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Nduva GM, Otieno F, Kimani J, Sein Y, Arimide DA, Mckinnon LR, Cholette F, Lawrence MK, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Medstrand P, Sanders EJ, Esbjörnsson J, Hassan AS. Temporal trends and transmission dynamics of pre-treatment HIV-1 drug resistance within and between risk groups in Kenya, 1986-2020. J Antimicrob Chemother 2024; 79:287-296. [PMID: 38091580 PMCID: PMC10832587 DOI: 10.1093/jac/dkad375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/26/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Evidence on the distribution of pre-treatment HIV-1 drug resistance (HIVDR) among risk groups is limited in Africa. We assessed the prevalence, trends and transmission dynamics of pre-treatment HIVDR within and between MSM, people who inject drugs (PWID), female sex workers (FSWs), heterosexuals (HETs) and perinatally infected children in Kenya. METHODS HIV-1 partial pol sequences from antiretroviral-naive individuals collected from multiple sources between 1986 and 2020 were used. Pre-treatment reverse transcriptase inhibitor (RTI), PI and integrase inhibitor (INSTI) mutations were assessed using the Stanford HIVDR database. Phylogenetic methods were used to determine and date transmission clusters. RESULTS Of 3567 sequences analysed, 550 (15.4%, 95% CI: 14.2-16.6) had at least one pre-treatment HIVDR mutation, which was most prevalent amongst children (41.3%), followed by PWID (31.0%), MSM (19.9%), FSWs (15.1%) and HETs (13.9%). Overall, pre-treatment HIVDR increased consistently, from 6.9% (before 2005) to 24.2% (2016-20). Among HETs, pre-treatment HIVDR increased from 6.6% (before 2005) to 20.2% (2011-15), but dropped to 6.5% (2016-20). Additionally, 32 clusters with shared pre-treatment HIVDR mutations were identified. The majority of clusters had R0 ≥ 1.0, indicating ongoing transmissions. The largest was a K103N cluster involving 16 MSM sequences sampled between 2010 and 2017, with an estimated time to the most recent common ancestor (tMRCA) of 2005 [95% higher posterior density (HPD), 2000-08], indicating propagation over 12 years. CONCLUSIONS Compared to HETs, children and key populations had higher levels of pre-treatment HIVDR. Introduction of INSTIs after 2017 may have abrogated the increase in pre-treatment RTI mutations, albeit in the HET population only. Taken together, our findings underscore the need for targeted efforts towards equitable access to ART for children and key populations in Kenya.
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Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Yiakon Sein
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
| | - Dawit A Arimide
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Lyle R Mckinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Morris K Lawrence
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - Moses Masika
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Gaudensia Mutua
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Susan M Graham
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
- Department of Medicine, Global Health and Epidemiology, University of Washington, Seattle, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Matt A Price
- IAVI, NewYork, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology & Biostatistics, University of Illinois at Chicago, Chicago, IL, USA
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Eduard J Sanders
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Department of HIV/STI, KEMRI/Wellcome Trust Research Programme, PO Box 230-80108 Kilifi, Kenya
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2
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Yuan D, Yu B, Li Y, Wang Z, Liu M, Ye L, Huang Y, Su L, Zhang Y, Api L, Chen M, Zhou C, Liu L, Zhang L, Liang S, Jia P, Yang S. Prevalence and Molecular Epidemiology of Transmitted Drug Resistance and Genetic Transmission Networks Among Newly Diagnosed People Living With HIV/AIDS in a Minority Area, China. Front Public Health 2021; 9:731280. [PMID: 34708015 PMCID: PMC8542729 DOI: 10.3389/fpubh.2021.731280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: Transmitted drug resistance (TDR) can compromise antiretroviral therapy (ART) efficacy. We aimed to understand the molecular epidemiology of TDR and its genetic transmission networks among newly diagnosed people living with HIV/AIDS (PLWH). Methods: A total of 1,318 newly diagnosed PLWH, identified in all population-based HIV screening in an HIV-affected county of a minority area of China (i.e., Butuo county), were enrolled between January 1, 2018, and November 31, 2018. HIV-1 pol gene sequences were used for phylogenetic and genotypic drug resistance analyses. The genetic transmission networks were identified. Results: The prevalence of TDR among newly diagnosed PLWH was 8.12% (107/1,318). Patients in the stage of AIDS (adjusted odds ratio, OR: 2.32) and who had a history of sharing a needle ≥5 times (adjusted OR: 3.89) were more likely to have an increased risk of TDR. The prevalence of TDR for non-nucleoside reverse transcriptase inhibitors (NNRTIs) is higher than that of other inhibitors, with a relatively high prevalence of three mutations [V179D/E/DE (4.93%), K103N/KN (3.11%), and E138A/G (1.52%)]. A total of 577 (43.78%) pol sequences were involved in the genetic transmission network, with 171 clusters ranging in size from 2 to 91 pol sequences; 37.38% (40/107) of individuals carrying TDR were involved in the network, and individuals with the same TDR-associated mutations were usually cross-linked. Conclusions: Our data suggest a relatively high level of TDR and many transmission clusters among the newly diagnosed PLWH. Targeted intervention, early identification, and monitoring of resistance are warranted to reduce the TDR and prevent HIV-1 transmission in areas with a high rate of HIV-1.
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Affiliation(s)
- Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Bin Yu
- West China Second University Hospital of Sichuan University and Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Zixin Wang
- Centre for Health Behaviours Research, The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Meijing Liu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yuling Huang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Ling Su
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yan Zhang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Laze Api
- Butuo Center for Disease Control and Prevention, Liangshan, China
| | - Maogang Chen
- Liangshan Center for Disease Control and Prevention, Xichang, China
| | - Chang Zhou
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Li Liu
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Linglin Zhang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Peng Jia
- School of Resources and Environmental Science, Wuhan University, Wuhan, China.,International Institute of Spatial Lifecourse Epidemiology (ISLE), Wuhan University, Wuhan, China
| | - Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.,International Institute of Spatial Lifecourse Epidemiology (ISLE), Wuhan University, Wuhan, China
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3
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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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4
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Yuan D, Liu M, Li Y, Jia P, Su L, Ye L, Zhang Y, Ling P, Zhou C, Liang S, Yang H, Liu H, Yang S. Genetic transmission networks of HIV-1 CRF07_BC strain among HIV-1 infections with virologic failure of ART in a minority area of China: a population-based study. BMC Infect Dis 2020; 20:631. [PMID: 32842977 PMCID: PMC7448482 DOI: 10.1186/s12879-020-05347-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/13/2020] [Indexed: 12/16/2022] Open
Abstract
Background The drug resistance and the virologic failure of antiretroviral therapy (ART) are quite severe in Liangshan. A better understanding of the virologic failure of ART and the HIV-1 transmission network dynamics is essential for the surveillance and prevention of HIV. Here, we analyzed the HIV-1 CRF07_BC strain genetic transmission networks and their associated factors among people living with HIV-1 (PLWH) who had virologic failure of ART by using close genetic links. Methods The drug-resistant mutations were determined using the Stanford University HIV Drug Resistance Database. HIV-1 pol genes sequences were used for phylogenetic and genotypic drug resistance analysis. The genetic transmission networks were performed by comparing sequences, constructing the phylogenetic tree, calculating the pairwise distance, and visualizing the network. Results A total of 1050 PLWH with CRF07_BC pol sequences were finally identified and included in the genetic transmission network analysis from 2016 to 2017. Of the 1050 CRF07_BC pol sequences, 346 (32.95%) fell into clusters at a genetic distance of 0.006, resulting in 137 clusters ranging in size from 2 to 40 individuals. Subjects who were widowed or divorced were less likely to form a genetic transmission network (adjusted OR: 0.50), while subjects who had shared a needle ≥ five times were more likely to form a network (adjusted OR: 1.88). Conclusions The genetic transmission networks revealed the complex transmission pattern, highlighting the urgent need for transmission monitoring of virologic failure of ART and selection of more effective therapeutic regimens to promote viral suppression.
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Affiliation(s)
- Dan Yuan
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China.,International Institute of Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China
| | - Meijing Liu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Number16, Section 3, South Renmin Road, Chengdu, 610041, Sichuan, China
| | - Yiping Li
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Peng Jia
- International Institute of Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China.,Department of Land Surveying and Geo-Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Ling Su
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Li Ye
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yan Zhang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Pan Ling
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Chang Zhou
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Shu Liang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Hong Yang
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Honglu Liu
- Center for AIDS/STD Control and Prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China.
| | - Shujuan Yang
- International Institute of Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China. .,West China School of Public Health and West China Fourth Hospital, Sichuan University, Number16, Section 3, South Renmin Road, Chengdu, 610041, Sichuan, China.
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5
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Geretti AM, White E, Orkin C, Tostevin A, Tilston P, Chadwick D, Leen C, Sabin C, Dunn DT. Virological outcomes of boosted protease inhibitor-based first-line ART in subjects harbouring thymidine analogue-associated mutations as the sole form of transmitted drug resistance. J Antimicrob Chemother 2020; 74:746-753. [PMID: 30544247 PMCID: PMC6376847 DOI: 10.1093/jac/dky468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/06/2018] [Accepted: 10/13/2018] [Indexed: 12/13/2022] Open
Abstract
Objectives In subjects with transmitted thymidine analogue mutations (TAMs), boosted PIs (PI/b) are often chosen to overcome possible resistance to the NRTI backbone. However, data to guide treatment selection are limited. Our aim was to obtain firmer guidance for clinical practice using real-world cohort data. Methods We analysed 1710 subjects who started a PI/b in combination with tenofovir or abacavir plus emtricitabine or lamivudine, and compared their virological outcomes with those of 4889 patients who started an NNRTI (predominantly efavirenz), according to the presence of ≥1 TAM as the sole form of transmitted drug resistance. Results Participants with ≥1 TAM comprised predominantly MSM (213 of 269, 79.2%), subjects of white ethnicity (206 of 269, 76.6%) and HIV-1 subtype B infections (234 of 269, 87.0%). Most (203 of 269, 75.5%) had singleton TAMs, commonly a revertant of T215Y or T215F (112 of 269, 41.6%). Over a median of 2.5 years of follow-up, 834 of 6599 (12.6%) subjects experienced viraemia (HIV-1 RNA >50 copies/mL). The adjusted HR for viraemia was 2.17 with PI/b versus NNRTI-based therapy (95% CI 1.88–2.51; P < 0.001). Other independent predictors of viraemia included injecting drug use, black ethnicity, higher viral load and lower CD4 cell count at baseline, and receiving abacavir instead of tenofovir. Resistance showed no overall impact (adjusted HR 0.77 with ≥1 TAM versus no resistance; 95% CI 0.54–1.10; P = 0.15). Conclusions In this cohort, patients harbouring ≥1 TAM as the sole form of transmitted drug resistance gained no apparent virological advantage from starting first-line ART with a PI/b.
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Affiliation(s)
- Anna Maria Geretti
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Ellen White
- MRC Clinical Trials Unit at University College London, London, UK
| | - Chloe Orkin
- Department of Infection & Immunity, Barts Health NHS Trust, London, UK
| | - Anna Tostevin
- Institute for Global Health, University College London, London, UK
| | - Peter Tilston
- Department of Clinical Virology, Manchester Royal Infirmary, Manchester, UK
| | - David Chadwick
- Department of Infectious Diseases, South Tees Hospitals NHS Trust, Middlesbrough, UK
| | - Clifford Leen
- Regional Infectious Diseases Unit, NHS Lothian, Edinburgh, UK
| | - Caroline Sabin
- Institute for Global Health, University College London, London, UK
| | - David T Dunn
- Institute for Global Health, University College London, London, UK
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6
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Aulicino PC, Zapiola I, Kademian S, Valle MM, Fernandez Giuliano S, Toro R, Barbas G, Cañizal AM, Mayon P, Golemba MD, Ortiz de Zarate M, Corazza MS, Cudola A, Mecikovsky D, Bologna R, Mangano A, Sen L. Pre-treatment drug resistance and HIV-1 subtypes in infants from Argentina with and without exposure to antiretroviral drugs for prevention of mother-to-child transmission. J Antimicrob Chemother 2020; 74:722-730. [PMID: 30517632 DOI: 10.1093/jac/dky486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES To assess the prevalence and patterns of pre-treatment HIV drug resistance (PDR) and HIV-1 subtype in infants from Argentina with exposure to different antiretroviral drugs (ARVs) for the prevention of mother-to-child transmission (PMTCT). PATIENTS AND METHODS HIV-1 genotyping was performed in 115 infants (median age = 2.3 months) born between 2007 and 2014 to screen for drug resistance mutations (DRMs) before starting first-line ART. HIV-1 subtype was characterized by phylogenetic and recombination analysis. RESULTS Overall, DRMs were found in 34 of 115 infants (PDR level 30% to any ARV, 3.5% to PIs, 12% to NRTIs and 22% to NNRTIs). Of the 115 infants, 22 (19.1%) were ARV-unexposed. Another 93 were ARV-exposed: 28 (24.3%) to short-course zidovudine monotherapy ARV prophylaxis; 25 (21.7%) to nevirapine-based ARV prophylaxis; 12 (10.4%) to perinatal infant zidovudine prophylaxis + maternal combination ART with NNRTIs; and 28 (24.3%) to perinatal infant zidovudine prophylaxis+maternal combination ART with PIs. Transmitted drug resistance among ARV-unexposed infants was 32% (5% to PIs, 9% to NRTIs and 18% to NNRTIs). ART-exposed infants showed multi-class ARV resistance. Importantly, vertical transmission of a triple-class-resistant virus was confirmed in one case. Patterns of DRMs predicted high-level resistance to NNRTIs in a similar and high proportion (>50%) of infants with at least one DRM independently of ARV exposure. BF recombinants were found in 74%, subtype B in 20%, subtype C in 3% and novel AG and AB recombinants in 3%. CONCLUSIONS PDR in HIV-1-infected children from Argentina is among the highest reported, jeopardizing successful lifelong suppressive ART as well as the efficacy of current PMTCT regimens.
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Affiliation(s)
- Paula C Aulicino
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | - Ines Zapiola
- Unidad de Virología, Hospital de Infecciosas "Francisco J. Muñiz", Buenos Aires, Argentina
| | - Silvia Kademian
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - María M Valle
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | | | - Rosana Toro
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Gabriela Barbas
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - Ana M Cañizal
- Unidad de Virología, Hospital de Infecciosas "Francisco J. Muñiz", Buenos Aires, Argentina
| | - Paula Mayon
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Marcelo D Golemba
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | | | - Marisa S Corazza
- Centro Provincial VIH/SIDA y Hepatitis Virales de la Provincia de Buenos Aires, Instituto Biológico Dr Tomás Perón, La Plata, Argentina
| | - Analía Cudola
- Laboratorio Central, Ministerio de Salud, Córdoba, Argentina
| | - Débora Mecikovsky
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Rosa Bologna
- Servicio de Epidemiología e Infectología, Hospital de Pediatría "Juan P. Garrahan", Buenos Aires, Argentina
| | - Andrea Mangano
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
| | - Luisa Sen
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría "Juan P. Garrahan"-CONICET, Buenos Aires, Argentina
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7
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Ye M, Chen X, Wang Y, Zhou YH, Pang W, Zhang C, Zheng YT. HIV-1 Drug Resistance in ART-Naïve Individuals in Myanmar. Infect Drug Resist 2020; 13:1123-1132. [PMID: 32368103 PMCID: PMC7182463 DOI: 10.2147/idr.s246462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/31/2020] [Indexed: 01/29/2023] Open
Abstract
Background Estimating the prevalence and characterizing the transmission of HIV-1 drug resistance in treatment-naïve individuals are very important in the prevention and control of HIV/AIDS. As one of the areas most affected by HIV/AIDS, few data are currently available for HIV-1 drug resistance in antiretroviral therapy (ART)-naïve individuals in Myanmar, which borders Yunnan, China. Methods HIV-1 pol sequences from ART-naïve HIV-1-infected individuals during 2008 and 2014 in Myanmar were retrieved from our previous studies. HIV-1 transmitted drug resistance (TDR) and susceptibility to antiretroviral drugs were predicted using the Stanford HIVdb program. HIV-1 transmission cluster (TC) was determined by Cluster Picker. Results A total of 169 partial pol sequences from ART-naïve HIV-1 positive Burmese were analyzed. The prevalence of TDR was 20.1%. CRF01_AE and BC recombinants appeared to have a higher prevalence of TDR than other subtypes. The V179D/T was found to be very common in the China–Myanmar border region and was involved in half of the transmission clusters formed by HIV-1 drug-resistance strains in this region. Comparison showed that drug-resistance mutation profile in Myanmar was very similar to that in Dehong prefecture of Yunnan. By further phylogenetic analysis with all available sequences from the China–Myanmar border region, four HIV-1 drug-resistance-related TCs were identified. Three of them were formed by Burmese long-distance truck drivers and the Burmese staying in Yunnan, and another was formed by Burmese injection drug users staying in Myanmar and Yunnan. These results suggest a potential transmission link of HIV-1 drug resistance between Myanmar and Yunnan. Conclusion Given the high prevalence of TDR in Myanmar, and the potential risk of cross-border transmission of HIV-1 drug-resistant strains between Myanmar and Yunnan, China, ongoing monitoring of HIV-1 drug resistance in ART-naïve individuals will provide a guideline for clinical antiretroviral treatment and benefit the prevention and control of HIV/AIDS in this border region.
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Affiliation(s)
- Mei Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China.,Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou 341000, People's Republic of China
| | - Yu Wang
- KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215000, People's Republic of China
| | - Yan-Heng Zhou
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, People's Republic of China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
| | - Chiyu Zhang
- Pathogen Discovery and Evolution Unit, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China.,KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215000, People's Republic of China
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8
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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9
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Günthard HF, Kouyos R. Can Directionality of HIV Transmission be Predicted by Next-Generation Sequencing Data? J Infect Dis 2019; 220:1393-1395. [PMID: 30590738 DOI: 10.1093/infdis/jiy737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Switzerland
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10
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Bandera A, Gori A, Clerici M, Sironi M. Phylogenies in ART: HIV reservoirs, HIV latency and drug resistance. Curr Opin Pharmacol 2019; 48:24-32. [PMID: 31029861 DOI: 10.1016/j.coph.2019.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 11/17/2022]
Abstract
Combination antiretroviral therapy (ART) has significantly reduced the morbidity and mortality resulting from HIV infection. ART is, however, unable to eradicate HIV, which persists latently in several cell types and tissues. Phylogenetic analyses suggested that the proliferation of cells infected before ART initiation is mainly responsible for residual viremia, although controversy still exists. Conversely, it is widely accepted that drug resistance mutations (DRMs) do not appear during ART in patients with suppressed viral loads. Studies based on sequence clustering have in fact indicated that, at least in developed countries, HIV-infected ART-naive patients are the major source of drug-resistant viruses. Analysis of longitudinally sampled sequences have also shown that DRMs have variable fitness costs, which are strongly influenced by the viral genetic background.
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Affiliation(s)
- Alessandra Bandera
- Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy; Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy; Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy; IRCCS Fondazione Don Carlo Gnocchi, 20148 Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy.
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11
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Integration of Contact Tracing and Phylogenetics in an Investigation of Acute HIV Infection. Sex Transm Dis 2019; 45:222-228. [PMID: 29465708 DOI: 10.1097/olq.0000000000000726] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND The integration of traditional contact tracing with HIV sequence analyses offers opportunities to mitigate some of the barriers to effective network construction. We used combined analyses during an outbreak investigation of spatiotemporally clustered acute HIV infections to evaluate if the observed clustering was the product of a single outbreak. METHODS We investigated acute and recent HIV index cases reported in North Carolina from 2013 to 2014 and their reported contacts. Contact tracing networks were constructed with surveillance data and compared with phylogenetic transmission clusters involving an index case using available HIV-1 pol sequences including 1672 references. Clusters were defined as clades of 2 or more sequences with a less than 1.5% genetic distance and a bootstrap of at least 98% on maximum-likelihood phylogenies. RESULTS In total, 68 index cases and 210 contacts (71 HIV infected) were reported. The contact tracing network involved 58 components with low overall density (1.2% statewide); 33% of first-degree contacts could not be located. Among 38 (56%) of 68 index cases and 34 (48%) of 71 contacts with sequences, 13 phylogenetic clusters were identified (size 2-4 members). Four clusters connected network components that were not linked in contact tracing. The largest component (n = 28 cases) included 2 distinct phylogenetic clusters and spanned 2 regions. CONCLUSIONS We identified the concurrent expansion of multiple small transmission clusters rather than a single outbreak in a largely disconnected contact tracing network. Integration of phylogenetic analyses provided timely information on transmission networks during the investigation. Our findings highlight the potential of combined methods to better identify high-risk networks for intervention.
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12
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Abstract
OBJECTIVES Molecular epidemiology is applied to various aspects of HIV transmission analyses. With ultradeep sequencing (UDS), in-depth characterization of transmission episodes involving minority variants is permitted. We explored HIV-1 epidemiological linkage and evaluated characteristics of transmission dynamics and transmitted drug resistance (TDR) detection through the added value of UDS. DESIGN HIV pol gene fragments were sequenced by UDS and Sanger sequencing on samples of 70 HIV-1-infected, treatment-naive recently diagnosed MSM. METHODS Pairwise genetic distances and maximum likelihood phylogenies were computed. Transmission events were identified as clades with branch support at least 70% and intraclade genetic difference less than 4.5%. TDR mutations were recognized from the TDR consensus list. Transmission directionality, directness and inoculum size were inferred from tree topologies. RESULTS Both datasets concurred in the identification of seven transmission pairs and one cluster of three patients. With UDS, direction of transmission was inferred in four out of eight chains. Evidence for multiple founder viruses was found in two out of eight chains. No transmission of minority-resistant variants was evidenced. TDR mutations prevalence in protease and reverse transcriptase fragments was 4.3% with Sanger sequencing and 18.6% with UDS. CONCLUSION Although Sanger sequencing and UDS identified the same transmission chains, UDS provided additional information on founder viruses, direction of transmission and levels of TDR. Nevertheless, topology of clusters was not always consistent across gene fragments, calling for a cautious interpretation of the data. Moreover, unobserved intermediary links cannot be excluded. Phylogenetic analysis use as a forensic technique for HIV transmission investigations is risky.
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13
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Insights on transmission of HIV from phylogenetic analysis to locally optimize HIV prevention strategies. Curr Opin HIV AIDS 2019; 13:95-101. [PMID: 29266012 DOI: 10.1097/coh.0000000000000443] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Phylogenetic analysis can identify transmission networks by clustering genetically related HIV genotypes that are routinely collected. In this study, we will review phylogenetic insights gained on transmission of HIV and phylogenetically optimized HIV prevention strategies. RECENT FINDINGS Phylogenetic analysis reports that HIV transmission varies by geographical region and by route of transmission. In high-income countries, HIV is predominantly transmitted between recently infected MSM who live in the same country. In rural Uganda, transmission of HIV is frequently between different communities. Age-discrepant transmission has been reported across the world. Four studies have used phylogenetic optimization of HIV prevention. Three studies predict that immediate treatment after diagnosis would have prevented 19-42% of infections, and that preexposure prophylaxis would have prevented 66% of infections. One phylogenetic study guided a public health response to an actively ongoing HIV outbreak. Phylogenetic clustering requires a dense sample of patients and small time-gaps between infection and diagnosis. SUMMARY Phylogenetic analysis can be an important tool to identify a local strategy that prevents most infections. Future studies that use phylogenetic analysis for optimizing HIV prevention strategies should also include cost-effectiveness so that the most cost-effective prevention method is identified.
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14
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Hassan AS, Esbjörnsson J, Wahome E, Thiong’o A, Makau GN, Price MA, Sanders EJ. HIV-1 subtype diversity, transmission networks and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya. PLoS One 2018; 13:e0206177. [PMID: 30562356 PMCID: PMC6298690 DOI: 10.1371/journal.pone.0206177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/08/2018] [Indexed: 11/21/2022] Open
Abstract
Background HIV-1 molecular epidemiology amongst men who have sex with men (MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR) in acute and early infected MSM from Coastal Kenya. Methods Analysis of HIV-1 partial pol sequences from MSM recruited 2005–2017 and sampled within six months of the estimated date of infection. Volunteers were classified as men who have sex with men exclusively (MSME) or with both men and women (MSMW). HIV-1 subtype and transmission clusters were determined by maximum-likelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug resistance database. Results Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters, with substantial mixing between MSME and MSMW. Majority of volunteer sequences were either not linked to any reference sequence (56%) or clustered exclusively with sequences of Kenyan origin (19%). Eight (8% [95% CI: 4–16]) had at least one TDR mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with sequences forming transmission clusters of two and three taxa each. There were no significant differences in HIV-1 subtype distribution and TDR between MSME and MSMW. Conclusions This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan origin, with many transmission clusters and having intermediate level of TDR. Targeted HIV-1 prevention, early identification and care interventions are warranted to break the transmission cycle amongst MSM from Coastal Kenya.
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Affiliation(s)
- Amin S. Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
- * E-mail:
| | | | | | | | - George N. Makau
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
| | - Mathew A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Oxford University, Oxford, United Kingdom
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15
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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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16
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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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17
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Increase in transmitted drug resistance in migrants from sub-Saharan Africa diagnosed with HIV-1 in Sweden. AIDS 2018; 32:877-884. [PMID: 29369826 DOI: 10.1097/qad.0000000000001763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To study the trends of transmitted drug resistance (TDR) in HIV-1 patients newly diagnosed in Sweden, 2010-2016. DESIGN Register-based study including all antiretroviral therapy-naive patients ≥18 years diagnosed with HIV-1 in Sweden 2010-2016. METHODS Patient data and viral pol sequences were extracted from the national InfCareHIV database. TDR was defined as the presence of surveillance drug resistance mutations (SDRMs). A CD4 T-cell decline trajectory model estimated time of infection. Phylogenetic inference was used for cluster analysis. Chi-square tests and logistic regressions were used to investigate relations between TDR, epidemiological and viral factors. RESULTS One thousand, seven hundred and thirteen pol sequences were analyzed, corresponding to 71% of patients with a new HIV-1 diagnosis (heterosexuals: 53%; MSM: 34%). The overall prevalence of TDR was 7.1% (95% CI 5.8-8.3%). Nonnucleoside reverse transcriptase inhibitor (NNRTI) TDR increased significantly from 1.5% in 2010 to 6.2% in 2016, and was associated to infection and/or origin in sub-Saharan Africa (SSA). An MSM transmission cluster dating back to the 1990s with the M41L SDRM was identified. Twenty-five (1.5%) patients exhibited TDR to tenofovir (TDF; n = 8), emtricitabine/lamivudine (n = 9) or both (n = 8). CONCLUSION NNRTI TDR has increased from 2010 to 2016 in HIV-1-infected migrants from SSA diagnosed in Sweden, mirroring the situation in SSA. TDR to tenofovir/emtricitabine, used in preexposure prophylaxis, confirms the clinical and epidemiological need for resistance testing in newly diagnosed patients.
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18
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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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19
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Paraskevis D, Kostaki E, Gargalianos P, Xylomenos G, Lazanas M, Chini M, Skoutelis A, Papastamopoulos V, Paraskeva D, Antoniadou A, Papadopoulos A, Psichogiou M, Daikos GL, Chrysos G, Paparizos V, Kourkounti S, Sambatakou H, Sipsas NV, Lada M, Panagopoulos P, Maltezos E, Drimis S, Hatzakis A. Transmission Dynamics of HIV-1 Drug Resistance among Treatment-Naïve Individuals in Greece: The Added Value of Molecular Epidemiology to Public Health. Genes (Basel) 2017; 8:genes8110322. [PMID: 29137167 PMCID: PMC5704235 DOI: 10.3390/genes8110322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 11/16/2022] Open
Abstract
The presence of human immunodeficiency virus type 1 (HIV-1) drug resistance among drug-naïve patients remains stable, although the proportion of patients with virological failure to therapy is decreasing. The dynamics of transmitted resistance among drug-naïve patients remains largely unknown. The prevalence of non-nucleoside reverse transcriptase inhibitors (NNRTI) resistance was 16.9% among treatment-naïve individuals in Greece. We aimed to investigate the transmission dynamics and the effective reproductive number (Re) of the locally transmitted NNRTI resistance. We analyzed sequences with dominant NNRTI resistance mutations (E138A and K103N) found within monophyletic clusters (local transmission networks (LTNs)) from patients in Greece. For the K103N LTN, the Re was >1 between 2008 and the first half of 2013. For all E138A LTNs, the Re was >1 between 1998 and 2015, except the most recent one (E138A_4), where the Re was >1 between 2006 and 2011 and approximately equal to 1 thereafter. K103N and E138A_4 showed similar characteristics with a more recent origin, higher Re during the first years of the sub-epidemics, and a declining trend in the number of transmissions during the last two years. In the remaining LTNs the epidemic was still expanding. Our study highlights the added value of molecular epidemiology to public health.
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Affiliation(s)
- Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; (E.K.); (A.H.)
- Correspondence:
| | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; (E.K.); (A.H.)
| | - Panagiotis Gargalianos
- 1st Department of Internal Medicine, G. Genimatas GH, 11527 Athens, Greece; (P.G.); (G.X.)
| | - Georgios Xylomenos
- 1st Department of Internal Medicine, G. Genimatas GH, 11527 Athens, Greece; (P.G.); (G.X.)
| | - Marios Lazanas
- 3rd Internal Medicine Department-Infectious Diseases, Red Cross Hospital, 11526 Athens, Greece; (M.L.); (M.C.)
| | - Maria Chini
- 3rd Internal Medicine Department-Infectious Diseases, Red Cross Hospital, 11526 Athens, Greece; (M.L.); (M.C.)
| | - Athanasios Skoutelis
- 5th Department of Medicine and Infectious Diseases, Evaggelismos GH, 10676 Athens, Greece; (A.S.); (V.P.)
| | - Vasileios Papastamopoulos
- 5th Department of Medicine and Infectious Diseases, Evaggelismos GH, 10676 Athens, Greece; (A.S.); (V.P.)
| | - Dimitra Paraskeva
- Hellenic Center for Disease Control & Prevention, 15123 Athens, Greece;
| | - Anastasia Antoniadou
- 4th Department of Medicine, Attikon GH, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (A.A.); (A.P.)
| | - Antonios Papadopoulos
- 4th Department of Medicine, Attikon GH, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (A.A.); (A.P.)
| | - Mina Psichogiou
- 1st Department of Medicine, Laikon GH, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.P.); (G.L.D.)
| | - Georgios L. Daikos
- 1st Department of Medicine, Laikon GH, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (M.P.); (G.L.D.)
| | - Georgios Chrysos
- Department of Internal Medicine, Tzaneio GH, 18536 Piraeus, Greece; (G.C.); (S.D.)
| | - Vasileios Paparizos
- HIV/AIDS Unit, A. Syngros Hospital of Dermatology and Venereology, 16121 Athens, Greece; (V.P.); (S.K.)
| | - Sofia Kourkounti
- HIV/AIDS Unit, A. Syngros Hospital of Dermatology and Venereology, 16121 Athens, Greece; (V.P.); (S.K.)
| | - Helen Sambatakou
- HIV Unit, 2nd Department of Internal Medicine, Hippokration GH, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Nikolaos V. Sipsas
- Department of Pathophysiology, Laikon GH, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Malvina Lada
- 2nd Department of Internal Medicine, Sismanogleion GH, 15126 Athens, Greece;
| | - Periklis Panagopoulos
- Department of Internal Medicine, University GH, Democritus University of Thrace, 67100 Alexandroupolis, Greece; (P.P.); (E.M.)
| | - Efstratios Maltezos
- Department of Internal Medicine, University GH, Democritus University of Thrace, 67100 Alexandroupolis, Greece; (P.P.); (E.M.)
| | - Stylianos Drimis
- Department of Internal Medicine, Tzaneio GH, 18536 Piraeus, Greece; (G.C.); (S.D.)
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; (E.K.); (A.H.)
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Paraskevis D, Kostaki E, Magiorkinis G, Gargalianos P, Xylomenos G, Magiorkinis E, Lazanas M, Chini M, Nikolopoulos G, Skoutelis A, Papastamopoulos V, Antoniadou A, Papadopoulos A, Psichogiou M, Daikos GL, Oikonomopoulou M, Zavitsanou A, Chrysos G, Paparizos V, Kourkounti S, Sambatakou H, Sipsas NV, Lada M, Panagopoulos P, Maltezos E, Drimis S, Hatzakis A. Prevalence of drug resistance among HIV-1 treatment-naive patients in Greece during 2003-2015: Transmitted drug resistance is due to onward transmissions. INFECTION GENETICS AND EVOLUTION 2017; 54:183-191. [PMID: 28688977 DOI: 10.1016/j.meegid.2017.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND The prevalence of HIV-1 drug resistance among treatment-naïve patients ranges between 8.3% and 15% in Europe and North America. Previous studies showed that subtypes A and B were the most prevalent in the Greek HIV-1 epidemic. Our aim was to estimate the prevalence of resistance among drug naïve patients in Greece and to investigate the levels of transmission networking among those carrying resistant strains. METHODS HIV-1 sequences were determined from 3428 drug naïve HIV-1 patients, in Greece sampled during 01/01/2003-30/6/2015. Transmission clusters were estimated by means of phylogenetic analysis including as references sequences from patients failing antiretroviral treatment in Greece and sequences sampled globally. RESULTS The proportion of sequences with SDRMs was 5.98% (n=205). The most prevalent SDRMs were found for NNRTIs (3.76%), followed by N(t)RTIs (2.28%) and PIs (1.02%). The resistance prevalence was 22.2% based on all mutations associated with resistance estimated using the HIVdb resistance interpretation algorithm. Resistance to NNRTIs was the most common (16.9%) followed by PIs (4.9%) and N(t)RTIs (2.8%). The most frequently observed NNRTI resistant mutations were E138A (7.7%), E138Q (4.0%), K103N (2.3%) and V179D (1.3%). The majority of subtype A sequences (89.7%; 245 out of 273) with the dominant NNRTI resistance mutations (E138A, K103N, E138Q, V179D) were found to belong to monophyletic clusters suggesting regional dispersal. For subtype B, 68.1% (139 out of 204) of resistant strains (E138A, K103N, E138Q V179D) belonged to clusters. For N(t)RTI-resistance, evidence for regional dispersal was found for 27.3% and 21.6% of subtype A and B sequences, respectively. CONCLUSIONS The TDR rate based on the prevalence of SDRM is lower than the average rate in Europe. However, the prevalence of NNRTI resistance estimated using the HIVdb approach, is high in Greece and it is mostly due to onward transmissions among drug-naïve patients.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece.
| | - E Kostaki
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - G Magiorkinis
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - P Gargalianos
- 1st Department of Internal Medicine, G. Genimatas GH, Athens, Greece
| | - G Xylomenos
- 1st Department of Internal Medicine, G. Genimatas GH, Athens, Greece
| | - E Magiorkinis
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - M Lazanas
- 3rd Internal Medicine Department-Infectious Diseases, Red Cross Hospital, Athens, Greece
| | - M Chini
- 3rd Internal Medicine Department-Infectious Diseases, Red Cross Hospital, Athens, Greece
| | | | - A Skoutelis
- 5th Department of Medicine and Infectious Diseases, Evaggelismos GH, Athens, Greece
| | - V Papastamopoulos
- 5th Department of Medicine and Infectious Diseases, Evaggelismos GH, Athens, Greece
| | - A Antoniadou
- 4th Department of Medicine, Attikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Papadopoulos
- 4th Department of Medicine, Attikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Psichogiou
- 1st Department of Medicine, Laikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - G L Daikos
- 1st Department of Medicine, Laikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Oikonomopoulou
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - A Zavitsanou
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | - G Chrysos
- Department of Internal Medicine, Tzaneio GH, Piraeus, Greece
| | - V Paparizos
- HIV/AIDS Unit, A. Syngros Hospital of Dermatology and Venereology, Athens, Greece
| | - S Kourkounti
- HIV/AIDS Unit, A. Syngros Hospital of Dermatology and Venereology, Athens, Greece
| | - H Sambatakou
- HIV Unit, 2nd Department of Internal Medicine, Hippokration GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - N V Sipsas
- 1st Department of Pathophysiology, Laikon GH, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Lada
- 2nd Department of Internal Medicine, Sismanogleion GH, Athens, Greece
| | - P Panagopoulos
- Department of Internal Medicine, University GH, Democritus University of Thrace, Alexandroupolis, Greece
| | - E Maltezos
- Department of Internal Medicine, University GH, Democritus University of Thrace, Alexandroupolis, Greece
| | - S Drimis
- Department of Internal Medicine, Tzaneio GH, Piraeus, Greece
| | - A Hatzakis
- Department of Hygiene,, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
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Hauser A, Hofmann A, Hanke K, Bremer V, Bartmeyer B, Kuecherer C, Bannert N. National molecular surveillance of recently acquired HIV infections in Germany, 2013 to 2014. ACTA ACUST UNITED AC 2017; 22:30436. [PMID: 28105988 PMCID: PMC5404484 DOI: 10.2807/1560-7917.es.2017.22.2.30436] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 08/23/2016] [Indexed: 11/20/2022]
Abstract
To enable an up-to-date molecular analysis of human immunodeficiency virus (HIV) genotypes circulating in Germany we have established a surveillance system based on recently acquired HIV infections. New HIV infections are reported to the Robert Koch Institute as a statutory duty for anonymous notification. In 2013 and 2014, a dried serum spot (DSS) sample was received from 6,371 newly diagnosed HIV-cases; their analysis suggested that 1,797 samples originated from a recent infection. Of these, 809 were successfully genotyped in the pol region to identify transmitted drug resistance (TDR) mutations and to determine the HIV-1 subtype. Total TDR was 10.8%, comprising 4.3% with mono-resistance to nucleoside reverse transcriptase inhibitors (NRTIs), 2.6% to non-NRTIs, 3.0% to protease inhibitors and 0.6% and 0.2%, respectively, with dual- and triple-class resistances. HIV-1 subtype B was most prevalent with 77.0%. Non-B infections were identified more often in men and women with heterosexual transmission compared with intravenous drug users or men who have sex with men (79% and 76%, 33%, 12%; all p < 0.05). Non-B subtypes were also more frequently found in patients originating from countries other than Germany (46% vs 14%; p < 0.05) and in patients infected outside of Germany (63% vs 14%; p < 0.05).
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Affiliation(s)
- Andrea Hauser
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Alexandra Hofmann
- Division of HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin,
Germany.,Charité - Universitätsmedizin, Berlin, Germany
| | - Kirsten Hanke
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Viviane Bremer
- Division of HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin,
Germany
| | - Barbara Bartmeyer
- Division of HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin,
Germany
| | - Claudia Kuecherer
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
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22
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Gorbach PM, Javanbakht M, Bornfleth L, Bolan RK, Lewis Blum M. Drug resistant HIV: Behaviors and characteristics among Los Angeles men who have sex with men with new HIV diagnosis. PLoS One 2017; 12:e0173892. [PMID: 28333950 PMCID: PMC5363913 DOI: 10.1371/journal.pone.0173892] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/28/2017] [Indexed: 11/18/2022] Open
Abstract
Epidemiology of drug resistant HIV has focused on trends and less attention has been given to identification of factors, especially behaviors including substance use, in acquisition of drug-resistant HIV. From 2009 to 2012 The Metromates Study enrolled and followed for one year men who have sex with men (MSM) seeking testing for HIV in a community clinic in Los Angeles assessing those testing positive for acute and recent HIV infection. Behavioral data were collected via Computer-Assisted Self-Interview from 125 classified as newly HIV infected and 91 as chronically infected (newly HIV-diagnosed); specimens were available and viable for resistance testing for 154 of the 216 HIV positives with new diagnoses. In this community clinic we found prevalence of resistance among MSM with new HIV-diagnosis was 19.5% (n = 30/154) with no difference by recency of HIV infection. Sexual partnership characteristics were associated with resistance; those who reported transgendered sex partners had a higher prevalence of resistance as compared to those who did not report transgendered sex partners (40% vs. 17%; p value = 0.04), while those who reported having a main partner had a lower prevalence of drug resistance (12% vs. 24%; p value = 0.07). In multivariable analyses adjusting for HIV recency and antiviral use, reporting a main partner decreased odds [adjusted odds ratio (AOR) 0.34; 95% confidence interval (CI) 0.13-0.87], reporting a transgendered partnered increased odds (AOR = 3.37; 95% CI 0.95-12.43); and being African American increased odds of drug resistance (AOR = 5.63, 95%CI 1.41-22.38). This suggests African American MSM and TG individuals in Los Angeles represent pockets of exceptional risk that will require special approaches to prevention and care to enhance their own health and reduce their likelihood to support transmission of drug resistance in the US.
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Affiliation(s)
- Pamina M. Gorbach
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, United States of America
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, United States of America
- * E-mail:
| | - Marjan Javanbakht
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, United States of America
| | - Lorelei Bornfleth
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, United States of America
| | - Robert K. Bolan
- The Los Angeles Gay, Lesbian and Transgender Health Center, Los Angeles, CA, United States of America
| | - Martha Lewis Blum
- Department of Medicine, Community Hospital of the Monterey Peninsula, Monterey County, Department of Public Health, Monterey, CA, United States of America
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Abstract
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis.
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Affiliation(s)
- Charlotte J. Houldcroft
- Department of Infection, UK; and the Division of Biological Anthropology, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, University of Cambridge, Cambridge CB2 3QG, UK.,
- and the Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3QG, UK.,
| | - Mathew A. Beale
- Division of Infection and Immunity, University College London, London, WC1E 6BT UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
- and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
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24
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Tostevin A, White E, Dunn D, Croxford S, Delpech V, Williams I, Asboe D, Pozniak A, Churchill D, Geretti AM, Pillay D, Sabin C, Leigh‐Brown A, Smit E. Recent trends and patterns in HIV-1 transmitted drug resistance in the United Kingdom. HIV Med 2017; 18:204-213. [PMID: 27476929 PMCID: PMC5297994 DOI: 10.1111/hiv.12414] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2016] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Transmission of drug-resistant HIV-1 has decreased in the UK since the early 2000s. This analysis reports recent trends and characteristics of transmitted drug resistance (TDR) in the UK from 2010 to 2013. METHODS Resistance tests conducted in antiretroviral treatment (ART)-naïve individuals between 2010 and 2013 were analysed for the presence of transmitted drug resistance mutations (TDRMs), defined as any mutations from a modified 2009 World Health Organization surveillance list, or a modified 2013 International Antiviral Society-USA list for integrase tests. Logistic regression was used to examine associations between demographics and the prevalence of TDRMs. RESULTS TDRMs were observed in 1223 (7.5%) of 16 425 individuals; prevalence declined from 8.1% in 2010 to 6.6% in 2013 (P = 0.02). The prevalence of TDRMs was higher among men who have sex with men (MSM) compared with heterosexual men and women (8.7% versus 6.4%, respectively) with a trend for decreasing TDRMs among MSM (P = 0.008) driven by a reduction in nucleoside reverse transcriptase inhibitor (NRTI)-related mutations. The most frequently detected TDRMs were K103N (2.2%), T215 revertants (1.6%), M41L (0.9%) and L90M (0.7%). Predicted phenotypic resistance to first-line ART was highest to the nonnucleoside reverse transcriptase inhibitors (NNRTIs) rilpivirine and efavirenz (6.2% and 3.4%, respectively) but minimal to NRTIs, including tenofovir, and protease inhibitors (PIs). No major integrase TDRMs were detected among 101 individuals tested while ART-naïve. CONCLUSIONS We observed a decrease in TDRMs in recent years. However, this was confined to the MSM population and rates remained stable in those with heterosexually acquired HIV infection. Resistance to currently recommended first-line ART, including integrase inhibitors, remained reassuringly low.
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Affiliation(s)
- A Tostevin
- MRC Clinical Trials Unit at UCLUniversity College LondonLondonUK
| | - E White
- MRC Clinical Trials Unit at UCLUniversity College LondonLondonUK
| | - D Dunn
- MRC Clinical Trials Unit at UCLUniversity College LondonLondonUK
| | - S Croxford
- Centre for Infectious Disease Surveillance and Control (CIDSC)Public Health EnglandLondonUK
| | - V Delpech
- Centre for Infectious Disease Surveillance and Control (CIDSC)Public Health EnglandLondonUK
| | - I Williams
- Mortimer Market CentreUniversity College London Hospitals NHS TrustLondonUK
| | - D Asboe
- Chelsea & Westminster HospitalLondonUK
| | - A Pozniak
- Chelsea & Westminster HospitalLondonUK
| | - D Churchill
- Brighton and Sussex University Hospitals NHS TrustBrightonUK
| | | | - D Pillay
- Division of Infection and ImmunityUniversity College LondonLondonUK
- Africa Centre for Health and Population StudiesUniversity of KwaZulu‐NatalMtubatubaSouth Africa
| | - C Sabin
- Research Department of Infection and Population HealthUniversity College LondonLondonUK
| | | | - E Smit
- Public Health EnglandBirmingham Heartlands HospitalBirminghamUK
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25
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Zhong Q, Carratalà A, Nazarov S, Guerrero-Ferreira RC, Piccinini L, Bachmann V, Leiman PG, Kohn T. Genetic, Structural, and Phenotypic Properties of MS2 Coliphage with Resistance to ClO 2 Disinfection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:13520-13528. [PMID: 27709908 DOI: 10.1021/acs.est.6b04170] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Common water disinfectants like chlorine have been reported to select for resistant viruses, yet little attention has been devoted to characterizing disinfection resistance. Here, we investigated the resistance of MS2 coliphage to inactivation by chlorine dioxide (ClO2). ClO2 inactivates MS2 by degrading its structural proteins, thereby disrupting the ability of MS2 to attach to and infect its host. ClO2-resistant virus populations emerged not only after repeated cycles of ClO2 disinfection followed by regrowth but also after dilution-regrowth cycles in the absence of ClO2. The resistant populations exhibited several fixed mutations which caused the substitution of ClO2-labile by ClO2-stable amino acids. On a phenotypic level, these mutations resulted in a more stable host binding during inactivation compared to the wild-type, thus resulting in a greater ability to maintain infectivity. This conclusion was supported by cryo-electron microscopy reconstruction of the virus particle, which demonstrated that most structural modification occurred in the putative A protein, an important binding factor. Resistance was specific to the inactivation mechanism of ClO2 and did not result in significant cross-resistance to genome-damaging disinfectants. Overall, our data indicate that resistant viruses may emerge even in the absence of ClO2 pressure but that they can be inactivated by other common disinfectants.
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Affiliation(s)
- Qingxia Zhong
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, and ‡Laboratory of Structural Biology and Biophysics, Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Anna Carratalà
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, and ‡Laboratory of Structural Biology and Biophysics, Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Sergey Nazarov
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, and ‡Laboratory of Structural Biology and Biophysics, Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ricardo Cesar Guerrero-Ferreira
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, and ‡Laboratory of Structural Biology and Biophysics, Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Laura Piccinini
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, and ‡Laboratory of Structural Biology and Biophysics, Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Virginie Bachmann
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, and ‡Laboratory of Structural Biology and Biophysics, Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Petr G Leiman
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, and ‡Laboratory of Structural Biology and Biophysics, Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, and ‡Laboratory of Structural Biology and Biophysics, Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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26
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Increasing prevalence of K65K and K66K in HIV-1 subtype B reverse transcriptase. AIDS 2016; 30:2787-2793. [PMID: 27677159 DOI: 10.1097/qad.0000000000001272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Synonymous substitutions K65K/K66K in HIV-1 reverse transcriptase alleviate fitness and fidelity defects in HIV-1 molecular clones harboring thymidine analogue mutations (TAMs); however, their potential for transmission and persistence is unknown. Here, we investigated the temporal appearance of K65K/K66K relative to TAMs in a HIV-1 cohort, their prevalence over time, and their impact on viral fitness in the context of patient-derived reverse transcriptase sequences. METHODS Retrospective analyses of the temporal appearance and longitudinal prevalence of synonymous substitutions and drug resistance mutations were performed using the British Columbia Centre for Excellence in HIV/AIDS Drug Treatment Program (DTP) database. Plasma-derived HIV-1 from the DTP was used to generate infectious molecular clones. Growth competition assays were performed to determine viral fitness. RESULTS The prevalence of K65K/K66K in drug-naïve individuals tripled from 11% in 1997 to 37% in 2014 (P < 0.0001, n = 5221), with K66K mainly accounting for the increase. These mutations emerged in drug-treated individuals without TAMs in 14% of the cohort and conferred a fitness advantage in the context of patient-derived multidrug-resistant (MDR) virus in the absence of drug. CONCLUSION The appearance of K65K/K66K in drug-treated individuals was largely independent of TAMs, suggesting alternative factors are likely associated with their emergence. The increasing K65K/K66K prevalence to over a third of treatment-naïve individuals in the mostly subtype B DTP cohort and their ability to confer a fitness advantage to multidrug-resistant virus might explain the transmission and persistence of virus harbouring K65K/K66K in untreated individuals, and highlights their role in adaptive HIV-1 evolution.
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27
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Gill VC, Lynch T, Ramazani S, Krentz HB. Reporting on the prevalence of antiretroviral drug resistance in a regional HIV population over 20 years: a word of caution. Antivir Ther 2016; 22:277-286. [PMID: 27805572 DOI: 10.3851/imp3105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Failure to achieve complete viral suppression with antiretroviral drugs (ARV) may lead to uncontrolled HIV replication, ARV resistance and negative outcomes. Monitoring and reporting of HIV resistance trends is important but problematic. We examined prevalent resistance rates in an HIV population over 20 years and document how rates may appear to vary greatly based solely on which parameters are utilized. METHODS We determined the annual use of genotypic antiretroviral resistance testing (GART) from 1995 to 2014 for all patients receiving HIV care in southern Alberta, Canada, and the presence of resistance mutations in those tested. The impact on prevalent resistance rates of using cumulative or latest GART was also determined. RESULTS Between 1995 and 2014, the number of patients with GART increased from <1% to 71%. Prevalent resistance in patients with GART decreased from a high of 52% in 2003 to 25.8% in 2014. However, if prevalence rates were reported using all active patients as denominator, including those without GART, prevalence increased from 0.7% to 18.5%. Prevalence rates were 7% to 9% higher in any given year if cumulative GART rather than latest GART results were used. CONCLUSIONS While prevalence resistance rates are decreasing, the precise rates being reported may vary due to increasing number of patients tested annually, using either the entire population as denominator or only patients with GART, and using either last or cumulative GART. Defining these parameters is critical if prevalence is to be compared over time or between HIV populations.
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Affiliation(s)
| | - Tarah Lynch
- Southern Alberta Clinic, Calgary, AB, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Hartmut B Krentz
- Southern Alberta Clinic, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
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28
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Cunningham E, Chan YT, Aghaizu A, Bibby DF, Murphy G, Tosswill J, Harris RJ, Myers R, Field N, Delpech V, Cane PA, Gill ON, Mbisa JL. Enhanced surveillance of HIV-1 drug resistance in recently infected MSM in the UK. J Antimicrob Chemother 2016; 72:227-234. [PMID: 27742812 DOI: 10.1093/jac/dkw404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 08/19/2016] [Accepted: 08/26/2016] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the prevalence of inferred low-frequency HIV-1 transmitted drug resistance (TDR) in MSM in the UK and its predicted effect on first-line therapy. METHODS The HIV-1 pol gene was amplified from 442 newly diagnosed MSM identified as likely recently infected by serological avidity testing in 2011-13. The PCR products were sequenced by next-generation sequencing with a mutation frequency threshold of >2% and TDR mutations defined according to the 2009 WHO surveillance drug resistance mutations list. RESULTS The majority (75.6%) were infected with subtype B and 6.6% with rare complex or unique recombinant forms. At a mutation frequency threshold of >20%, 7.2% (95% CI 5.0%-10.1%) of the sequences had TDR and this doubled to 15.8% (95% CI 12.6%-19.6%) at >2% mutation frequency (P < 0.0001). The majority (26/42, 62%) of low-frequency variants were against PIs. The most common mutations detected at >20% and 2%-20% mutation frequency differed for each drug class, these respectively being: L90M (n = 7) and M46IL (n = 10) for PIs; T215rev (n = 9) and D67GN (n = 4) for NRTIs; and K103N (n = 5) and G190E (n = 2) for NNRTIs. Combined TDR was more frequent in subtype B than non-B (OR = 0.38; 95% CI = 0.17-0.88; P = 0.024) and had minimal predicted effect on recommended first-line therapies. CONCLUSIONS The data suggest differences in the types of low-frequency compared with majority TDR variants that require a better understanding of the origins and clinical significance of low-frequency variants. This will better inform diagnostic and treatment strategies.
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Affiliation(s)
- Emma Cunningham
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Yuen-Ting Chan
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Adamma Aghaizu
- HIV and STI Department, National Infection Service, Public Health England, London, UK
| | - David F Bibby
- Virus Reference Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Gary Murphy
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Jennifer Tosswill
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Ross J Harris
- Statistics, Modelling and Economics Department, National Infection Service, Public Health England, London, UK
| | - Richard Myers
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Nigel Field
- HIV and STI Department, National Infection Service, Public Health England, London, UK
| | - Valerie Delpech
- HIV and STI Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Patricia A Cane
- Virus Reference Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - O Noel Gill
- HIV and STI Department, National Infection Service, Public Health England, London, UK.,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
| | - Jean L Mbisa
- Virus Reference Department, National Infection Service, Public Health England, London, UK .,National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, University College London, London, UK
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29
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Zoufaly A, Kraft C, Schmidbauer C, Puchhammer-Stoeckl E. Prevalence of integrase inhibitor resistance mutations in Austrian patients recently diagnosed with HIV from 2008 to 2013. Infection 2016; 45:165-170. [PMID: 27530391 DOI: 10.1007/s15010-016-0936-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 08/02/2016] [Indexed: 01/08/2023]
Abstract
PURPOSE Treatment guidelines often do not advocate testing for integrase inhibitor resistance associated mutations (IRAM) before initiation of first line ART given the extremely low prevalence of mutations found in older surveillance studies. We aimed to describe the prevalence of IRAM in Austrian patients recently diagnosed with HIV in the 5 years following introduction of integrase inhibitors and to analyse trends and factors associated with their detection. METHODS Samples of antiretroviral treatment (ART) naïve patients recently diagnosed with HIV in Austria between 2008 and 2013 were analysed for the existence of IRAM and drug penalty scores were calculated to estimate response to drugs. Demographic and virological data were extracted from a database. Descriptive and comparative statistics were used. RESULTS A total of 303 samples were analysed. 78 % were male and mean age was 38 years. Overall prevalence of IRAM was 2.3 %. Six percent had at least potentially low-level resistance to raltegravir or elvitegravir, versus 1 % for dolutegravir. One primary mutation was observed (F121Y) in a patient sample from 2012 leading to 5-10-fold reduced susceptibility to raltegravir and elvitegravir. Two patients carried the accessory mutations E138K and G140A, respectively, where both lie on the Q148 pathway. No temporal trend of IRAM prevalence was observed (p = 0.16). DISCUSSION Primary IRAM are still rarely found despite the increasing use of INSTI in Austria, but there is a potential for reduced susceptibility to these drugs in selected patients. Routine resistance testing seems prudent to avoid the consequences including accumulation of further mutations and therapeutic failure.
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Affiliation(s)
- A Zoufaly
- Department of Medicine IV, Kaiser Franz Josef Hospital, Kundratstrasse 3, 1100, Vienna, Austria.
| | - C Kraft
- Department of Medicine IV, Kaiser Franz Josef Hospital, Kundratstrasse 3, 1100, Vienna, Austria
| | - C Schmidbauer
- Department of Medicine IV, Kaiser Franz Josef Hospital, Kundratstrasse 3, 1100, Vienna, Austria
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Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation. J Clin Microbiol 2016; 54:1605-1615. [PMID: 27076656 DOI: 10.1128/jcm.00030-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/01/2016] [Indexed: 12/29/2022] Open
Abstract
Deep sequencing of plasma RNA or proviral DNA may be an interesting alternative to population sequencing for the detection of baseline transmitted HIV-1 drug resistance. Using a Roche 454 GS Junior HIV-1 prototype kit, we performed deep sequencing of the HIV-1 protease and reverse transcriptase genes on paired plasma and buffy coat samples from newly diagnosed HIV-1-positive individuals. Selection was based on the outcome of population sequencing and included 12 patients with either a revertant amino acid at codon 215 of the reverse transcriptase or a singleton resistance mutation, 4 patients with multiple resistance mutations, and 4 patients with wild-type virus. Deep sequencing of RNA and DNA detected 6 and 43 mutations, respectively, that were not identified by population sequencing. A subsequently performed hypermutation analysis, however, revealed hypermutation in 61.19% of 3,188 DNA reads with a resistance mutation. The removal of hypermutated reads dropped the number of additional mutations in DNA from 43 to 17. No hypermutation evidence was found in the RNA reads. Five of the 6 additional RNA mutations and all additional DNA mutations, after full exclusion of hypermutation bias, were observed in the 3 individuals with multiple resistance mutations detected by population sequencing. Despite focused selection of patients with T215 revertants or singleton mutations, deep sequencing failed to identify the resistant T215Y/F or M184V or any other resistance mutation, indicating that in most of these cases there is no hidden resistance and that the virus detected at diagnosis by population sequencing is the original infecting variant.
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31
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Kouyos RD, Günthard HF. Editorial Commentary: The Irreversibility of HIV Drug Resistance. Clin Infect Dis 2015; 61:837-9. [PMID: 25991467 PMCID: PMC4530727 DOI: 10.1093/cid/civ400] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/09/2015] [Indexed: 11/12/2022] Open
Affiliation(s)
- Roger D. Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich
- Institute of Medical Virology, University of Zurich, Switzerland
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