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Semengue ENJ, Armenia D, Inzaule S, Santoro MM, Dambaya B, Takou D, Teto G, Nka AD, Yagai B, Fabeni L, Chenwi C, Angong Beloumou G, Djupsa Ndjeyep SC, Colizzi V, Perno CF, Ceccherini-Silberstein F, Fokam J. Baseline integrase drug resistance mutations and conserved regions across HIV-1 clades in Cameroon: implications for transition to dolutegravir in resource-limited settings. J Antimicrob Chemother 2021; 76:1277-1285. [PMID: 33501504 DOI: 10.1093/jac/dkab004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Transition to dolutegravir-based regimens in resource-limited settings (RLS) requires prior understanding of HIV-1 integrase variants and conserved regions. Therefore, we evaluated integrase drug resistance mutations (DRMs) and conserved regions amongst integrase strand transfer inhibitor (INSTI)-naive patients harbouring diverse HIV-1 clades in Cameroon. METHODS A cross-sectional study was conducted amongst 918 INSTI-naive patients from Cameroon (89 ART-naive and 829 ART-experienced patients). HIV-1 sequences were interpreted regarding INSTI-DRMs using the Stanford HIVdb v8.9-1 and the 2019 IAS-USA list. Amino acid positions with <1% variability were considered as highly conserved. Subtyping was performed by phylogeny. RESULTS Overall prevalence (95% CI) of INSTI-DRMs was 0.8% (0.4-1.7), with 0.0% (0.0-4.0) amongst ART-naive versus 0.9% (0.5-1.9) amongst ART-experienced patients; P = 0.44. Accessory mutations (95% CI) were found in 33.8% (30.9-37.0), with 38.2% (28.1-49.1) amongst ART-naive versus 33.4% (30.4-36.7) amongst ART-experienced patients; P = 0.21. Of 288 HIV-1 integrase amino acid positions, 58.3% were highly conserved across subtypes in the following major regions: V75-G82, E85-P90, H114-G118, K127-W132, E138-G149, Q168-L172, T174-V180, W235-A239 and L241-D253. Wide genetic diversity was found (37 clades), including groups M (92.3%), N (1.4%), O (6.2%) and P (0.1%). Amongst group M, CRF02_AG was predominant (47.4%), with a significantly higher frequency (95% CI) of accessory mutations compared with non-AG [41.4% (36.8-46.0) versus 27.1% (23.3-31.2) respectively; P < 0.001]. CONCLUSIONS The low baseline of INSTI-DRMs (<1%) in Cameroon suggests effectiveness of dolutegravir-based regimens. In spite of high conservation across clades, the variability of accessory mutations between major circulating strains underscores the need for monitoring the selection of INSTI-DRMs while scaling up dolutegravir-based regimens in RLS.
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Affiliation(s)
- Ezechiel Ngoufack Jagni Semengue
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Daniele Armenia
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
| | - Seth Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | | | - Béatrice Dambaya
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Désiré Takou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Georges Teto
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Alex Durand Nka
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Bouba Yagai
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" - IRCCS, Rome, Italy
| | - Collins Chenwi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Grâce Angong Beloumou
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Sandrine Claire Djupsa Ndjeyep
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Vittorio Colizzi
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Evangelical University of Cameroon, Bandjoun, Cameroon
| | - Carlo-Federico Perno
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Bambino Gesu Children's Hospital, IRCCS, Rome, Italy
| | | | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon.,National HIV Drug Resistance Working Group, Ministry of Public Health, Cameroon.,Faculty of Health Sciences, University of Buea, Buea, Cameroon
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Mikasi SG, Isaacs D, Ikomey GM, Shimba H, Cloete R, Jacobs GB. Short Communication: HIV-1 Drug Resistance Mutation Analyses of Cameroon-Derived Integrase Sequences. AIDS Res Hum Retroviruses 2021; 37:54-56. [PMID: 32640829 DOI: 10.1089/aid.2020.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
HIV-1 integrase (IN) is a primary target for combination antiretroviral therapy. Only a limited number of studies report on the emergence of resistance-associated mutations (RAMs) in Cameroon. We observed that 1.4% of sequence from treatment-naive patients had IN strand transfer inhibitor (INSTI) RAMs. These mutations confer resistance to raltegravir and elvitegravir. We also observed that 10.1% of the sequences have INSTI accessory RAMs. HIV-1 CRF02_AG was the predominant subtype (44.7%) in this study analyses. The occurrence of INSTI RAMs among the sequences at baseline needs to be monitored carefully.
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Affiliation(s)
- Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Darren Isaacs
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - George Mondinde Ikomey
- Centre for the Study and Control of Communicable Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon
| | - Henerico Shimba
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - Ruben Cloete
- Centre for the Study and Control of Communicable Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Mboumba Bouassa RS, Mossoro-Kpinde CD, Gody JC, Veyer D, Péré H, Matta M, Robin L, Grésenguet G, Charpentier C, Bélec L. High predictive efficacy of integrase strand transfer inhibitors in perinatally HIV-1-infected African children in therapeutic failure of first- and second-line antiretroviral drug regimens recommended by the WHO. J Antimicrob Chemother 2020; 74:2030-2038. [PMID: 30891603 PMCID: PMC6587428 DOI: 10.1093/jac/dkz099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 12/23/2022] Open
Abstract
Objectives The predictive efficacy of integrase (IN) strand transfer inhibitors (INSTIs) was investigated in HIV-infected children born to HIV-infected mothers in Africa. Methods Plasma was collected at the Complexe Pédiatrique of Bangui, Central African Republic, from INSTI-naive children (n = 8) and adolescents (n = 10) in virological failure (viral load >1000 copies/mL) after 5 years of first- and/or second-line combination ART (cART). IN, reverse transcriptase (RT) and protease (P) genes were genotyped and drug resistance mutations (DRMs) to INSTIs, NRTIs, NNRTIs and PIs were interpreted using the Stanford algorithm. Results Successful IN, RT and P genotypes were obtained for 18, 13 and 15 children (median age 11 years, range 5–18; 8 were female), respectively. Two (2/18; 11.1%) viruses from children treated with a first-line regimen had INSTI DRMs at codon 138 (E138K and E138T), which is known to harbour major resistance mutations, and also had the accessory mutations L74I, G140K, G140R and G163R. The majority (16/18; 88.9%) of HIV-1 IN sequences demonstrated full susceptibility to all major INSTIs with a high frequency of natural polymorphic mutations. Most (12/15; 80%) genotyped viruses harboured at least one major DRM conferring resistance to at least one of the WHO-recommended antiretroviral drugs (NNRTIs, NRTIs and PIs) prescribed in first- and second-line regimens. Conclusions INSTIs could be proposed in first-line regimens in the majority of African children or adolescents and may constitute relevant therapeutic alternatives as second- and third-line cART regimens in HIV-infected children and adolescents living in sub-Saharan Africa.
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Affiliation(s)
- Ralph-Sydney Mboumba Bouassa
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France.,Ecole Doctorale (ED562) Bio Sorbonne Paris Cité (BioSPC), Université Paris Descartes, Paris, France.,Ecole Doctorale Régionale en Infectiologie Tropicale, Franceville, Gabon
| | - Christian Diamant Mossoro-Kpinde
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, République Centrafricaine.,Faculté des Sciences de la Santé, Université de Bangui, Bangui, République Centrafricaine
| | - Jean-Chrysostome Gody
- Faculté des Sciences de la Santé, Université de Bangui, Bangui, République Centrafricaine.,Complexe Pédiatrique de Bangui, Bangui, République Centrafricaine
| | - David Veyer
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Hélène Péré
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Mathieu Matta
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Leman Robin
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Gérard Grésenguet
- Faculté des Sciences de la Santé, Université de Bangui, Bangui, République Centrafricaine
| | - Charlotte Charpentier
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, Paris, France
| | - Laurent Bélec
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Mikasi SG, Gichana JO, Van der Walt C, Brado D, Obasa AE, Njenda D, Messembe M, Lyonga E, Assoumou O, Cloete R, Ikomey GM, Jacobs GB. HIV-1 Integrase Diversity and Resistance-Associated Mutations and Polymorphisms Among Integrase Strand Transfer Inhibitor-Naive HIV-1 Patients from Cameroon. AIDS Res Hum Retroviruses 2020; 36:450-455. [PMID: 31830799 DOI: 10.1089/aid.2019.0264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The World Health Organization (WHO) has put forth recommendations for the use of integrase (IN) strand transfer inhibitors (INSTIs) to be part of the first-line combination antiretroviral therapy regimen to treat HIV infections. The knowledge of pretreatment drug resistance against INSTIs is still scarce in resource-limited settings (RLS). We characterized the integrase gene to identify resistance-associated mutations (RAMs) in 56 INSTI-naive patient viral sequences from Cameroon. Study analysis used 37 sequences with fragment size ≥500 bp or of good quality .The majority of the sequences were identified as CRF02_AG 54.% (n = 20/37) and 45.9% (n = 17/37), other subtype viral sequences include (A, CRF36_cpx, F,G, and C). A total of 18.9% (n = 7/37) of the sequences had RAMs, with only 5.4% (n = 2/37) having major RAMs (Y143R/C/D/G and P145S), against INSTIs. Accessory RAMs were present in 8.1% (n = 3/37) of the sequences, of which one sequence contained solely E157Q, and another Q95K. One patient sequence had three accessory RAMs (G140E, E157Q, and G163R). We identified major RAMs to INSTIs, which might have a potential clinical impact to dolutegravir rollout in RLS, including Cameroon. This is the first study to describe RAMs among INSTI-naive people living with HIV-1 (PLHIV-1) infected with CRF02_AG and other subtypes in Cameroon.
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Affiliation(s)
- Sello Given Mikasi
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Josiah Otwoma Gichana
- Division of Oral Surgery, Department of Pathology Laboratory, University of Nairobi, Nairobi, Kenya
| | - Cheri Van der Walt
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dominik Brado
- Division of Virology, Faculty of Medicine, Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Adetayo Emmanuel Obasa
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Duncan Njenda
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, University of Stockholm, Stockholm, Sweden
| | - Martha Messembe
- Faculty of Medicine and Biomedical Sciences, Centre for the Study and Control of Communicable Diseases, University of Yaoundé I, Yaoundé, Cameroon
| | - Emilia Lyonga
- Faculty of Medicine and Biomedical Sciences, Centre for the Study and Control of Communicable Diseases, University of Yaoundé I, Yaoundé, Cameroon
| | - Okomo Assoumou
- Faculty of Medicine and Biomedical Sciences, Centre for the Study and Control of Communicable Diseases, University of Yaoundé I, Yaoundé, Cameroon
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - George Mondinde Ikomey
- Faculty of Medicine and Biomedical Sciences, Centre for the Study and Control of Communicable Diseases, University of Yaoundé I, Yaoundé, Cameroon
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Differences among HIV-1 subtypes in drug resistance against integrase inhibitors. INFECTION GENETICS AND EVOLUTION 2016; 46:286-291. [PMID: 27353185 DOI: 10.1016/j.meegid.2016.06.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 11/22/2022]
Abstract
Three integrase strand transfer inhibitors (INSTIs), raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG), have been approved by the FDA. Resistance against these three INSTIs have been reported and cross-resistance among them has been documented. Due to extensive and dynamic genetic diversity in different HIV-1 variants, significant differences in susceptibility to the INSTIs have been observed among HIV subtypes. This review summarizes what is known about this topic and discusses possible clinical implications.
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Mulu A, Maier M, Liebert UG. Lack of integrase inhibitors associated resistance mutations among HIV-1C isolates. J Transl Med 2015; 13:377. [PMID: 26626277 PMCID: PMC4665939 DOI: 10.1186/s12967-015-0734-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Although biochemical analysis of HIV-1 integrase enzyme suggested the use of integrase inhibitors (INIs) against HIV-1C, different viral subtypes may favor different mutational pathways potentially leading to varying levels of drug resistance. Thus, the aim of this study was to search for the occurrence and natural evolution of integrase polymorphisms and/or resistance mutations in HIV-1C Ethiopian clinical isolates prior to the introduction of INIs. Methods Plasma samples from chronically infected drug naïve patients (N = 45), of whom the PR and RT sequence was determined previously, were used to generate population based sequences of HIV-1 integrase. HIV-1 subtype was determined using the REGA HIV-1 subtyping tool. Resistance mutations were interpreted according to the Stanford HIV drug resistance database (http://hivdb.stanford.edu) and the updated International Antiviral Society (IAS)-USA mutation lists. Moreover, rates of polymorphisms in the current isolates were compared with South African and global HIV-1C isolates. Results All subjects were infected with HIV-1C concordant to the protease (PR) and reverse transcriptase (RT) regions. Neither major resistance-associated IN mutations (T66I/A/K, E92Q/G, T97A, Y143HCR, S147G, Q148H/R/K, and N155H) nor silent mutations known to change the genetic barrier were observed. Moreover, the DDE-catalytic motif (D64G/D116G/E152 K) and signature HHCC zinc-binding motifs at codon 12, 16, 40 and 43 were found to be highly conserved. However, compared to other South African subtype C isolates, the rate of polymorphism was variable at various positions. Conclusion Although the sample size is small, the findings suggest that this drug class could be effective in Ethiopia and other southern African countries where HIV-1C is predominantly circulating. The data will contribute to define the importance of integrase polymorphism and to improve resistance interpretation algorithms in HIV-1C isolates.
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Affiliation(s)
- Andargachew Mulu
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany. .,Department of Microbiology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
| | - Melanie Maier
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.
| | - Uwe Gerd Liebert
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.
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Llácer Delicado T, Torrecilla E, Holguín Á. Deep analysis of HIV-1 natural variability across HIV-1 variants at residues associated with integrase inhibitor (INI) resistance in INI-naive individuals. J Antimicrob Chemother 2015; 71:362-6. [PMID: 26546669 DOI: 10.1093/jac/dkv333] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/15/2015] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES We evaluated variant-associated variability at positions related to resistance to the integrase (IN) inhibitors (INIs) raltegravir, elvitegravir and dolutegravir using HIV-1 IN sequences from naive individuals retrieved from GenBank. METHODS We evaluated the frequency of major, secondary and rare amino acid changes associated with INI resistance (INI-R) in 6706 sequences from 3791 INI-naive individuals carrying a large panel of different HIV-1 variants retrieved from GenBank, including four groups: M (6663), O (24), N (15) and P (4). HIV-1 group M sequences included 4599 sequences from the nine group M subtypes and 2064 recombinants ascribed to 54 circulating recombinant forms (CRFs). RESULTS Primary INI-R mutations were rare in INI-naive participants and only present at a low rate in subtypes B, C and D and recombinants CRF01_AE and CRF14_BG, ranging from one to five per variant. Three secondary INI-R changes appeared with variable frequency in INI-naive individuals carrying specific HIV-1 variants: L74M in CRF43_02G (33.3%); T97A in group P (50%), J (33.3%), CRF18_cpx (20%) and F2 (11.5%); and G163RK in CRF44_BF (100%), CRF46_BF (66.7%), CRF17_BF (28.6%), F1 (21.7%), CRF12_BF (16.7%) and CRF29_BF (12.5%). Rare mutations were absent. CONCLUSIONS Natural variability in INI-R positions across HIV-1 variants should be studied as they may facilitate or delay the emergence of INI-R viruses.
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Affiliation(s)
- Teresa Llácer Delicado
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, Madrid, SpainInstituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, SpainCIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Esther Torrecilla
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, Madrid, SpainInstituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, SpainCIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, Madrid, SpainInstituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, SpainCIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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Doyle T, Dunn DT, Ceccherini-Silberstein F, De Mendoza C, Garcia F, Smit E, Fearnhill E, Marcelin AG, Martinez-Picado J, Kaiser R, Geretti AM. Integrase inhibitor (INI) genotypic resistance in treatment-naive and raltegravir-experienced patients infected with diverse HIV-1 clades. J Antimicrob Chemother 2015; 70:3080-6. [PMID: 26311843 PMCID: PMC4613743 DOI: 10.1093/jac/dkv243] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/14/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The aim of this study was to characterize the prevalence and patterns of genotypic integrase inhibitor (INI) resistance in relation to HIV-1 clade. METHODS The cohort comprised 533 INI-naive subjects and 255 raltegravir recipients with viraemia who underwent integrase sequencing in routine care across Europe, including 134/533 (25.1%) and 46/255 (18.0%), respectively, with non-B clades (A, C, D, F, G, CRF01, CRF02, other CRFs, complex). RESULTS No major INI resistance-associated mutations (RAMs) occurred in INI-naive subjects. Among raltegravir recipients with viraemia (median 3523 HIV-1 RNA copies/mL), 113/255 (44.3%) had one or more major INI RAMs, most commonly N155H (45/255, 17.6%), Q148H/R/K + G140S/A (35/255, 13.7%) and Y143R/C/H (12/255, 4.7%). In addition, four (1.6%) raltegravir recipients showed novel mutations at recognized resistance sites (E92A, S147I, N155D, N155Q) and novel mutations at other integrase positions that were statistically associated with raltegravir exposure (K159Q/R, I161L/M/T/V, E170A/G). Comparing subtype B with non-B clades, Q148H/R/K occurred in 42/209 (20.1%) versus 2/46 (4.3%) subjects (P = 0.009) and G140S/A occurred in 36/209 (17.2%) versus 1/46 (2.2%) subjects (P = 0.005). Intermediate- to high-level cross-resistance to twice-daily dolutegravir was predicted in 40/255 (15.7%) subjects, more commonly in subtype B versus non-B clades (39/209, 18.7% versus 1/46, 2.2%; P = 0.003). A glycine (G) to serine (S) substitution at integrase position 140 required one nucleotide change in subtype B and two nucleotide changes in all non-B clades. CONCLUSIONS No major INI resistance mutations occurred in INI-naive subjects. Reduced occurrence of Q148H/R/K + G140S/A was seen in non-B clades versus subtype B, and was explained by the higher genetic barrier to the G140S mutation observed in all non-B clades analysed.
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Affiliation(s)
- Tomas Doyle
- Department of Infectious Diseases, King's College London, London, UK
| | | | | | | | | | - Erasmus Smit
- Heart of England NHS Foundation Trust, Birmingham, UK
| | | | - Anne-Genevieve Marcelin
- AP-HP, Hôpital Pitié-Salpêtrière, INSERM-Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Paris, France
| | | | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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Falasca F, Montagna C, Maida P, Bucci M, Fantauzzi A, Mezzaroma I, Antonelli G, Turriziani O. Analysis of intracellular human immunodeficiency virus (HIV)-1 drug resistance mutations in multi-failed HIV-1-infected patients treated with a salvage regimen: 72-week follow-up. Clin Microbiol Infect 2013; 19:E318-21. [PMID: 23438096 DOI: 10.1111/1469-0691.12175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/28/2012] [Accepted: 01/25/2013] [Indexed: 11/29/2022]
Abstract
The human immunodeficiency virus (HIV) mutational archive of proviral DNA was monitored during a 72-week follow-up in 20 multidrug-experienced HIV-1-infected patients treated with a darunavir/ritonavir-based salvage therapy. At the beginning of the study, all patients harboured a number of intracellular drug resistance-associated mutations (RAMs) in peripheral blood mononuclear cells. In some patients, a significant fluctuation in the number of RAMs was observed during the observation period. However, all patients, notwithstanding the presence or the fluctuation of intracellular RAMs, showed a persistently undetectable viraemia. The data suggest that the archived resistant viral variants change during suppressive therapy, but that the variants are unable to re-emerge and to affect virological response.
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Affiliation(s)
- F Falasca
- Department of Molecular Medicine, Sapienza University, Rome, Italy
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Parczewski M, Bander D, Urbańska A, Boroń-Kaczmarska A. HIV-1 integrase resistance among antiretroviral treatment naive and experienced patients from Northwestern Poland. BMC Infect Dis 2012; 12:368. [PMID: 23259737 PMCID: PMC3547692 DOI: 10.1186/1471-2334-12-368] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 12/18/2012] [Indexed: 12/02/2022] Open
Abstract
Background HIV integrase inhibitor use is limited by low genetic barrier to resistance and possible cross-resistance among representatives of this class of antiretrovirals. The aim of this study was to analyse integrase sequence variability among antiretroviral treatment naive and experienced patients with no prior integrase inhibitor (InI) exposure and investigate development of the InI drug resistance mutations following the virologic failure of the raltegravir containing regimen. Methods Sequencing of HIV-1 integrase region from plasma samples of 80 integrase treatment naive patients and serial samples from 12 patients with observed virologic failure on raltegravir containing treatment whenever plasma vireamia exceeded >50 copies/ml was performed. Drug resistance mutations were called with Stanford DB database and grouped into major and minor variants. For subtyping bootstrapped phylogenetic analysis was used; Bayesian Monte Carlo Marcov Chain (MCMC) model was implemented to infer on the phylogenetic relationships between the serial sequences from patients failing on raltegravir. Results Majority of the integrase region sequences were classified as subtype B; the remaining ones being subtype D, C, G, as well as CRF01_AE , CRF02_AG and CRF13_cpx recombinants. No major integrase drug resistance mutations have been observed in InI-treatment naive patients. In 30 (38.5%) cases polymorphic variation with predominance of the E157Q mutation was observed. This mutation was more common among subtype B (26 cases, 54.2%) than non-B sequences (5 cases, 16.7%), p=0.00099, OR: 5.91 (95% CI:1.77-22.63)]. Other variants included L68V, L74IL, T97A, E138D, V151I, R263K. Among 12 (26.1%) raltegravir treated patients treatment failure was observed; major InI drug resistance mutations (G140S, Q148H and N155H, V151I, E92EQ, V151I, G163R) were noted in four of these cases (8.3% of the total InI-treated patients). Time to the development of drug resistance ranged from 2.6 to 16.3 months with mean increase of HIV viral load of 4.34 (95% CI:1.86-6.84) log HIV-RNA copies/ml at the time of emergence of the major mutations. Baseline polymorphisms, including E157Q were not associated with the virologic failure on raltegravir. Conclusions In InI treatment naive patients polymorphic integrase sequence variation was common, with no major resistance mutants. In the treatment failing patients selection of drug resistance occurred rapidly and followed the typical drug resistance pathways. Preexisting integrase polymorphisms were not associated with the treatment failure.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland.
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