and R263K comparable to the WT structure. Except for accessory mutant structure E157Q, only one MG contact was made with DTG, while DTG had no MG ion contacts and no DDE motif residue contacts for structure D232N. CONCLUSIONS Our analysis indicated that all RAM's that resulted in a change in the number of interactions with encompassing residues does not affect DTG binding, while accessory mutations E157Q and D232N could affect DTG binding leading to possible DTG resistance. However, further experimental validation is required to validate the in silico findings of our study.
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Affiliation(s)
- Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Darren Isaacs
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa
| | - Rumbidzai Chitongo
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa
| | - George Mondide Ikomey
- Centre for the Study and Control of Communicable Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Rd, Bellville, P.O. Box X17, Cape Town, 7535, South Africa.
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17
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Tzou PL, Rhee SY, Descamps D, Clutter DS, Hare B, Mor O, Grude M, Parkin N, Jordan MR, Bertagnolio S, Schapiro JM, Harrigan PR, Geretti AM, Marcelin AG, Shafer RW. Integrase strand transfer inhibitor (INSTI)-resistance mutations for the surveillance of transmitted HIV-1 drug resistance. J Antimicrob Chemother 2021; 75:170-182. [PMID: 31617907 DOI: 10.1093/jac/dkz417] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Integrase strand transfer inhibitors (INSTIs) are expected to be widely adopted globally, requiring surveillance of resistance emergence and transmission. OBJECTIVES We therefore sought to develop a standardized list of INSTI-resistance mutations suitable for the surveillance of transmitted INSTI resistance. METHODS To characterize the suitability of the INSTI-resistance mutations for transmitted HIV-1 drug resistance (TDR) surveillance, we classified them according to their presence on published expert lists, conservation in INSTI-naive persons, frequency in INSTI-treated persons and contribution to reduced in vitro susceptibility. Mutation prevalences were determined using integrase sequences from 17302 INSTI-naive and 2450 INSTI-treated persons; 53.3% of the INSTI-naive sequences and 20.0% of INSTI-treated sequences were from non-B subtypes. Approximately 10% of sequences were from persons who received dolutegravir alone or a first-generation INSTI followed by dolutegravir. RESULTS Fifty-nine previously recognized (or established) INSTI-resistance mutations were present on one or more of four published expert lists. They were classified into three main non-overlapping groups: 29 relatively common non-polymorphic mutations, occurring in five or more individuals and significantly selected by INSTI treatment; 8 polymorphic mutations; and 22 rare mutations. Among the 29 relatively common INSTI-selected mutations, 24 emerged as candidates for inclusion on a list of INSTI surveillance drug-resistance mutations: T66A/I/K, E92G/Q, G118R, F121Y, E138A/K/T, G140A/C/S, Y143C/H/R/S, S147G, Q148H/R/K, N155H, S230R and R263K. CONCLUSIONS A set of 24 non-polymorphic INSTI-selected mutations is likely to be useful for quantifying INSTI-associated TDR. This list may require updating as more sequences become available from INSTI-experienced persons infected with HIV-1 non-subtype B viruses and/or receiving dolutegravir.
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Affiliation(s)
- Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Diane Descamps
- Université de Paris, IAME, INSERM, F-75018, Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Virologie, F-75018, Paris, France
| | - Dana S Clutter
- Kaiser-Permanente Medical Care Program - Northern California, South San Francisco, CA, USA
| | - Bradley Hare
- Kaiser-Permanente Medical Care Program - Northern California, San Francisco, CA, USA
| | - Orna Mor
- Central Virology Laboratory, Sheba Medical Center, Ministry of Health, Ramat-Gan, Israel and Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Israel
| | - Maxime Grude
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Department of Virology, F-75013, Paris, France
| | - Neil Parkin
- Data First Consulting Inc., Sebastopol, CA, USA
| | | | - Silvia Bertagnolio
- Department of HIV and Global Hepatitis Programme, WHO, Geneva, Switzerland
| | | | - P Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Department of Virology, F-75013, Paris, France
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
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18
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Abstract
Purpose of Review With the expanded roll-out of antiretrovirals for treatment and prevention of HIV during the last decade, the emergence of HIV drug resistance (HIVDR) has become a growing challenge. This review provides an overview of the epidemiology and trajectory of HIVDR globally with an emphasis on pediatric and adolescent populations. Recent Findings HIVDR is associated with suboptimal virologic suppression and treatment failure, leading to an increased risk of HIV transmission to uninfected people and increased morbidity and mortality among people living with HIV. High rates of HIVDR to non-nucleoside reverse transcriptase inhibitors globally are expected to decline with the introduction of the integrase strand transfer inhibitors and long-acting combination regimens, while challenge remains for HIVDR to other classes of antiretroviral drugs. Summary We highlight several solutions including increased HIV viral load monitoring, expanded HIVDR surveillance, and adopting antiretroviral regimens with a high-resistance barrier to decrease HIVDR. Implementation studies and programmatic changes are needed to determine the best approach to prevent and combat the development of HIVDR.
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Lai J, Liu Y, Han X, Huang A, Lin J, Ao W, Ye H, Chen Y. Low Frequency of Integrase Inhibitor Resistance Mutations Among Therapy-Naïve HIV Patients in Southeast China. Drug Des Devel Ther 2021; 15:889-894. [PMID: 33679129 PMCID: PMC7924127 DOI: 10.2147/dddt.s286863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/03/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND With the widespread use of integrase strand transfer inhibitors (INSTIs) in the clinical setting, transmission of INSTIs-resistance mutations may increase. Data regarding transmitted drug resistance mutations (TDRM) to INSTIs in Chinese HIV patients are limited. The aim of this study was to summarize the INSTIs TDRM, including the frequency of protease inhibitors (PIs) and reverse transcriptase (RT) inhibitors (RTIs) mutations in treatment-naïve patients in Southeast China. METHODS HIV-1 positive patients were retrospectively selected between April 2018 and October 2020 from the Mengchao Hepatobiliary Hospital of Fujian Medical University, the largest designated HIV/AIDS care hospital in Southeast China. Individuals who were antiretroviral therapy-naïve and received antiretroviral drug resistance testing at baseline were included. Clinical data including demographic data, CD4 counts, HIV-RNA loads, and drug resistance mutations were collected. RESULTS A total of 147 patients were enrolled. INSTIs TDRM was rare, with only one primary integrase mutation E138K observed in one sample and one secondary mutation E157Q detected in another sample. The overall prevalence of INSTIs TDRM was 1.36%. A substantial proportion of patients harbored common INSTIs-associated polymorphic variants. Two samples harbored the T215S, M184V and K70E mutations related to nucleoside RTIs (NRTIs). Twelve patients carried nonnucleoside RTIs (NNRTIs)-resistance mutations. Two individuals harbored PIs-resistance mutations: Q58E in one patient and M46I, I54V, V82A, L10F, and Q58E mutations in another patient. The total TDRM rate for RTIs and PIs was 10.20% (15/147), but only 0.68% (1/147) was according to the WHO recommendations on TDRM. CONCLUSION The rate of INSTIs TDRM was low among therapy-naïve HIV patients in Southeast China. INSTIs as a first-line regimen are suitable for untreated HIV-1 patients in Southeast China. But special attention must be still paid to INSTIs TDRM in clinical practice.
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Affiliation(s)
- Jinglan Lai
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Infectious Diseases Hospital of Fuzhou, Fuzhou, Fujian, People’s Republic of China
| | - Yuming Liu
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Infectious Diseases Hospital of Fuzhou, Fuzhou, Fujian, People’s Republic of China
| | - Xiao Han
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Infectious Diseases Hospital of Fuzhou, Fuzhou, Fujian, People’s Republic of China
| | - Aiqiong Huang
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Infectious Diseases Hospital of Fuzhou, Fuzhou, Fujian, People’s Republic of China
| | - Jin Lin
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Infectious Diseases Hospital of Fuzhou, Fuzhou, Fujian, People’s Republic of China
| | - Wen Ao
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Infectious Diseases Hospital of Fuzhou, Fuzhou, Fujian, People’s Republic of China
| | - Hanhui Ye
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Infectious Diseases Hospital of Fuzhou, Fuzhou, Fujian, People’s Republic of China
| | - Yahong Chen
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Infectious Diseases Hospital of Fuzhou, Fuzhou, Fujian, People’s Republic of China
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Pang X, Tang K, He Q, Huang J, Fang N, Zhou X, Zhu Q, Wu X, Shen Z, Liang S. HIV drug resistance and HIV transmission risk factors among newly diagnosed individuals in Southwest China. BMC Infect Dis 2021; 21:160. [PMID: 33557775 PMCID: PMC7871613 DOI: 10.1186/s12879-021-05854-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
Background The widespread use of antiretroviral therapy (ART) has resulted in the development of transmitted drug resistance (TDR), which reduces ART efficacy. We explored TDR prevalence and its associated risk factors in newly diagnosed individuals in Guangxi. Methods We enrolled 1324 participants who were newly diagnosed with HIV-1 and had not received ART at voluntary counselling and testing centres (VCT) in Guangxi, China, who had not received ART. Phylogenetic relationship, transmission cluster, and genotypic drug resistance analyses were performed using HIV-1 pol sequences. We analysed the association of demographic and virological factors with TDR. Results In total, 1151 sequences were sequenced successfully, of which 83 (7.21%) showed evidence of TDR. Multivariate logistic regression analysis revealed that there was significant difference between the prevalence of TDR and unmarried status (adjusted odds ratio (aOR) = 2.41, 95% CI: 1.23–4.71), and CRF08_BC subtype (aOR = 2.03, 95% CI: 1.13–3.64). Most cases of TDR were related to resistance to non-nucleoside reverse transcriptase inhibitors (4.87%) and V179E was the most common mutation detected. We identified a total of 119 HIV transmission clusters (n = 585, 50.8%), of which 18 (15.1%) clusters showed evidence of TDR (36, 41.86%). Three clusters were identified that included drug-resistant individuals having a transmission relationship with each other. The following parameters were associated with TDR transmission risk: Unmarried status, educational level of junior high school or below, and CRF08_BC subtype may be a risk of the transmission of TDR. Conclusions Our findings indicated that moderate TDR prevalence and highlighted the importance of continuous TDR monitoring and designing of strategies for TDR mitigation.
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Affiliation(s)
- Xianwu Pang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China.,Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Kailing Tang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China
| | - Qin He
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China
| | - Jinghua Huang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China
| | - Ningye Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China
| | - Xinjuan Zhou
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China
| | - Qiuying Zhu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China
| | - Xiuling Wu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China
| | - Zhiyong Shen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China.
| | - Shujia Liang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, 530028, Guangxi, China.
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21
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Richardson D, Fitzpatrick C, Parkes L, Roberts J, Mulka L. HIV-1 transmitted drug resistance in Brighton, UK, from 2014 to 2020. Int J STD AIDS 2020; 32:199-201. [PMID: 33327896 DOI: 10.1177/0956462420953043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
HIV-1 transmitted drug resistance (TDR) is associated with transmission in men who have sex with men (MSM), non MSM clusters, sexually transmitted infections (STIs) and can lead to antiretroviral failure. UK guidelines recommend performing TDR testing in all newly-diagnosed people living with HIV. We audited performance of TDR in our large tertiary HIV department from 2014-2020. All new patients had TDR testing attempted in the study period. The rate of TDR was 8% and was associated with increasing age and having non-B subtype. Having non-B subtype was not associated with being non-UK born. Thirty-four percent of people were diagnosed with a bacterial STI at the time of HIV diagnosis, but STI diagnosis was not associated with TDR. There was no significant change in TDR over the 6-year audit period. TDR remains a small but significant problem. Identifying these populations and providing effective HIV prevention interventions will reduce HIV incidence and TDR.
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Affiliation(s)
- Daniel Richardson
- Sexual Health & HIV Medicine, Brighton & Sussex University Hospitals NHS Trust, Brighton, UK
- Sexual Health & HIV Medicine, Brighton & Sussex Medical School, Brighton, UK
| | - Colin Fitzpatrick
- Sexual Health & HIV Medicine, Brighton & Sussex University Hospitals NHS Trust, Brighton, UK
| | - Luke Parkes
- Sexual Health & HIV Medicine, Brighton & Sussex University Hospitals NHS Trust, Brighton, UK
| | - Jonathan Roberts
- Sexual Health & HIV Medicine, Brighton & Sussex University Hospitals NHS Trust, Brighton, UK
| | - Larissa Mulka
- Sexual Health & HIV Medicine, Brighton & Sussex University Hospitals NHS Trust, Brighton, UK
- Sexual Health & HIV Medicine, King's College Hospital, London, UK
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Pingarilho M, Pimentel V, Diogo I, Fernandes S, Miranda M, Pineda-Pena A, Libin P, Theys K, O. Martins MR, Vandamme AM, Camacho R, Gomes P, Abecasis A. Increasing Prevalence of HIV-1 Transmitted Drug Resistance in Portugal: Implications for First Line Treatment Recommendations. Viruses 2020; 12:E1238. [PMID: 33143301 PMCID: PMC7693025 DOI: 10.3390/v12111238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Treatment for All recommendations have allowed access to antiretroviral (ARV) treatment for an increasing number of patients. This minimizes the transmission of infection but can potentiate the risk of transmitted (TDR) and acquired drug resistance (ADR). OBJECTIVE To study the trends of TDR and ADR in patients followed up in Portuguese hospitals between 2001 and 2017. METHODS In total, 11,911 patients of the Portuguese REGA database were included. TDR was defined as the presence of one or more surveillance drug resistance mutation according to the WHO surveillance list. Genotypic resistance to ARV was evaluated with Stanford HIVdb v7.0. Patterns of TDR, ADR and the prevalence of mutations over time were analyzed using logistic regression. RESULTS AND DISCUSSION The prevalence of TDR increased from 7.9% in 2003 to 13.1% in 2017 (p < 0.001). This was due to a significant increase in both resistance to nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleotide reverse transcriptase inhibitors (NNRTIs), from 5.6% to 6.7% (p = 0.002) and 2.9% to 8.9% (p < 0.001), respectively. TDR was associated with infection with subtype B, and with lower viral load levels (p < 0.05). The prevalence of ADR declined from 86.6% in 2001 to 51.0% in 2017 (p < 0.001), caused by decreasing drug resistance to all antiretroviral (ARV) classes (p < 0.001). CONCLUSIONS While ADR has been decreasing since 2001, TDR has been increasing, reaching a value of 13.1% by the end of 2017. It is urgently necessary to develop public health programs to monitor the levels and patterns of TDR in newly diagnosed patients.
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Affiliation(s)
- Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Andrea Pineda-Pena
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Pieter Libin
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
- Artificial Intelligence Lab, Department of computer science, Vrije Universiteit Brussel, 1000 Brussels, Belgium
- Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, 3500 Hasselt, Belgium
| | - Kristof Theys
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Anne-Mieke Vandamme
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - Ricardo Camacho
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
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Pyngottu A, Scherrer AU, Kouyos R, Huber M, Hirsch H, Perreau M, Yerly S, Calmy A, Cavassini M, Stöckle M, Furrer H, Vernazza P, Bernasconi E, Günthard HF. Predictors of virological failure and time to viral suppression of first line integrase inhibitor based antiretroviral treatment. Clin Infect Dis 2020; 73:e2134-e2141. [PMID: 33095848 PMCID: PMC8492202 DOI: 10.1093/cid/ciaa1614] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/19/2020] [Indexed: 11/12/2022] Open
Abstract
Background Integrase strand transfer inhibitors (InSTIs) are recommended for first-line treatment of persons with human immunodeficiency virus (HIV). We identified risk factors, including baseline minor InSTI resistance mutations, for treatment failure of InSTI-based regimens. Methods We studied time-to-treatment failure and time to viral suppression among 1419 drug-naive patients in the Swiss HIV Cohort Study. We performed Cox regression models adjusted for demographic factors, baseline HIV RNA/CD4 cell counts, AIDS-defining events, and the type of InSTI. In 646 patients with a baseline genotypic resistance test of the integrase, we studied the impact of minor integrase resistance mutations. Results We observed 121 virological failures during 18 447 person-years of follow-up. A baseline viral load ≥100 000 copies/mL (multivariable hazard ratio [mHR], 2.2; 95% confidence interval [CI], 1.3–3.6) and an AIDS-defining event (mHR, 1.8; 95% CI. 1.1–3.0) were associated with treatment failure. CD4 counts between 200 and 500 cells/µL (mHR, 0.5; 95% CI, .3–.8) and >500 cells/µL (mHR, 0.4; 95% CI, .2–.7) were protective. Time to suppression was shorter in lower viral load strata (mHR, 0.7; 95% CI, .6–.8) and in dolutegravir-based therapy (mHR, 1.2; 95% CI, 1.0–1.4). Minor resistance mutations were found at baseline in 104 of 646 (16%) patients with no effect on treatment outcome. Conclusions Factors associated with treatment failure on InSTI-based first-line regimen remained similar to those of older treatments, in particular high viral load and low CD4 counts.
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Affiliation(s)
- Ashima Pyngottu
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Vannappagari V, Ragone L, Henegar C, van Wyk J, Brown D, Demarest J, Quercia R, St Clair M, Underwood M, Gatell JM, de Ruiter A, Aboud M. Prevalence of pretreatment and acquired HIV-1 mutations associated with resistance to lamivudine or rilpivirine: a systematic review. Antivir Ther 2020; 24:393-404. [PMID: 31503008 DOI: 10.3851/imp3331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Pretreatment and acquired drug resistance mutations (DRMs) can limit antiretroviral therapy effectiveness. METHODS We review prevalence of DRMs with resistance to nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs), focusing on lamivudine and rilpivirine, from 127 articles with >100,000 individuals with HIV-1 infection. RESULTS Estimated global prevalence of pretreatment resistance to any NRTI was 4% and to any NNRTI was 6%. Most prevalent DRMs resistant to lamivudine or rilpivirine were at positions E138 (4%), V179 (1%) and M184 (1%). Estimated acquired DRM prevalence was 58% for any NRTIs and 67% for any NNRTIs, most frequently at positions M184 (58%) and Y181 (21%). CONCLUSIONS This review suggests low risk of lamivudine- or rilpivirine-resistant mutations in treatment-naive, HIV-1-infected individuals.
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Affiliation(s)
| | - Leigh Ragone
- ViiV Healthcare, Research Triangle Park, NC, USA
| | | | | | | | | | | | | | | | - Jose M Gatell
- Hospital Clinic/IDIBAPS, University of Barcelona, Barcelona, Spain.,ViiV Healthcare, Barcelona, Spain
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Calza L, Tamburello M, Borderi M, Colangeli V, Testi D, Amedeo A, Re MC, Bon I. Prevalence of transmitted drug resistance mutations among newly diagnosed HIV‐1‐infected patients in a large teaching hospital of the Northern Italy. J Med Virol 2020; 92:929-931. [DOI: 10.1002/jmv.25896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Leonardo Calza
- Unit of Infectious Diseases, S. Orsola‐Malpighi Hospital“Alma Mater Studiorum” University of Bologna Bologna Italy
| | - Martina Tamburello
- Unit of Microbiology, S. Orsola‐Malpighi Hospital“Alma Mater Studiorum” University of Bologna Bologna Italy
| | - Marco Borderi
- Unit of Infectious Diseases, S. Orsola‐Malpighi Hospital“Alma Mater Studiorum” University of Bologna Bologna Italy
| | - Vincenzo Colangeli
- Unit of Infectious Diseases, S. Orsola‐Malpighi Hospital“Alma Mater Studiorum” University of Bologna Bologna Italy
| | - Diletta Testi
- Unit of Infectious Diseases, S. Orsola‐Malpighi Hospital“Alma Mater Studiorum” University of Bologna Bologna Italy
| | - Alberto Amedeo
- Unit of Infectious Diseases, S. Orsola‐Malpighi Hospital“Alma Mater Studiorum” University of Bologna Bologna Italy
| | - Maria Carla Re
- Unit of Microbiology, S. Orsola‐Malpighi Hospital“Alma Mater Studiorum” University of Bologna Bologna Italy
| | - Isabella Bon
- Unit of Microbiology, S. Orsola‐Malpighi Hospital“Alma Mater Studiorum” University of Bologna Bologna Italy
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Long-Acting Rilpivirine (RPV) Preexposure Prophylaxis Does Not Inhibit Vaginal Transmission of RPV-Resistant HIV-1 or Select for High-Frequency Drug Resistance in Humanized Mice. J Virol 2020; 94:JVI.01912-19. [PMID: 31969438 PMCID: PMC7108851 DOI: 10.1128/jvi.01912-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 01/12/2020] [Indexed: 11/20/2022] Open
Abstract
The antiretroviral drug rilpivirine was developed into a long-acting formulation (RPV LA) to improve adherence for preexposure prophylaxis (PrEP) to prevent HIV-1 transmission. A concern is that RPV LA will not inhibit transmission of drug-resistant HIV-1 and may select for drug-resistant virus. In female humanized mice, we found that RPV LA inhibited vaginal transmission of WT or 3-fold RPV-resistant HIV-1 but not virus with 30-fold RPV resistance. In animals that became infected despite RPV LA PrEP, WT HIV-1 dissemination was delayed until genital and plasma RPV concentrations waned. RPV resistance was detected at similar low frequencies in untreated and PrEP-treated mice that became infected. These results indicate the importance of maintaining RPV at a sustained threshold after virus exposure to prevent dissemination of HIV-1 after vaginal infection and low-frequency resistance mutations conferred low-level resistance, suggesting that RPV resistance is difficult to develop after HIV-1 infection during RPV LA PrEP. As a long-acting formulation of the nonnucleoside reverse transcriptase inhibitor rilpivirine (RPV LA) has been proposed for use as preexposure prophylaxis (PrEP) and the prevalence of transmitted RPV-resistant viruses can be relatively high, we evaluated the efficacy of RPV LA to inhibit vaginal transmission of RPV-resistant HIV-1 in humanized mice. Vaginal challenges of wild-type (WT), Y181C, and Y181V HIV-1 were performed in mice left untreated or after RPV PrEP. Plasma viremia was measured for 7 to 10 weeks, and single-genome sequencing was performed on plasma HIV-1 RNA in mice infected during PrEP. RPV LA significantly prevented vaginal transmission of WT HIV-1 and Y181C HIV-1, which is 3-fold resistant to RPV. However, it did not prevent transmission of Y181V HIV-1, which has 30-fold RPV resistance in the viruses used for this study. RPV LA did delay WT HIV-1 dissemination in infected animals until genital and plasma RPV concentrations waned. Animals that became infected despite RPV LA PrEP did not acquire new RPV-resistant mutations above frequencies in untreated mice or untreated people living with HIV-1, and the mutations detected conferred low-level resistance. These data suggest that high, sustained concentrations of RPV were required to inhibit vaginal transmission of HIV-1 with little or no resistance to RPV but could not inhibit virus with high resistance. HIV-1 did not develop high-level or high-frequency RPV resistance in the majority of mice infected after RPV LA treatment. However, the impact of low-frequency RPV resistance on virologic outcome during subsequent antiretroviral therapy still is unclear. IMPORTANCE The antiretroviral drug rilpivirine was developed into a long-acting formulation (RPV LA) to improve adherence for preexposure prophylaxis (PrEP) to prevent HIV-1 transmission. A concern is that RPV LA will not inhibit transmission of drug-resistant HIV-1 and may select for drug-resistant virus. In female humanized mice, we found that RPV LA inhibited vaginal transmission of WT or 3-fold RPV-resistant HIV-1 but not virus with 30-fold RPV resistance. In animals that became infected despite RPV LA PrEP, WT HIV-1 dissemination was delayed until genital and plasma RPV concentrations waned. RPV resistance was detected at similar low frequencies in untreated and PrEP-treated mice that became infected. These results indicate the importance of maintaining RPV at a sustained threshold after virus exposure to prevent dissemination of HIV-1 after vaginal infection and low-frequency resistance mutations conferred low-level resistance, suggesting that RPV resistance is difficult to develop after HIV-1 infection during RPV LA PrEP.
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Acharya A, Tagny CT, Mbanya D, Fonsah JY, Nchindap E, Kenmogne L, Jihyun M, Njamnshi AK, Kanmogne GD. Variability in HIV-1 Integrase Gene and 3'-Polypurine Tract Sequences in Cameroon Clinical Isolates, and Implications for Integrase Inhibitors Efficacy. Int J Mol Sci 2020; 21:ijms21051553. [PMID: 32106437 PMCID: PMC7084836 DOI: 10.3390/ijms21051553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 01/06/2023] Open
Abstract
Integrase strand-transfer inhibitors (INSTIs) are now included in preferred first-line antiretroviral therapy (ART) for HIV-infected adults. Studies of Western clade-B HIV-1 show increased resistance to INSTIs following mutations in integrase and nef 3′polypurine tract (3′-PPT). With anticipated shifts in Africa (where 25.6-million HIV-infected people resides) to INSTIs-based ART, it is critical to monitor patients in African countries for resistance-associated mutations (RAMs) affecting INSTIs efficacy. We analyzed HIV-1 integrase and 3′-PPT sequences in 345 clinical samples from INSTIs-naïve HIV-infected Cameroonians for polymorphisms and RAMs that affect INSTIs. Phylogeny showed high genetic diversity, with the predominance of HIV-1 CRF02_AG. Major INSTIs RAMs T66A and N155K were found in two (0.6%) samples. Integrase polymorphic and accessory RAMs found included T97A, E157Q, A128T, M50I, S119R, L74M, L74I, S230N, and E138D (0.3′23.5% of samples). Ten (3.2%) samples had both I72V+L74M, L74M+T97A, or I72V+T97A mutations; thirty-one (9.8%) had 3′-PPT mutations. The low frequency of major INSTIs RAMs shows that INSTIs-based ART can be successfully used in Cameroon. Several samples had ≥1 INSTIs accessory RAMs known to reduce INSTIs efficacy; thus, INSTIs-based ART would require genetic surveillance. The 3′-PPT mutations could also affect INSTIs. For patients failing INSTIs-based ART with no INSTIs RAMs, monitoring 3′-PPT sequences could reveal treatment failure etiology.
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Affiliation(s)
- Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Claude T. Tagny
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Julius Y. Fonsah
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Department of Neurology, Yaoundé Central Hospital/Brain Research Africa Initiative (BRAIN), P.O. Box 25625 Yaoundé, Cameroon
| | - Emilienne Nchindap
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Léopoldine Kenmogne
- Yaoundé University Teaching Hospital, Department of Haematology, P.O. Box 5739 Yaoundé, Cameroon; (E.N.); (L.K.)
| | - Ma Jihyun
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Alfred K. Njamnshi
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, P.O. Box 1364 Yaoundé, Cameroon (D.M.); (J.Y.F.); (A.K.N.)
- Department of Neurology, Yaoundé Central Hospital/Brain Research Africa Initiative (BRAIN), P.O. Box 25625 Yaoundé, Cameroon
| | - Georgette D. Kanmogne
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Correspondence: ; Tel.: +402-559-4084
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Gibson KM, Jair K, Castel AD, Bendall ML, Wilbourn B, Jordan JA, Crandall KA, Pérez-Losada M. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Sci Rep 2020; 10:1989. [PMID: 32029767 PMCID: PMC7004982 DOI: 10.1038/s41598-020-58410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/31/2019] [Indexed: 11/08/2022] Open
Abstract
Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40-49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9-33.8% of the participants into clusters. HIV-TRACE grouped 2.9-12.8% of participants when using consensus sequences and 9.0-64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.
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Grants
- P30 AI117970 NIAID NIH HHS
- U01 AI069503 NIAID NIH HHS
- UM1 AI069503 NIAID NIH HHS
- This study was supported by the DC Cohort Study (U01 AI69503-03S2), a supplement from the Women’s Interagency Study for HIV-1 (410722_GR410708), a DC D-CFAR pilot award, and a 2015 HIV-1 Phylodynamics Supplement award from the District of Columbia for AIDS Research, an NIH funded program (AI117970), which is supported by the following NIH Co-Funding and Participating Institutes and Centers: NIAID, NCI, NICHD, NHLBI, NIDA, NIMH, NIA, FIC, NIGMS, NIDDK and OAR. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
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Affiliation(s)
- Keylie M Gibson
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA.
| | - Kamwing Jair
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Amanda D Castel
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Matthew L Bendall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Brittany Wilbourn
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Jeanne A Jordan
- Department of Epidemiology, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Keith A Crandall
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
| | - Marcos Pérez-Losada
- Computational Biology Institute, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- Department of Biostatistics and Bioinformatics, The Milken Institute School of Public Health, The George Washington University, Washington, DC, 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
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29
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Günthard HF, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Jacobsen DM, Richman DD. Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel. Clin Infect Dis 2020; 68:177-187. [PMID: 30052811 PMCID: PMC6321850 DOI: 10.1093/cid/ciy463] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/28/2018] [Indexed: 12/16/2022] Open
Abstract
Background Contemporary antiretroviral therapies (ART) and management strategies have diminished both human immunodeficiency virus (HIV) treatment failure and the acquired resistance to drugs in resource-rich regions, but transmission of drug-resistant viruses has not similarly decreased. In low- and middle-income regions, ART roll-out has improved outcomes, but has resulted in increasing acquired and transmitted resistances. Our objective was to review resistance to ART drugs and methods to detect it, and to provide updated recommendations for testing and monitoring for drug resistance in HIV-infected individuals. Methods A volunteer panel of experts appointed by the International Antiviral (formerly AIDS) Society–USA reviewed relevant peer-reviewed data that were published or presented at scientific conferences. Recommendations were rated according to the strength of the recommendation and quality of the evidence, and reached by full panel consensus. Results Resistance testing remains a cornerstone of ART. It is recommended in newly-diagnosed individuals and in patients in whom ART has failed. Testing for transmitted integrase strand-transfer inhibitor resistance is currently not recommended, but this may change as more resistance emerges with widespread use. Sanger-based and next-generation sequencing approaches are each suited for genotypic testing. Testing for minority variants harboring drug resistance may only be considered if treatments depend on a first-generation nonnucleoside analogue reverse transcriptase inhibitor. Different HIV-1 subtypes do not need special considerations regarding resistance testing. Conclusions Testing for HIV drug resistance in drug-naive individuals and in patients in whom antiretroviral drugs are failing, and the appreciation of the role of testing, are crucial to the prevention and management of failure of ART.
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Affiliation(s)
- Huldrych F Günthard
- University Hospital Zürich and Institute of Medical Virology, University of Zurich, Switzerland
| | - Vincent Calvez
- Pierre et Marie Curie University and Pitié-Salpêtriere Hospital, Paris, France
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,Africa Health Research Institute, KwaZulu Natal, South Africa
| | | | | | | | | | - Douglas D Richman
- Veterans Affairs San Diego Healthcare System and University of California San Diego
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30
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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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31
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Jewsbury S, Ward C. A case of M184V mutant human immunodeficiency virus in a patient using daily pre-exposure prophylaxis. Int J STD AIDS 2019; 31:85-87. [PMID: 31801029 DOI: 10.1177/0956462419879620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study presents a case report of a 31-year-old gay man who acquired human immunodeficiency virus while using daily emtricitabine (FTC)/tenofovir disoproxil fumarate (TDF) pre-exposure prophylaxis (PrEP). He had an M184V nucleoside reverse-transcriptase inhibitor mutation at diagnosis. Either he acquired a pre-existing M184V mutation or he acquired a wild-type virus but then suboptimal use of FTC/TDF led to the development of resistance. For PrEP to be safely managed and seroconvertors to be identified quickly, PrEP should be commissioned by the NHS and managed within sexual health clinics. Notwithstanding the current provision of PrEP, those accessing it must be reminded about the importance of regular testing and optimal adherence.
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Affiliation(s)
- Sally Jewsbury
- The Northern Contraception Sexual Health and HIV Service, Central Manchester NHS Foundation Trust, Manchester, UK
| | - Chris Ward
- The Northern Contraception Sexual Health and HIV Service, Central Manchester NHS Foundation Trust, Manchester, UK
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32
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Marjani A, Bokharaei-Salim F, Jahanbakhshi F, Monavari SH, Esghaei M, Kalantari S, Kiani SJ, Ataei-Pirkooh A, Fakhim A, Keyvani H. HIV-1 integrase drug-resistance mutations in Iranian treatment-experienced HIV-1-infected patients. Arch Virol 2019; 165:115-125. [PMID: 31741096 DOI: 10.1007/s00705-019-04463-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/09/2019] [Indexed: 11/29/2022]
Abstract
The latest class of antiretrovirals (ARVs), including integrase strand transfer inhibitors (INSTIs), has been demonstrated to be effective for antiretroviral therapy (ART). Despite all the distinguishing characteristics of these drugs, including a high genetic barrier to resistance and lower toxicity than other ARVs, unfortunately, INSTI drug resistance mutations (DRMs) have occasionally been observed. The aim of this study was to investigate the presence of DRMs associated with INSTIs among treatment-experienced HIV-1-infected patients. From June 2012 to December 2018, a total of 655 treatment-experienced HIV-1-infected patients enrolled in this cross-sectional survey. Following amplification and sequencing of the HIV-1 integrase region of the pol gene, DRM and phylogenetic analysis were successfully carried out on the plasma samples of patients who had a viral load over 1,000 IU/ml after at least 6 months of ART. Out of the 655 patients evaluated, 62 (9.5%) had a viral load higher than 1,000 IU/ml after at least 6 months of ART. Phylogenetic analysis showed that all of the 62 HIV-1 patients experiencing treatment failure were infected with CRF35_AD, and one of these patients (1.6%) was infected with HIV-1 variants with DRMs. The DRMs that were identified belonged to the INSTI class, including E138K, G140A, S147G, and Q148R. This survey shows that DRMs belonging to the INSTI class were detected in an Iranian HIV patient who has experienced treatment failure. Therefore, regarding the presence of DRMs to INSTIs in ART-experienced patients, it seems better to perform drug resistance mutation testing in HIV patients experiencing treatment failure before changing the ART regimen and prescribing this class of medication.
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Affiliation(s)
- Arezoo Marjani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | | | | | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Kalantari
- Departments of Infectious Diseases and Tropical Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Jalal Kiani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Angila Ataei-Pirkooh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Atousa Fakhim
- Department of Architectural Engineering, Faculty of Engineering, Islamic Azad University, South Tehran Branch, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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33
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Gatanaga H, Oka S. Comment on: Tenofovir DF/emtricitabine/rilpivirine as HIV post-exposure prophylaxis: results from a multicentre prospective study. J Antimicrob Chemother 2019; 74:3402-3403. [DOI: 10.1093/jac/dkz301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hiroyuki Gatanaga
- AIDS Clinical Centre, National Centre for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Centre, National Centre for Global Health and Medicine, Tokyo, Japan
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Abstract
Approximately 20% of people with HIV in the United States prescribed antiretroviral therapy are not virally suppressed. Thus, optimal management of virologic failure has a critical role in the ability to improve viral suppression rates to improve long-term health outcomes for those infected and to achieve epidemic control. This article discusses the causes of virologic failure, the use of resistance testing to guide management after failure, interpretation and relevance of HIV drug resistance patterns, considerations for selection of second-line and salvage therapies, and management of virologic failure in special populations.
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Affiliation(s)
- Suzanne M McCluskey
- Division of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, GRJ5, Boston, MA 02114, USA.
| | - Mark J Siedner
- Division of Infectious Diseases, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, GRJ5, Boston, MA 02114, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Department of Global Health, Emory University School of Medicine, Rollins School of Public Health, Health Sciences Research Building, 1760 Haygood Dr NE, Room W325, Atlanta, GA 30322, USA
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35
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Weng YW, Chen IT, Tsai HC, Wu KS, Tseng YT, Sy CL, Chen JK, Lee SSJ, Chen YS. Trend of HIV transmitted drug resistance before and after implementation of HAART regimen restriction in the treatment of HIV-1 infected patients in southern Taiwan. BMC Infect Dis 2019; 19:741. [PMID: 31443633 PMCID: PMC6708193 DOI: 10.1186/s12879-019-4389-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
Background The use of fixed combination antiretroviral therapy with a low genetic barrier for the treatment of patients infected with human immunodeficiency virus (HIV) may affect the local HIV transmitted drug resistance (TDR) pattern. The present study aimed to investigate changes in the prevalence of HIV TDR following the implementation of a fixed regimen of HIV treatment in Taiwan in 2012. Methods TDR was measured in antiretroviral treatment-naïve HIV-1-infected individuals who participated in voluntary counseling and testing between 2007 and 2015 in southern Taiwan. Antiretroviral resistance mutations were interpreted using the HIVdb program from the Stanford University HIV Drug Resistance Database. Results Sequences were obtained from 377 consecutive individuals between 2007 and 2015. The overall prevalence rates of TDR HIV among the study population from 2007 to 2011 and 2012–2015 were 10.6 and 7.9%, respectively. Among the detected mutations, K103 N and V179D + K103R were more frequently observed after 2012. Four HIV-infected patients with K103 N variants were detected after 2012, and 4 of the 5 patients with V179D + K103R variants were found after 2012. No significant differences were observed in the TDRs among nucleoside reverse transcriptase inhibitors (NRTIs), non-NRTIs (NNRTIs), protease inhibitors, multiple drug resistance, and any drug resistance between period 1 (2007–2011) and period 2 (2012–2015). Conclusions A fixed treatment regimen with zidovudine/lamivudine + efavirenz or nevirapine as first-line therapy for treatment-naïve patients infected with HIV did not significantly increase the TDR during the 4-year follow-up period. Due to the increase in NNRTI resistance associated with mutations after 2012, a longer follow-up period and larger sample size are needed in future studies.
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Affiliation(s)
- Ya-Wei Weng
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - I-Tzu Chen
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hung-Chin Tsai
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan. .,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan. .,Department of Parasitology, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan.
| | - Kuan-Sheng Wu
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Ting Tseng
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Cheng-Len Sy
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Jui-Kuang Chen
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Susan Shin-Jung Lee
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yao-Shen Chen
- Division of Infectious Diseases, Department of Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
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36
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Soodla P, Huik K, Pauskar M, Cuypers L, Van Laethem K, Rajasaar H, Kallas E, Lepa H, Velts-Lindh A, Jõgeda EL, Lutsar I, Avi R. Stable level of HIV transmitted drug resistance in Estonia despite significant scale-up of antiretroviral therapy. INFECTION GENETICS AND EVOLUTION 2019; 75:103901. [PMID: 31146045 DOI: 10.1016/j.meegid.2019.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 03/31/2019] [Accepted: 05/25/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND Due to the widespread use of non-nucleoside reverse transcriptase inhibitors (NNRTI) as part of first-line therapies to curb the human immunodeficiency virus (HIV) epidemic in Eastern-European countries, transmitted drug resistance (TDR) is of serious concern in this region. Therefore, TDR and its associated risk factors were investigated among newly diagnosed HIV-1 subjects in Estonia. METHODS This nationwide observational study included all newly diagnosed HIV-1 subjects from January 1 until December 31, 2013. Demographic and clinical data were collected using the national surveillance system and the Estonian HIV-positive patient database (E-HIV). Starting from RNA, the HIV-1 protease (PR) and reverse transcriptase (RT) region was sequenced and surveillance drug resistance mutations (SDRM) were determined. Sequences from previous studies in Estonia and from public databases were included to study epidemic trends and to determine TDR clusters by phylogenetic analysis. RESULTS Out of 325 newly diagnosed HIV-1 infections, 224 were successfully sequenced (68%). As in previous studies from Estonia, the circulating recombinant form CRF06_cpx was the most prevalent HIV subtype (164/224, 74%). Fifteen strains displayed SDRM, giving a TDR rate of 6.7% (95% CI 3.9; 11.0). The most common SDRMs were associated with NNRTI (10/15, 4.5%), followed by PI (3/15, 1.3%) and NRTI (2/15, 0.9%). K103 N (8/15, 53%) was the most common SDRM. The level of TDR and mutational patterns were comparable to previous years. Twenty-six transmission clusters containing Estonian sequences were observed, of which 23/26 belonged to CRF06_cpx and 2/26 displayed evidence of TDR. The only risk factor associated with the presence of TDR was imprisonment (OR 5.187, CI 1.139-25.565, p = 0.034). CONCLUSIONS TDR remained stable at a moderate level in Estonia, K103N is the main SDRM with only one transmission-pair detected. We suggest screening for TDR at the time of diagnosis or prior to antiretroviral treatment initiation to tailor first-line regimens accordingly. SUMMARY The third consecutive transmitted drug resistance (TDR) study demonstrated a stable TDR in Estonia. TDR reached 6.7% (moderate level) in 2013, with imprisonment being the only associated risk factor. Few drug resistance-associated transmission clusters were identified.
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Affiliation(s)
- Pilleriin Soodla
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia.
| | - Kristi Huik
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Merit Pauskar
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Lize Cuypers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Kristel Van Laethem
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Heli Rajasaar
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Eveli Kallas
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Helen Lepa
- West-Tallinn Central Hospital Laboratory, Tallinn, Estonia
| | | | - Ene-Ly Jõgeda
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Irja Lutsar
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Radko Avi
- Faculty of Medicine, Department of Microbiology, University of Tartu, Tartu, Estonia
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Günthard HF, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Jacobsen DM, Richman DD. Reply to Ambrosioni et al. Clin Infect Dis 2019; 68:1977-1978. [PMID: 30520997 DOI: 10.1093/cid/ciy1022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/03/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Huldrych F Günthard
- University Hospital Zürich and Institute of Medical Virology, University of Zurich, Switzerland
| | - Vincent Calvez
- Pierre et Marie Curie University and Pitié-Salpêtrieŕe Hospital, Paris, France
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu Natal, South Africa.,University College London, United Kingdom
| | | | | | | | - Douglas D Richman
- Veterans Affairs San Diego Healthcare System.,University of California San Diego
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Soria J, Mugruza R, Levine M, León SR, Arévalo J, Ticona E, Beck IA, Frenkel LM. Pretreatment HIV Drug Resistance and Virologic Outcomes to First-Line Antiretroviral Therapy in Peru. AIDS Res Hum Retroviruses 2019; 35:150-154. [PMID: 30560685 DOI: 10.1089/aid.2018.0239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Access to nucleoside reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTI) first-line antiretroviral therapy (ART) for HIV has been increasing in Peru since a national ART program was initiated in 2004. Between 2007 and 2009, we found a 1% prevalence of pre-ART HIV drug resistance (PDR) among antiretroviral (ARV)-naive Peruvians. Given that PDR has been associated with virologic failure (VF) of ART, in 2014-2015 we enrolled a follow-up cohort at the same institution to determine whether the rate of transmitted resistance had increased and compared virologic outcomes of those with and without PDR. Blood specimens from ARV-naive individuals were assessed for PDR to NNRTI-based ART by an oligonucleotide ligation assay (OLA) sensitive to 2% mutant within an individual's HIV quasispecies at reverse transcriptase codons M41L, K65R, K103N, Y181C, M184V, and G190A, and by Sanger consensus sequencing (CS). Rates of VF (plasma HIV RNA >200 copies/mL) were compared between those with and without PDR. Among 122 ARV-naive adults, PDR was detected by OLA in 17 (13.9%) adults. Compared with the 2007-2009 cohort, the proportion with PDR at OLA codons was significantly increased (p < .001). A total of 11 of 19 OLA mutations conferring high-level drug resistance were also detected by CS, and 8 additional participants had mutations encoding low-level resistance detected by CS for a total of 25 participants (20.5%). VF at month 6 of NNRTI-ART appeared greater in participants with versus without PDR [4/18 (22.2%) vs. 3/71 (4.2%); p = .03]. An increasing prevalence of PDR was detected among ARV-naive Peruvians. Studies are needed to determine risks of specific PDR mutations.
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Affiliation(s)
- Jaime Soria
- Infectious and Tropical Diseases Department. Hospital Nacional Dos de Mayo, Lima, Peru
- Northern Pacific Global Health Research Fellows Training Consortium, University of Washington, Seattle, Washington
| | - Raquel Mugruza
- Infectious and Tropical Diseases Department. Hospital Nacional Dos de Mayo, Lima, Peru
| | - Molly Levine
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, Washington
| | | | - Jorge Arévalo
- Infectious and Tropical Diseases Department. Hospital Nacional Dos de Mayo, Lima, Peru
| | - Eduardo Ticona
- Infectious and Tropical Diseases Department. Hospital Nacional Dos de Mayo, Lima, Peru
- Faculty of Medicine. Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ingrid A. Beck
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, Washington
| | - Lisa M. Frenkel
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, Washington
- Department of Pediatric, University of Washington, Seattle, Washington
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
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The effect of primary drug resistance on CD4+ cell decline and the viral load set-point in HIV-positive individuals before the start of antiretroviral therapy. AIDS 2019; 33:315-326. [PMID: 30325769 DOI: 10.1097/qad.0000000000002046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To evaluate the effect of primary resistance and selected polymorphic amino-acid substitutions in HIV reverse transcriptase and protease on the CD4 cell count and viral load set point before the start of antiretroviral treatment. DESIGN Prospective cohort study. METHODS A total of 6180 individuals with a resistance test prior to starting antiretroviral treatment accessing care in HIV clinics across Europe who had at least one viral load and one CD4+ test available were included in the analysis. The impact of amino-acid substitutions variants on viral load and CD4+ trends was investigated using linear mixed models. Clusters of mutations were studied using principal component analysis. RESULTS Overall, the detection of any primary resistance was not associated with either the speed of CD4+ cell decline or the viral load set point. However, transmitted nucleoside reverse transcriptase inhibitor and protease inhibitor resistance appeared to be weakly associated with lower viral load set points, as were the polymorphic G16E or Q92K protease mutations. There was some evidence suggesting that these effects varied according to HIV subtype, with the effects of transmitted nucleoside reverse transcriptase inhibitor and protease resistance being particularly marked among individuals with a subtype B virus. A cluster of five polymorphic protease substitutions at position 20, 13, 36, 69 and 89 was associated with less steep CD4+ cell declines and lower viral load set points. CONCLUSION Although we found little evidence for an association between primary resistance and CD4+ speed of decline and viral load set point, the potential role of polymorphic protease (alone or in clusters) and their interplay with HIV subtype needs to be further evaluated.
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Resistance Testing for Integrase Strand Transfer Inhibitors in Naive, Human Immunodeficiency Virus–infected Individuals. Clin Infect Dis 2018; 68:1976-1977. [DOI: 10.1093/cid/ciy1019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
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Silver N, Paynter M, McAllister G, Atchley M, Sayir C, Short J, Winner D, Alouani DJ, Sharkey FH, Bergefall K, Templeton K, Carrington D, Quiñones-Mateu ME. Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Res Ther 2018; 15:18. [PMID: 30409215 PMCID: PMC6223033 DOI: 10.1186/s12981-018-0206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals. METHODS We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals. RESULTS Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4+ T cell counts in the NHS Lothian patients. CONCLUSIONS This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
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Increasing proportions of HIV-1 non-B subtypes and of NNRTI resistance between 2013 and 2016 in Germany: Results from the national molecular surveillance of new HIV-diagnoses. PLoS One 2018; 13:e0206234. [PMID: 30408827 PMCID: PMC6224275 DOI: 10.1371/journal.pone.0206234] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/09/2018] [Indexed: 12/12/2022] Open
Abstract
Background Molecular surveillance of newly diagnosed HIV-infections is important for tracking trends in circulating HIV-variants, including those with transmitted drug resistances (TDR) to sustain ART efficacy. Methods Dried serum spots (DSS) are received together with the statutory notification of a new diagnosis. 'Recent infections' (<155 days) classified by a 'recent infection test algorithm' (BED-CEIA and clinical data) are genotyped in HIV-protease (PR), reverse transcriptase (RT) and integrase (INT) to determine the HIV-1 subtype, to calculate prevalence and trends of TDR, to predict baseline susceptibility and to identify potential transmission clusters for resistant variants. Results Between January 2013 and December 2016, 1,885 recent infections were analysed regarding the PR/RT genomic region, with 43.5% of these also being subjected to the analysis of INT. The proportion of HIV-1 non-B viruses (31.3%; 591/1,885) increased from 21.6% to 36.0%, particularly the subtypes A (5.0% to 8.3%) and C (3.2% to 7.7%; all ptrends < 0.01). The subtype A increment is mainly due to transmissions within men who have sex with men (MSM) while subtype C transmissions are associated with heterosexuals and people who inject drugs. The prevalence of TDR was stable at 11.0% (208/1,885) over the study period. Resistances to nucleotide RT inhibitors (NRTI) and PR inhibitors (PI) were 4.5% and 3.2%, respectively, without identifiable trends. In contrast, resistances to non-NRTIs (NNRTI, 4.7%) doubled between 2014 and 2016 from 3.2% to 6.4% (ptrend = 0.02) mainly due to the K103N mutation (from 1.7% to 4.1%; ptrend = 0.03) predominantly detected in recently infected German MSM not linked to transmission clusters. Transmitted INSTI mutations were present in only one case (T66I) and resistance to dolutegravir was not identified at all. Reduced susceptibility to recommended first-line therapies was low with 1.0% for PIs, 1.3% for NRTIs and 0.7% for INSTIs, but high for the NNRTIs efavirence (4.9%) and rilpivirine (6.0%) due to the K103N mutation and the polymorphic mutation E138A. These trends in therapy-naïve individuals impact current first-line regimens and require awareness and vigilant surveillance.
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Petersen A, Cowan SA, Nielsen J, Fischer TK, Fonager J. Characterisation of HIV-1 transmission clusters and drug-resistant mutations in Denmark, 2004 to 2016. Euro Surveill 2018; 23:1700633. [PMID: 30401010 PMCID: PMC6337072 DOI: 10.2807/1560-7917.es.2018.23.44.1700633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This study describes the prevalence of human immunodeficiency virus (HIV) drug resistance mutations among 1,815 patients in Denmark from 2004 to 2016 and characterises transmission clusters. POL sequences were analysed for subtype, drug resistance mutations and phylogenetic relationship. The prevalence of surveillance drug resistance mutations (SDRM) was 6.7%, while the prevalence of drug resistance mutations (DRM) with a clinical impact was 12.3%. We identified 197 transmission clusters with 706 patients. Patients 40 years or older were less likely to be members of a transmission cluster and patients in transmission clusters were less likely to be infected abroad. The proportion of late presenters (LP) was lower in active compared with inactive clusters. Large active clusters consisted of more men who have sex with men (MSM), had members more frequently infected in Denmark and contained a significantly lower proportion of LP and significantly fewer patients with DRM than small active clusters. Subtyping demonstrated that the Danish HIV epidemic is gradually becoming more composed of non-B subtypes/circulating recombinant forms. This study shows that active HIV-1 transmission has become increasingly MSM-dominated and that the recent increase in SDRM and DRM prevalence is not associated with more sustained transmission within identified transmission networks or clusters.
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Affiliation(s)
- Andreas Petersen
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark,European Public Health Microbiology (EUPHEM) training programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Susan A Cowan
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Nielsen
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Thea K Fischer
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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Prevalence of Transmitted HIV drug resistance in antiretroviral treatment naïve newly diagnosed individuals in China. Sci Rep 2018; 8:12273. [PMID: 30115986 PMCID: PMC6095875 DOI: 10.1038/s41598-018-29202-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/24/2018] [Indexed: 12/17/2022] Open
Abstract
To investigate the prevalence and temporal trend of transmitted drug resistance (TDR), a nationwide cross-sectional survey was conducted among 5627 ART naïve newly diagnosed HIV-infected individuals in 2015 in China. Totally 4704 partial pol sequences were obtained. Among them, the most common HIV-1 circulating recombinant form (CRF) or subtype was CRF01_AE (39.0%), followed by CRF07_BC (35.6%), CRF08_BC (8.9%), and subtype B (5.5%). TDR mutations were found in 3.6% of the cases, with 1.1% harboring TDR to protease inhibitors (PIs), 1.3% having TDR to nucleoside reverse transcriptase inhibitors (NRTIs), and 1.6% to non-nucleoside reverse transcriptase inhibitors (NNRTIs). No significant difference was found in the prevalence of TDR, as compared with the results of another nationwide survey performed among ART naïve HIV-infected people in between 2004 and 2005, except in the 16-25 year-old group. In addition, four drug-resistant transmission clusters were identified in phylogenetic trees, accounting for 6.2% (9/145) of the individuals with TDR. Although the rate of TDR remained relatively low in the past 10 years in China, surveillance is still needed to monitor the trend of TDR and to optimize the first-line regimens.
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Saag MS, Benson CA, Gandhi RT, Hoy JF, Landovitz RJ, Mugavero MJ, Sax PE, Smith DM, Thompson MA, Buchbinder SP, Del Rio C, Eron JJ, Fätkenheuer G, Günthard HF, Molina JM, Jacobsen DM, Volberding PA. Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2018 Recommendations of the International Antiviral Society-USA Panel. JAMA 2018; 320:379-396. [PMID: 30043070 PMCID: PMC6415748 DOI: 10.1001/jama.2018.8431] [Citation(s) in RCA: 440] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
IMPORTANCE Antiretroviral therapy (ART) is the cornerstone of prevention and management of HIV infection. OBJECTIVE To evaluate new data and treatments and incorporate this information into updated recommendations for initiating therapy, monitoring individuals starting therapy, changing regimens, and preventing HIV infection for individuals at risk. EVIDENCE REVIEW New evidence collected since the International Antiviral Society-USA 2016 recommendations via monthly PubMed and EMBASE literature searches up to April 2018; data presented at peer-reviewed scientific conferences. A volunteer panel of experts in HIV research and patient care considered these data and updated previous recommendations. FINDINGS ART is recommended for virtually all HIV-infected individuals, as soon as possible after HIV diagnosis. Immediate initiation (eg, rapid start), if clinically appropriate, requires adequate staffing, specialized services, and careful selection of medical therapy. An integrase strand transfer inhibitor (InSTI) plus 2 nucleoside reverse transcriptase inhibitors (NRTIs) is generally recommended for initial therapy, with unique patient circumstances (eg, concomitant diseases and conditions, potential for pregnancy, cost) guiding the treatment choice. CD4 cell count, HIV RNA level, genotype, and other laboratory tests for general health and co-infections are recommended at specified points before and during ART. If a regimen switch is indicated, treatment history, tolerability, adherence, and drug resistance history should first be assessed; 2 or 3 active drugs are recommended for a new regimen. HIV testing is recommended at least once for anyone who has ever been sexually active and more often for individuals at ongoing risk for infection. Preexposure prophylaxis with tenofovir disoproxil fumarate/emtricitabine and appropriate monitoring is recommended for individuals at risk for HIV. CONCLUSIONS AND RELEVANCE Advances in HIV prevention and treatment with antiretroviral drugs continue to improve clinical management and outcomes for individuals at risk for and living with HIV.
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Affiliation(s)
| | | | - Rajesh T Gandhi
- Massachusetts General Hospital and Harvard Medical School, Boston
| | - Jennifer F Hoy
- The Alfred Hospital and Monash University, Melbourne, Australia
| | | | | | - Paul E Sax
- Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | - Susan P Buchbinder
- San Francisco Department of Public Health and University of California San Francisco
| | - Carlos Del Rio
- Emory University Rollins School of Public Health and School of Medicine, Atlanta, Georgia
| | - Joseph J Eron
- University of North Carolina at Chapel Hill School of Medicine
| | - Gerd Fätkenheuer
- University Hospital of Cologne, Department I of Internal Medicine, Cologne, Germany, and German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Huldrych F Günthard
- University Hospital Zurich and Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Levintow SN, Okeke NL, Hué S, Mkumba L, Virkud A, Napravnik S, Sebastian J, Miller WC, Eron JJ, Dennis AM. Prevalence and Transmission Dynamics of HIV-1 Transmitted Drug Resistance in a Southeastern Cohort. Open Forum Infect Dis 2018; 5:ofy178. [PMID: 30151407 PMCID: PMC6101542 DOI: 10.1093/ofid/ofy178] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/18/2018] [Indexed: 12/26/2022] Open
Abstract
Background Transmitted drug resistance (TDR) compromises clinical management and outcomes. Transmitted drug resistance surveillance and identification of growing transmission clusters are needed in the Southeast, the epicenter of the US HIV epidemic. Our study investigated prevalence and transmission dynamics in North Carolina. Methods We analyzed surveillance drug resistance mutations (SDRMs) using partial pol sequences from patients presenting to 2 large HIV outpatient clinics from 1997 to 2014. Transmitted drug resistance prevalence was defined as ≥1 SDRMs among antiretroviral therapy (ART)–naïve patients. Binomial regression was used to characterize prevalence by calendar year, drug class, and demographic and clinical factors. We assessed the transmission networks of patients with TDR with maximum likelihood trees and Bayesian methods including background pol sequences (n = 15 246). Results Among 1658 patients with pretherapy resistance testing, ≥1 SDRMs was identified in 199 patients, with an aggregate TDR prevalence of 12% (95% confidence interval, 10% to 14%) increasing over time (P = .02). Resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs; 8%) was common, followed by nucleoside reverse transcriptase inhibitors (4%) and protease inhibitors (2%). Factors associated with TDR were being a man reporting sex with men, white race, young age, higher CD4 cell count, and being a member of a transmission cluster. Transmitted drug resistance was identified in 106 clusters ranging from 2 to 26 members. Cluster resistance was primarily NNRTI and dominated by ART-naïve patients or those with unknown ART initiation. Conclusions Moderate TDR prevalence persists in North Carolina, predominantly driven by NNRTI resistance. Most TDR cases were identified in transmission clusters, signifying multiple local transmission networks and TDR circulation among ART-naïve persons. Transmitted drug resistance surveillance can detect transmission networks and identify patients for enhanced services to promote early treatment.
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Affiliation(s)
- Sara N Levintow
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Nwora Lance Okeke
- Division of Infectious Diseases, Duke University, Durham, North Carolina
| | - Stephane Hué
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Laura Mkumba
- Division of Infectious Diseases, Duke University, Durham, North Carolina
| | - Arti Virkud
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Sonia Napravnik
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina.,Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Joseph Sebastian
- Campbell University School of Osteopathic Medicine, South Lillington, North Carolina
| | - William C Miller
- Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Joseph J Eron
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina.,Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Ann M Dennis
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
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Fabeni L, Alteri C, Di Carlo D, Orchi N, Carioti L, Bertoli A, Gori C, Forbici F, Continenza F, Maffongelli G, Pinnetti C, Vergori A, Mondi A, Ammassari A, Borghi V, Giuliani M, De Carli G, Pittalis S, Grisetti S, Pennica A, Mastroianni CM, Montella F, Cristaudo A, Mussini C, Girardi E, Andreoni M, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. Dynamics and phylogenetic relationships of HIV-1 transmitted drug resistance according to subtype in Italy over the years 2000-14. J Antimicrob Chemother 2018; 72:2837-2845. [PMID: 29091206 DOI: 10.1093/jac/dkx231] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/09/2017] [Indexed: 11/14/2022] Open
Abstract
Background Transmitted drug-resistance (TDR) remains a critical aspect for the management of HIV-1-infected individuals. Thus, studying the dynamics of TDR is crucial to optimize HIV care. Methods In total, 4323 HIV-1 protease/reverse-transcriptase sequences from drug-naive individuals diagnosed in north and central Italy between 2000 and 2014 were analysed. TDR was evaluated over time. Maximum-likelihood and Bayesian phylogenetic trees with bootstrap and Bayesian-probability supports defined transmission clusters. Results Most individuals were males (80.2%) and Italian (72.1%), with a median (IQR) age of 37 (30-45) years. MSM accounted for 42.2% of cases, followed by heterosexuals (36.4%). Non-B subtype infections accounted for 30.8% of the overall population and increased over time (<2005-14: 19.5%-38.5%, P < 0.0001), particularly among Italians (<2005-14: 6.5%-28.8%, P < 0.0001). TDR prevalence was 8.8% and increased over time in non-B subtypes (<2005-14: 2%-7.1%, P = 0.018). Overall, 467 transmission clusters (involving 1207 individuals; 27.9%) were identified. The prevalence of individuals grouping in transmission clusters increased over time in both B (<2005-14: 12.9%-33.5%, P = 0.001) and non-B subtypes (<2005-14: 18.4%-41.9%, P = 0.006). TDR transmission clusters were 13.3% within the overall cluster observed and dramatically increased in recent years (<2005-14: 14.3%-35.5%, P = 0.005). This recent increase was mainly due to non-B subtype-infected individuals, who were also more frequently involved in large transmission clusters than those infected with a B subtype [median number of individuals in transmission clusters: 7 (IQR 6-19) versus 4 (3-4), P = 0.047]. Conclusions The epidemiology of HIV transmission changed greatly over time; the increasing number of transmission clusters (sometimes with drug resistance) shows that detection and proper treatment of the multi-transmitters is a major target for controlling HIV spread.
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Affiliation(s)
- L Fabeni
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - C Alteri
- University of Rome Tor Vergata, Rome, Italy
| | - D Di Carlo
- University of Rome Tor Vergata, Rome, Italy
| | - N Orchi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - L Carioti
- University of Rome Tor Vergata, Rome, Italy
| | - A Bertoli
- University of Rome Tor Vergata, Rome, Italy
| | - C Gori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Forbici
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - F Continenza
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C Pinnetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Vergori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Mondi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - A Ammassari
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - V Borghi
- Modena University Hospital, Modena, Italy
| | - M Giuliani
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - G De Carli
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Pittalis
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - S Grisetti
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | | | - F Montella
- S. Giovanni Addolorata Hospital, Rome, Italy
| | - A Cristaudo
- San Gallicano Dermatological Institute, IRCCS, Rome, Italy
| | - C Mussini
- Modena University Hospital, Modena, Italy
| | - E Girardi
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | - M Andreoni
- University Hospital Tor Vergata, Rome, Italy
| | - A Antinori
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
| | | | - C F Perno
- National Institute for Infectious Diseases L Spallanzani, IRCCS, Rome, Italy
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Epidemiological surveillance of HIV-1 transmitted drug resistance among newly diagnosed individuals in Shijiazhuang, northern China, 2014-2015. PLoS One 2018; 13:e0198005. [PMID: 29870534 PMCID: PMC5988301 DOI: 10.1371/journal.pone.0198005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/12/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The widespread use of antiretroviral therapy (ART) has led to considerable concerns about the prevalence of transmitted drug resistance (TDR). Sexual contact, particularly men who have sex with men (MSM) was the most prevalent form of HIV transmission in Shijiazhuang. Hence, we conducted an epidemiological surveillance study on TDR among newly diagnosed individuals who infected-HIV through sexual contact in from 2014-2015. METHODS Genotypic resistance mutations were defined using the WHO-2009 surveillance list. Potential impact on antiretroviral drug was predicted according to the Stanford HIV db program version 7.0. The role of transmission clusters in drug resistant strains was evaluated by phylogenetic and network analyses. RESULTS In this study, 589 individuals were recruited and 542 samples were amplified and sequenced successfully. The over prevalence of TDR was 6.1%: 1.8% to nucleoside reverse transcriptase inhibitors (NRTIs), 2.0% to non- NRTIs (NNRTIs) and 2.4% to protease inhibitors (PIs), respectively. We did not find significant differences in the TDR prevalence by demographic and clinical characteristics (p > 0.05). Using network and phylogenetic analysis, almost 60.0% sequences were clustered together. Of these clusters, 2 included at least two individuals carrying the same resistance mutation, accounting for 21.2% (7/33) individuals with TDR. No significant difference was observed in the clustering rate between the individuals with and without TDR. CONCLUSIONS We obtained a moderate level TDR rate in studied region. These findings enhance our understanding of HIV-1 drug resistance prevalence in Shijiazhuang, and may be helpful for the comprehensive prevention and control of HIV-1.
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Koullias Y, Sax PE, Fields NF, Walensky RP, Hyle EP. Should We Be Testing for Baseline Integrase Resistance in Patients Newly Diagnosed With Human Immunodeficiency Virus? Clin Infect Dis 2018; 65:1274-1281. [PMID: 28605418 DOI: 10.1093/cid/cix542] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/07/2017] [Indexed: 12/30/2022] Open
Abstract
Background Current guidelines recommend genotype resistance testing at diagnosis to guide initial selection of antiretroviral therapy (ART). Many standard resistance genotypes exclude testing for resistance to integrase inhibitors ("IR testing"), although this class of drugs is a component of most recommended first-line regimens. Methods We compared the 96-week clinical outcomes and cost-effectiveness of 2 strategies: no IR testing vs IR testing performed at human immunodeficiency virus (HIV) diagnosis. The base case prevalence of transmitted integrase strand transfer inhibitor (INSTI)-resistant (INSTI-R) virus is estimated at 0.1%. With no IR testing, all patients start dolutegravir (DTG)-based ART after genotype; 12-week suppression rates are 90% (INSTI-susceptible [INSTI-S] virus) and 35% (INSTI-R virus). Those not suppressed at 12 weeks undergo IR testing; if diagnosed with INSTI-R virus, they change to ritonavir-boosted darunavir (DRV/r)-based ART. With IR testing, all patients are diagnosed with INSTI-S/INSTI-R virus prior to ART initiation and start DTG- or DRV/r-based regimens, respectively. Costs include IR tests (175 US dollars [USD]) and ART (41100-44900 USD/year). We examined the impact of key parameters in sensitivity analyses. Results IR testing resulted in worse clinical outcomes compared to no IR testing and increased costs by 200 USD/person/year. Prevalence of transmitted INSTI-R virus did not affect the favored strategy. No IR testing remained clinically preferred unless DTG suppression of INSTI-R virus was <20% or 96-week DRV/r suppression was >92%. If quality of life was worse with DRV/r- than DTG-based ART, no IR testing was clinically preferred over an even broader range of parameters. Conclusions In patients with newly diagnosed HIV, IR testing is projected to result in worse outcomes and is not cost-effective. Pretreatment assessment for INSTI resistance should not be recommended in treatment guidelines.
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Affiliation(s)
- Yiannis Koullias
- Department of Medicine, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, Massachusetts
| | - Paul E Sax
- Harvard Medical School, Boston, Massachusetts.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA
| | - Naomi F Fields
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston
| | - Rochelle P Walensky
- Harvard Medical School, Boston, Massachusetts.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
| | - Emily P Hyle
- Harvard Medical School, Boston, Massachusetts.,Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
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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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