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Armenia D, Spagnuolo V, Bellocchi MC, Galli L, Duca L, Marchegiani G, Clemente T, Carioti L, Lolatto R, Calza L, Celesia BM, Cascio A, Francisci D, Saracino A, Torti C, Zazzi M, Castagna A, Santoro MM. Use of next-generation sequencing on HIV-1 DNA to assess archived resistance in highly treatment-experienced people with multidrug-resistant HIV under virological control: data from the PRESTIGIO Registry. J Antimicrob Chemother 2024:dkae236. [PMID: 39004997 DOI: 10.1093/jac/dkae236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND To clarify whether next-generation sequencing (NGS) can be useful for resistance assessment in virologically suppressed highly treatment-experienced (HTE) individuals with MDR HIV. METHODS Ninety-one participants from the PRESTIGIO Registry were included. NGS was performed on HIV-DNA at 1%, 5% and 20% cut-offs; major drug resistance mutations (DRMs) were evaluated and compared with those detected in historical plasma genotypic resistance testing (h-GRT). APOBEC editing was also characterized. RESULTS Participants had a complex and long treatment history [median 23 (IQR 21-25) years of ART exposure) and had been virologically suppressed since a median of 3 (IQR 2-5) years. Among all major DRMs detected by HIV-DNA NGS and/or h-GRT, 30% were exclusively found through NGS. The highest detection rate of historical major DRMs was reached with NGS set at 1%, but unusual substitutions and extensive APOBEC hypermutations suggest technical issues and poor clinical relevance in the 1%-5% interval. At NGS set at 5%, 67.2% of historical major DRMs were detected. The number of major DRMs detected exclusively by DNA-NGS as minority variants (frequency 5%-20%) was significantly higher in individuals who later experienced virological rebound compared with those who maintained virological control [median 2 (IQR 1-3) versus 1 (0-2), P = 0.030] and positively correlated with viraemia levels at rebound (rho = 0.474, P = 0.030). CONCLUSIONS In non-viraemic people with an MDR virus, HIV-1 DNA NGS set at 5% is an acceptable technical cut-off that might help to reveal mutations with a potential clinical relevance. Moreover, the number of minority resistance mutations additionally detected by NGS might be associated with loss of virological control.
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Affiliation(s)
- Daniele Armenia
- Departmental Faculty, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Vincenzo Spagnuolo
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
| | - Maria C Bellocchi
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Laura Galli
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
| | - Leonardo Duca
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Greta Marchegiani
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Tommaso Clemente
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Riccardo Lolatto
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
| | - Leonardo Calza
- Department of Medical and Surgical Sciences, Unit of Infectious Diseases, Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | | | - Antonio Cascio
- Infectious and Tropical Diseases Unit-Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Daniela Francisci
- Clinic of Infectious Diseases, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | | | - Carlo Torti
- Dipartimento di Scienze di Mediche e Chirurgiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Antonella Castagna
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Maria M Santoro
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
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Abdullahi A, Diaz AG, Fopoussi OM, Beloukas A, Defo VF, Kouanfack C, Torimiro J, Geretti AM. A detailed characterization of drug resistance during darunavir/ritonavir monotherapy highlights a high barrier to the emergence of resistance mutations in protease but identifies alternative pathways of resistance. J Antimicrob Chemother 2024; 79:339-348. [PMID: 38153241 PMCID: PMC10832591 DOI: 10.1093/jac/dkad386] [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: 12/29/2023] Open
Abstract
BACKGROUND Maintenance monotherapy with ritonavir-boosted darunavir has yielded variable outcomes and is not recommended. Trial samples offer valuable opportunities for detailed studies. We analysed samples from a 48 week trial in Cameroon to obtain a detailed characterization of drug resistance. METHODS Following failure of NNRTI-based therapy and virological suppression on PI-based therapy, participants were randomized to ritonavir-boosted darunavir (n = 81) or tenofovir disoproxil fumarate/lamivudine +ritonavir-boosted lopinavir (n = 39). At study entry, PBMC-derived HIV-1 DNA underwent bulk Protease and Reverse Transcriptase (RT) sequencing. At virological rebound (confirmed or last available HIV-1 RNA ≥ 60 copies/mL), plasma HIV-1 RNA underwent ultradeep Protease and RT sequencing and bulk Gag-Protease sequencing. The site-directed mutant T375A (p2/p7) was characterized phenotypically using a single-cycle assay. RESULTS NRTI and NNRTI resistance-associated mutations (RAMs) were detected in 52/90 (57.8%) and 53/90 (58.9%) HIV-1 DNA samples, respectively. Prevalence in rebound HIV-1 RNA (ritonavir-boosted darunavir, n = 21; ritonavir-boosted lopinavir, n = 2) was 9/23 (39.1%) and 10/23 (43.5%), respectively, with most RAMs detected at frequencies ≥15%. The resistance patterns of paired HIV-1 DNA and RNA sequences were partially consistent. No darunavir RAMs were found. Among eight participants experiencing virological rebound on ritonavir-boosted darunavir (n = 12 samples), all had Gag mutations associated with PI exposure, including T375N, T375A (p2/p7), K436R (p7/p1) and substitutions in p17, p24, p2 and p6. T375A conferred 10-fold darunavir resistance and increased replication capacity. CONCLUSIONS The study highlights the high resistance barrier of ritonavir-boosted darunavir while identifying alternative pathways of resistance through Gag substitutions. During virological suppression, resistance patterns in HIV-1 DNA reflect treatment history, but due to technical and biological considerations, cautious interpretation is warranted.
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Affiliation(s)
- Adam Abdullahi
- Takemi Program in International Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Ana Garcia Diaz
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK
| | - Olga Mafotsing Fopoussi
- Biomedical Sciences Department, University of West Attica, Athens, Greece
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention & Management (CIRCB), Yaoundé, Cameroon
| | - Apostolos Beloukas
- Biomedical Sciences Department, University of West Attica, Athens, Greece
- National AIDS Reference Centre of Southern Greece, School of Public Health, University of West Attica, Athens, Greece
| | - Victoire Fokom Defo
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention & Management (CIRCB), Yaoundé, Cameroon
- Department of HIV Medicine, Hôpital Central de Yaoundé, Ministry of Public Health, Yaoundé, Cameroon
| | - Charles Kouanfack
- Department of HIV Medicine, Hôpital Central de Yaoundé, Ministry of Public Health, Yaoundé, Cameroon
| | - Judith Torimiro
- Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention & Management (CIRCB), Yaoundé, Cameroon
| | - Anna Maria Geretti
- Department of Infectious Diseases, Fondazione PTV, University of Rome Tor Vergata, Rome, Italy
- Department of Infection, North Middlesex University Hospital, London, UK
- School of Immunity and Microbial Sciences, King’s College London, London, UK
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Armenia D, Gagliardini R, Alteri C, Svicher V, Cento V, Borghi V, Vergori A, Cicalini S, Forbici F, Fabeni L, Bertoli A, Brugneti M, Gennari W, Malagnino V, Andreoni M, Mussini C, Antinori A, Perno CF, Santoro MM, Ceccherini-Silberstein F. Temporal trend of drug-resistance and APOBEC editing in PBMC genotypic resistance tests from HIV-1 infected virologically suppressed individuals. J Clin Virol 2023; 168:105551. [PMID: 37573167 DOI: 10.1016/j.jcv.2023.105551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND We aimed at evaluating the temporal trend of drug-resistance and APOBEC editing from HIV-DNA genotypic resistance tests (GRT) in virologically suppressed individuals. MATERIAL AND METHODS Major resistance mutations (MRM), genotypic susceptibility score (GSS) for the current regimen and APOBEC-related mutations (APO-M) were evaluated. Potential changes in trends of MRM and APO-M over-time were assessed and predictors of MRM detection or sub-optimal GSS (GSS<2) at HIV-DNA-GRT were estimated through logistic regression analyses. RESULTS Among the 1126 individuals included, 396 (35.2%) harboured at least one MRM (23.4% to NRTI, 18.8% to NNRTI, 7.7% to PI and 1.4% to INSTI [N=724]); 132 (12.3%) individuals showed a GSS <2. APO-M and stop codons were found in 229 (20.3%) and 105 (9.3%) individuals, respectively. APO-DRMs were found in 16.8% of individuals and were more likely observed in those individuals with stop codons (40.0%) compared to those without (14.4%, P<0.001). From 2010 to 2021 no significant changes of resistance or APO-M were found. Positive predictors of MRM detection at HIV-DNA GRT were drug abuse, subtype B infection, and a prolonged and complex treatment history. Perinatal infection and having at least 2 stop codons were associated with a current suboptimal regimen. CONCLUSIONS In virologically suppressed individuals, resistance in HIV-DNA and the extent of APOBEC editing were generally stable in the last decade. A careful evaluation of APOBEC editing might be helpful to improve the reliability of HIV-DNA GRT. Further investigations are required to understand how to apply the estimation of APOBEC editing in refining genotypic evaluation.
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Affiliation(s)
- D Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - R Gagliardini
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - C Alteri
- University of Milan, Milan, Italy
| | - V Svicher
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - V Cento
- Humanitas Research Hospital, IRCCS, Milan, Italy
| | - V Borghi
- University of Modena and Reggio Emilia, Modena, Italy
| | - A Vergori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - S Cicalini
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - F Forbici
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - L Fabeni
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - A Bertoli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy; Polyclinic of Rome "Tor Vergata", Rome, Italy
| | - M Brugneti
- Polyclinic of Rome "Tor Vergata", Rome, Italy
| | - W Gennari
- University of Modena and Reggio Emilia, Modena, Italy
| | - V Malagnino
- Polyclinic of Rome "Tor Vergata", Rome, Italy
| | - M Andreoni
- Polyclinic of Rome "Tor Vergata", Rome, Italy
| | - C Mussini
- University of Modena and Reggio Emilia, Modena, Italy
| | - A Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - C F Perno
- Bambino Gesù Children's Hospital, Rome, Italy
| | - M M Santoro
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
| | - F Ceccherini-Silberstein
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
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Jaha B, Schenkel CD, Jörimann L, Huber M, Zaheri M, Neumann K, Leemann C, Calmy A, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ. Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018. J Antimicrob Chemother 2023; 78:2323-2334. [PMID: 37545164 PMCID: PMC10477134 DOI: 10.1093/jac/dkad240] [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: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Genotypic resistance testing (GRT) is routinely performed upon diagnosis of HIV-1 infection or during virological failure using plasma viral RNA. An alternative source for GRT could be cellular HIV-1 DNA. OBJECTIVES A substantial number of participants in the Swiss HIV Cohort Study (SHCS) never received GRT. We applied a method that enables access to the near full-length proviral HIV-1 genome without requiring detectable viraemia. METHODS Nine hundred and sixty-two PBMC specimens were received. Our two-step nested PCR protocol was applied to generate two overlapping long-range amplicons of the HIV-1 genome, sequenced by next-generation sequencing (NGS) and analysed by MinVar, a pipeline to detect drug resistance mutations (DRMs). RESULTS Six hundred and eighty-one (70.8%) of the samples were successfully amplified, sequenced and analysed by MinVar. Only partial information of the pol gene was contained in 82/681 (12%), probably due to naturally occurring deletions in the proviral sequence. All common HIV-1 subtypes were successfully sequenced. We detected at least one major DRM at high frequency (≥15%) in 331/599 (55.3%) individuals. Excluding APOBEC-signature (G-to-A mutation) DRMs, 145/599 (24.2%) individuals carried at least one major DRM. RT-inhibitor DRMs were most prevalent. The experienced time on ART was significantly longer in DRM carriers (P = 0.001) independent of inclusion or exclusion of APOBEC-signature DRMs. CONCLUSIONS We successfully applied a reliable and efficient method to analyse near full-length HIV-1 proviral DNA and investigated DRMs in individuals with undetectable or low viraemia. Additionally, our data underscore the need for new computational tools to exclude APOBEC-related hypermutated NGS sequence reads for reporting DRMs.
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Affiliation(s)
- Bashkim Jaha
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Corinne D Schenkel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Lisa Jörimann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Christine Leemann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
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Santoro MM, Armenia D, Teyssou E, Santos JR, Charpentier C, Lambert-Niclot S, Antinori A, Katlama C, Descamps D, Perno CF, Calvez V, Paredes R, Ceccherini-Silberstein F, Marcelin AG. Virological efficacy of switch to DTG plus 3TC in a retrospective observational cohort of suppressed HIV-1 patients with or without past M184V: the LAMRES study. J Glob Antimicrob Resist 2022; 31:52-62. [PMID: 35948240 DOI: 10.1016/j.jgar.2022.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES The aim of this study was to assess the efficacy of dolutegravir plus lamivudine (DTG+3TC) in a large set of virologically suppressed HIV-1 infected individuals with or without past M184V mutation. METHODS This observational study included individuals who switched to DTG+3TC with ≥1 genotype before switch. Survival analysis was used to evaluate the role of past M184V on virological rebound (VR) or blips after DTG+3TC switch. RESULTS A total of 712 individuals followed in several clinical centres in France, Italy and Spain were analysed. Past M184V was present in 60 (8.4%) individuals. By 3 years after switch, the overall probability of VR and blips was 6.7% and 6.9%, respectively, without any statistical significance according to the presence/absence of past M184V. A significantly higher probability of VR was found in individuals harbouring M184V before DTG+3TC with a duration of virological suppression (Ts) ≤.3.5 years compared to others (M184V+Ts ≤.3.5 years: 22.7%; M184M+Ts ≤.3.5 years: 9.0%; M184V+Ts >3.5 years: 7.8%; M184M+Ts >3.5 years: 4.9%; P = 0.007). This finding was not confirmed in multivariable models adjusting for behavioural and demographic variables. Genotypic resistance test after VR under DTG+3TC was available for 8/39 individuals; one poorly adherent individual developed M184V. No resistance to INIs was found. CONCLUSION In this retrospective observational study, the probability of VR and blips in patients switching to DTG+3TC was very low after 3 years of treatment regardless M184V. The effect of a short duration of previous virological suppression in individuals with M184V remains troubling and needs ad hoc clinical trials to be confirmed.
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Affiliation(s)
| | - Daniele Armenia
- Saint Camillus International University of Health Sciences, Rome, Italy
| | - Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - José Ramón Santos
- Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Charlotte Charpentier
- Service de Virologie, Université de Paris, INSERM, IAME, Hôpital Bichat-Claude Bernard, Paris, France
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Universitaire Saint Antoine, laboratoire de virologie, Paris, France
| | - Andrea Antinori
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases 'L. Spallanzani', IRCCS, Rome, Italy
| | - Christine Katlama
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - Diane Descamps
- Service de Virologie, Université de Paris, INSERM, IAME, Hôpital Bichat-Claude Bernard, Paris, France
| | - Carlo Federico Perno
- Multimodal Laboratory Research Department, Children Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - Roger Paredes
- Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | - Anne Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1738-1740. [DOI: 10.1093/jac/dkac082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/18/2022] [Indexed: 11/14/2022] Open
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Armenia D, Santoro MM, Bellocchi MC, Carioti L, Galli L, Galli A, Scutari R, Salsi E, Mussini C, Sterrantino G, Calza L, Rossetti B, Zazzi M, Castagna A. Viral resistance burden and APOBEC editing correlate with virological response in heavily treatment-experienced people living with multi-drug resistant HIV. Int J Antimicrob Agents 2021; 59:106492. [PMID: 34871747 DOI: 10.1016/j.ijantimicag.2021.106492] [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] [Received: 04/09/2021] [Revised: 09/15/2021] [Accepted: 11/24/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND The impact of drug resistance mutational load and APOBEC editing in heavily treatment-experienced (HTE) people living with multidrug-resistant HIV has not been investigated. MATERIAL AND METHODS This study explored the HIV-DNA and HIV-RNA mutational load of drug resistance and APOBEC-related mutations through next-generation sequencing (NGS, Illumina MiSeq) in 20 failing HTE participants enrolled in the PRESTIGIO registry. RESULTS The patients showed high levels of both HIV-DNA (4.5 [4.0-5.2] log10 copies/106 T-CD4+ cell) and HIV-RNA (4.5 [4.1-5.0] log10 copies/mL) with complex resistance patterns in both compartments. Among the 255 drug-resistant mutations found, 66.3% were concordantly detected in both HIV-DNA and HIV-RNA; 71.3% of mutations were already present in historical Sanger genotypes. At an intra-patient frequency > 5%, a considerable proportion of mutations detected through DNA-NGS were found in historical genotypes but not through RNA-NGS, and few patients had APOBEC-related mutations. Of 14 patients who switched therapy, the five who failed treatment had DNA resistance with higher intra-patient frequency and higher DNA/RNA mutational load in a context of tendentially less pronounced APOBEC editing compared with those who responded. CONCLUSIONS Using NGS in HIV-DNA and HIV-RNA together with APOBEC editing evaluation might help to identify HTE individuals with MDR who are more prone to experience virological failure.
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Affiliation(s)
- Daniele Armenia
- Saint Camillus International University of Health Sciences, Rome, Italy; Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Luca Carioti
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Laura Galli
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy
| | - Andrea Galli
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy
| | - Rossana Scutari
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Gaetana Sterrantino
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | | | | | - Antonella Castagna
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy; Clinic of Infectious Diseases, Vita-Salute San Raffaele University, Milan, Italy
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Delaugerre C, Nere ML, Eymard-Duvernay S, Armero A, Ciaffi L, Koulla-Shiro S, Sawadogo A, Ngom Gueye NF, Ndour CT, Mpoudi Ngolle M, Amara A, Chaix ML, Reynes J. Deep sequencing analysis of M184V/I mutation at the switch and at the time of virological failure of boosted protease inhibitor plus lamivudine or boosted protease inhibitor maintenance strategy (substudy of the ANRS-MOBIDIP trial). J Antimicrob Chemother 2021; 76:1286-1293. [PMID: 33624081 DOI: 10.1093/jac/dkab002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The ANRS12286/MOBIDIP trial showed that boosted protease inhibitor (bPI) plus lamivudine dual therapy was superior to bPI monotherapy as maintenance treatment in subjects with a history of M184V mutation. OBJECTIVES We aimed to deep analyse the detection of M184V/I variants at time of switch and at the time of virological failure (VF). METHODS Ultra-deep sequencing (UDS) was performed on proviral HIV-DNA at inclusion among 265 patients enrolled in the ANRS 12026/MOBIDIP trial, and on plasma from 31 patients experiencing VF. The proportion of M184V/I variants was described and the association between the M184V/I mutation at 1% of threshold and VF was explored with logistic regression models. RESULTS M184V and I mutations were detected in HIV-DNA for 173/252 (69%) and 31/252 (12%) of participants, respectively. Longer duration of first-line treatment, higher plasma viral load at first-line treatment failure and higher baseline HIV-DNA load were associated with the archived M184V. M184I mutation was always associated with a STOP codon, suggesting defective virus. The 48 week estimated probability of remaining free from VF was comparable with or without the M184V/I mutation for dual therapy. At failure, M184V and major PI mutations were detected in 1/17 and 5/15 patients in the bPI arm and in 2/2 and 0/3 in the bPI+lamivudine arm, respectively. CONCLUSIONS Using UDS evidenced that archiving of M184V in HIV-DNA is heterogeneous despite past historical M184V in 96% of cases. The antiviral efficacy of lamivudine-based dual therapy regimens is mainly due to the residual lamivudine activity.
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Affiliation(s)
- Constance Delaugerre
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM U944, University of Paris, Paris, France
| | - Marie-Laure Nere
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sabrina Eymard-Duvernay
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France
| | - Alix Armero
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laura Ciaffi
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France
| | - Sinata Koulla-Shiro
- Department of Infectious Diseases, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Adrien Sawadogo
- Day Care Center, University Hospital Souro Sanou, Bobo Dioulasso, Burkina Faso
| | | | | | | | - Ali Amara
- INSERM U944, University of Paris, Paris, France
| | - Marie-Laure Chaix
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM U944, University of Paris, Paris, France
| | - Jacques Reynes
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France.,Department of Infectious Diseases, Montpellier University Hospital, Montpellier, France
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9
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Dolutegravir Plus Lamivudine Two-Drug Regimen: Safety, Efficacy and Diagnostic Considerations for Its Use in Real-Life Clinical Practice-A Refined Approach in the COVID-19 Era. Diagnostics (Basel) 2021; 11:diagnostics11050809. [PMID: 33947009 PMCID: PMC8145545 DOI: 10.3390/diagnostics11050809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/17/2022] Open
Abstract
The diagnostic and therapeutic management of the Coronavirus Disease 2019 (COVID-19) pandemic in the HIV population brought some known criticalities (and opportunities) to the forefront, for both those who are facing their first therapeutic line today, and for those already well viro-suppressed. The clinical, socioeconomic, and psychological impact of the COVID-19 pandemic should not affect the long-term care of people living with HIV, which creates an urgent need to optimize the diagnostic and treatment approach to the first-line or switch regimens. The use of dolutegravir plus a lamivudine two-drug regimen is one of the most promising solutions to ease the management of HIV treatment in this difficult period. In this review, we report the most salient features related to the use of this regimen from real-life cohorts, meta-analyses, randomized clinical trials, and studies presented at international conferences up to March 2021. We focused on the diagnostic and clinical-management implications of its use in real life, and how these comply with the contingent historical situation. The issue of the timing and type of diagnostic procedures and the relevance of classical diagnostic tests (such as genotype for resistance detection) is also discussed. According to the currently available results, dolutegravir plus a lamivudine two-drug regimen represents an outstanding tool, whose expected advantages fulfill the current requirements for optimal daily care of our HIV patients.
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10
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Andreatta K, Willkom M, Martin R, Chang S, Wei L, Liu H, Liu YP, Graham H, Quirk E, Martin H, White KL. Switching to bictegravir/emtricitabine/tenofovir alafenamide maintained HIV-1 RNA suppression in participants with archived antiretroviral resistance including M184V/I. J Antimicrob Chemother 2020; 74:3555-3564. [PMID: 31430369 PMCID: PMC6857193 DOI: 10.1093/jac/dkz347] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/01/2019] [Accepted: 07/16/2019] [Indexed: 12/12/2022] Open
Abstract
Objectives Studies 1878 and 1844 demonstrated non-inferior efficacy of switching suppressed HIV-1-infected adults to bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) versus continuing boosted PI-based triple regimens or dolutegravir/abacavir/lamivudine (DTG/ABC/3TC). Here, detailed analyses of pre-existing resistance in the two BIC/FTC/TAF switch studies and efficacy at week 48 are described. Methods Pre-existing resistance was assessed from historical genotypes (documented resistance to study drugs was excluded) and by retrospective baseline proviral archive DNA genotyping from whole blood. Outcomes were based on HIV-1 RNA at week 48 with missing values imputed using the last on-treatment observation carried forward method. Results Cumulative pre-existing resistance data from historical and proviral genotypes were obtained for 95% (543/570) of participants who switched to BIC/FTC/TAF. Altogether, 40% (217/543) had one or more pre-existing primary resistance substitutions in protease, reverse transcriptase and/or integrase. Pre-switch NRTI resistance was detected in 16% (89/543) of BIC/FTC/TAF-treated participants, with M184V or M184I detected by proviral genotyping in 10% (54/543). At week 48, 98% (561/570) of all BIC/FTC/TAF-treated participants versus 98% (213/217) with pre-existing resistance and 96% (52/54) with archived M184V/I had HIV-1 RNA <50 copies/mL. No BIC/FTC/TAF-treated participants developed treatment-emergent resistance to study drugs. Conclusions Pre-existing resistance substitutions, notably M184V/I, were unexpectedly common among suppressed participants who switched to BIC/FTC/TAF. High rates of virological suppression were maintained in the overall study population and in those with pre-existing resistance, including M184V/I, for up to 48 weeks of BIC/FTC/TAF treatment with no resistance development. These results indicate that BIC/FTC/TAF is an effective treatment option for suppressed patients, including those with evidence of archived NRTI resistance.
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Affiliation(s)
- Kristen Andreatta
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Madeleine Willkom
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Ross Martin
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Silvia Chang
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Lilian Wei
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Hui Liu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Ya-Pei Liu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Hiba Graham
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Erin Quirk
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Hal Martin
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Kirsten L White
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
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11
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Quality Control of Next-Generation Sequencing-Based HIV-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework. Viruses 2020; 12:v12060645. [PMID: 32545906 PMCID: PMC7354600 DOI: 10.3390/v12060645] [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: 05/13/2020] [Revised: 05/29/2020] [Accepted: 06/11/2020] [Indexed: 01/24/2023] Open
Abstract
Next-generation sequencing (NGS) in HIV drug resistance (HIVDR) testing has the potential to improve both clinical and public health settings, however it challenges the normal operations of quality management systems to be more flexible due to its complexity, massive data generation, and rapidly evolving protocols. While guidelines for quality management in NGS data have previously been outlined, little guidance has been implemented for NGS-based HIVDR testing. This document summarizes quality control procedures for NGS-based HIVDR testing laboratories using a laboratory information systems (LIS) framework. Here, we focus in particular on the quality control measures applied on the final sequencing product aligned with the recommendations from the World Health Organization HIV Drug Resistance Laboratory Network.
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12
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Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences. PLoS One 2020; 15:e0225352. [PMID: 32102090 PMCID: PMC7043932 DOI: 10.1371/journal.pone.0225352] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/30/2020] [Indexed: 12/31/2022] Open
Abstract
Introduction At low mutation-detection thresholds, next generation sequencing (NGS) for HIV-1 genotypic resistance testing is susceptible to artifactual detection of mutations arising from PCR error and APOBEC-mediated G-to-A hypermutation. Methods We analyzed published HIV-1 pol Illumina NGS data to characterize the distribution of mutations at eight NGS mutation detection thresholds: 20%, 10%, 5%, 2%, 1%, 0.5%, 0.2%, and 0.1%. At each threshold, we determined proportions of amino acid mutations that were unusual (defined as having a prevalence <0.01% in HIV-1 group M sequences) or signature APOBEC mutations. Results Eight studies, containing 855 samples, in the NCBI Sequence Read Archive were analyzed. As detection thresholds were lowered, there was a progressive increase in the proportion of positions with usual and unusual mutations and in the proportion of all mutations that were unusual. The median proportion of positions with an unusual mutation increased gradually from 0% at the 20% threshold to 0.3% at the 1% threshold and then exponentially to 1.3% (0.5% threshold), 6.9% (0.2% threshold), and 23.2% (0.1% threshold). In two of three studies with available plasma HIV-1 RNA levels, the proportion of positions with unusual mutations was negatively associated with virus levels. Although the complete set of signature APOBEC mutations was much smaller than that of unusual mutations, the former outnumbered the latter in one-sixth of samples at the 0.5%, 1%, and 2% thresholds. Conclusions The marked increase in the proportion of positions with unusual mutations at thresholds below 1% and in samples with lower virus loads suggests that, at low thresholds, many unusual mutations are artifactual, reflecting PCR error or G-to-A hypermutation. Profiling the numbers of unusual and signature APOBEC pol mutations at different NGS mutation detection thresholds may be useful to avoid selecting a threshold that is too low and poses an unacceptable risk of identifying artifactual mutations.
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13
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Meybeck A, Alidjinou EK, Huleux T, Boucher A, Tetart M, Choisy P, Bocket L, Ajana F, Robineau O. Virological Outcome After Choice of Antiretroviral Regimen Guided by Proviral HIV-1 DNA Genotyping in a Real-Life Cohort of HIV-Infected Patients. AIDS Patient Care STDS 2020; 34:51-58. [PMID: 32049556 DOI: 10.1089/apc.2019.0198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Issues have been raised concerning clinical relevance of HIV-1 proviral DNA genotypic resistance test (DNA GRT). To assess impact of DNA GRT on choice of antiretroviral therapy (ART) and subsequent virological outcome, we retrospectively reviewed decision-making and viral load (VL) evolution following DNA GRT performed in our center between January 2012 and December 2017, except those prescribed within the framework of a clinical trial. A total of 304 DNA GRTs were included, 185 (62%) performed in a context of virological success. Only 34% of tests were followed by ART change, more frequently in situation of virological success (39% vs. 26%, p = 0.02). In this situation, ART change guided by DNA GRT led to VL >20 copies/mL after 6 months in 5% of cases. In multivariate analysis, higher HIV DNA quantification (p = 0.01) was associated with occurrence of viremia. A higher nadir of CD4 count (p = 0.04) and a longer time with VL <20 copies/mL (p = 0.04) were independently associated with a lower risk of viremia. In situation of low-level viremia, ART change guided by DNA GRT led to VL <20 copies/mL after 6 months in 52% of cases, while decision to maintain the same treatment led to VL <20 copies/mL in 74% of cases. In multivariate analysis, longer time with VL >20 copies/mL (p = 0.02) was associated with persistence of virological replication. In conclusion, in situation of virological success, use of DNA GRT in addition to analysis of historical RNA GRT to guide ART optimization appears safe. Its prescription framework in situation of low-level viremia deserves to be better defined.
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Affiliation(s)
- Agnès Meybeck
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | | | - Thomas Huleux
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Anne Boucher
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Macha Tetart
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Philippe Choisy
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Laurence Bocket
- Virology Department, Lille University Hospital, Lille, France
| | - Faiza Ajana
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Olivier Robineau
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
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14
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Zhang XL, Luo MT, Song JH, Pang W, Zheng YT. An Alu Element Insertion in Intron 1 Results in Aberrant Alternative Splicing of APOBEC3G Pre-mRNA in Northern Pig-Tailed Macaques ( Macaca leonina) That May Reduce APOBEC3G-Mediated Hypermutation Pressure on HIV-1. J Virol 2020; 94:e01722-19. [PMID: 31776266 PMCID: PMC6997765 DOI: 10.1128/jvi.01722-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/14/2019] [Indexed: 11/20/2022] Open
Abstract
APOBEC3 family members, particularly APOBEC3F and APOBEC3G, inhibit the replication and spread of various retroviruses by inducing hypermutation in newly synthesized viral DNA. Viral hypermutation by APOBEC3 is associated with viral evolution, viral transmission, and disease progression. In recent years, increasing attention has been paid to targeting APOBEC3G for AIDS therapy. Thus, a controllable model system using species such as macaques, which provide a relatively ideal in vivo system, is needed for the study of APOBEC3-related issues. To appropriately utilize this animal model for biomedical research, important differences between human and macaque APOBEC3s must be considered. In this study, we found that the ratio of APOBEC3G-mediated/APOBEC3-mediated HIV-1 hypermutation footprints was much lower in peripheral blood mononuclear cells (PBMCs) from northern pig-tailed macaques than in PBMCs from humans. Next, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and resulted from an Alu element insertion into macaque APOBEC3G gene intron 1. This alternative splicing pattern generating an aberrant APOBEC3G mRNA isoform may significantly dilute full-length APOBEC3G and reduce APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques, which was supported by the elimination of other possibilities accounting for this hypermutation difference between the two hosts.IMPORTANCE APOBEC3 family members, particularly APOBEC3F and APOBEC3G, are important cellular antiviral factors. Recently, more attention has been paid to targeting APOBEC3G for AIDS therapy. To appropriately utilize macaque animal models for the study of APOBEC3-related issues, it is important that the differences between human and macaque APOBEC3s are clarified. In this study, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and which may reduce the APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques (NPMs). Our work provides important information for the proper application of macaque animal models for APOBEC3-related issues in AIDS research and a better understanding of the biological functions of APOBEC3 proteins.
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Affiliation(s)
- Xiao-Liang Zhang
- 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, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Meng-Ting Luo
- 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, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jia-Hao Song
- 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, China
- Institute of Health Sciences, Anhui University, Hefei, Anhui, 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, 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, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
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15
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Inzaule SC, Hamers RL, Noguera-Julian M, Casadellà M, Parera M, Rinke de Wit TF, Paredes R. Primary resistance to integrase strand transfer inhibitors in patients infected with diverse HIV-1 subtypes in sub-Saharan Africa. J Antimicrob Chemother 2019; 73:1167-1172. [PMID: 29462322 DOI: 10.1093/jac/dky005] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023] Open
Abstract
Objectives To investigate the prevalence and patterns of major and accessory resistance mutations associated with integrase strand transfer inhibitors (INSTIs), across diverse HIV-1 subtypes in sub-Saharan Africa. Methods pol gene sequences were obtained using Illumina next-generation sequencing from 425 INSTI-naive HIV-infected adults from Kenya (21.2%), Nigeria (7.3%), South Africa (22.8%), Uganda (25.2%) and Zambia (23.5%). Drug resistance interpretation was based on the IAS 2017 mutation list and accessory mutations from Stanford HIVdb with resistance penalty scores of ≥10 to at least 1 INSTI. Resistance was further classified based on sensitivity thresholds of ≥20% (Sanger sequencing) and 1%-20% for low-frequency variants (next-generation sequencing). Results Of 425 genotypes, 48.7% were subtype C, 28.5% A, 10.1% D, 2.8% G and 9.9% were recombinants. Major INSTI resistance mutations were detected only at <20% threshold, at a prevalence of 2.4% (2.5% in subtype A, 2.4% C, 0% D, 8.3% G and 2.4% in recombinants) and included T66A/I (0.7%), E92G (0.5%), Y143C/S (0.7%), S147G (0.2%) and Q148R (0.5%). Accessory mutations occurred at a prevalence of 15.1% at the ≥20% threshold (23.1% in subtype A, 8.7% C, 11.6% D, 25% G and 23.8% in recombinants), and included L74I/M (10.4%), Q95K (0.5%), T97A (4%), E157Q (0.7%) and G163R/K (0.7%). Conclusions Major INSTI resistance mutations were rare and only occurred at low-level resistance detection thresholds. INSTI-based regimens are expected to be effective across the different major HIV-1 subtypes in the region.
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Affiliation(s)
- Seth C Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands.,Joep Lange Institute, Department of Global Health, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands
| | - Raph L Hamers
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands.,Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia, and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marc Noguera-Julian
- Infectious Diseases Unit & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500 Vic, Catalonia, Spain
| | - Maria Casadellà
- Infectious Diseases Unit & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - Mariona Parera
- Infectious Diseases Unit & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - Tobias F Rinke de Wit
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands.,Joep Lange Institute, Department of Global Health, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands
| | - Roger Paredes
- Infectious Diseases Unit & IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain.,Universitat de Vic-Universitat Central de Catalunya, C. Sagrada Família 7, 08500 Vic, Catalonia, Spain
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16
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Ikeda T, Molan AM, Jarvis MC, Carpenter MA, Salamango DJ, Brown WL, Harris RS. HIV-1 restriction by endogenous APOBEC3G in the myeloid cell line THP-1. J Gen Virol 2019; 100:1140-1152. [PMID: 31145054 DOI: 10.1099/jgv.0.001276] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
HIV-1 replication in CD4-positive T lymphocytes requires counteraction of multiple different innate antiviral mechanisms. Macrophage cells are also thought to provide a reservoir for HIV-1 replication but less is known in this cell type about virus restriction and counteraction mechanisms. Many studies have combined to demonstrate roles for APOBEC3D, APOBEC3F, APOBEC3G and APOBEC3H in HIV-1 restriction and mutation in CD4-positive T lymphocytes, whereas the APOBEC enzymes involved in HIV-1 restriction in macrophages have yet to be delineated fully. We show that multiple APOBEC3 genes including APOBEC3G are expressed in myeloid cell lines such as THP-1. Vif-deficient HIV-1 produced from THP-1 is less infectious than Vif-proficient virus, and proviral DNA resulting from such Vif-deficient infections shows strong G to A mutation biases in the dinucleotide motif preferred by APOBEC3G. Moreover, Vif mutant viruses with selective sensitivity to APOBEC3G show Vif null-like infectivity levels and similarly strong APOBEC3G-biased mutation spectra. Importantly, APOBEC3G-null THP-1 cells yield Vif-deficient particles with significantly improved infectivities and proviral DNA with background levels of G to A hypermutation. These studies combine to indicate that APOBEC3G is the main HIV-1 restricting APOBEC3 family member in THP-1 cells.
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Affiliation(s)
- Terumasa Ikeda
- 2 Institute for Molecular Virology, Minneapolis, MN 55455, USA.,3 Center for Genome Engineering, Minneapolis, MN 55455, USA.,5 Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA.,1 Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA.,4 Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amy M Molan
- 4 Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.,2 Institute for Molecular Virology, Minneapolis, MN 55455, USA.,3 Center for Genome Engineering, Minneapolis, MN 55455, USA.,1 Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA
| | - Matthew C Jarvis
- 3 Center for Genome Engineering, Minneapolis, MN 55455, USA.,1 Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA.,4 Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.,2 Institute for Molecular Virology, Minneapolis, MN 55455, USA
| | - Michael A Carpenter
- 3 Center for Genome Engineering, Minneapolis, MN 55455, USA.,1 Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA.,4 Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.,2 Institute for Molecular Virology, Minneapolis, MN 55455, USA.,5 Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel J Salamango
- 1 Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA.,4 Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.,2 Institute for Molecular Virology, Minneapolis, MN 55455, USA.,3 Center for Genome Engineering, Minneapolis, MN 55455, USA
| | - William L Brown
- 4 Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.,3 Center for Genome Engineering, Minneapolis, MN 55455, USA.,2 Institute for Molecular Virology, Minneapolis, MN 55455, USA.,1 Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA
| | - Reuben S Harris
- 3 Center for Genome Engineering, Minneapolis, MN 55455, USA.,1 Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN 55455, USA.,4 Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.,2 Institute for Molecular Virology, Minneapolis, MN 55455, USA.,5 Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
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17
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Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance. Heliyon 2019; 5:e01498. [PMID: 31025011 PMCID: PMC6475876 DOI: 10.1016/j.heliyon.2019.e01498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 04/05/2019] [Indexed: 01/04/2023] Open
Abstract
The APOBEC3 enzymes can induce mutagenesis of HIV-1 proviral DNA through the deamination of cytosine. HIV-1 overcomes this restriction through the viral protein Vif that induces APOBEC3 proteasomal degradation. Within this dynamic host-pathogen relationship, the APOBEC3 enzymes have been found to be beneficial, neutral, or detrimental to HIV-1 biology. Here, we assessed the ability of co-expressed APOBEC3F and APOBEC3G to induce HIV-1 resistance to antiviral drugs. We found that co-expression of APOBEC3F and APOBEC3G enabled partial resistance of APOBEC3F to Vif-mediated degradation with a corresponding increase in APOBEC3F-induced deaminations in the presence of Vif, in addition to APOBEC3G-induced deaminations. We recovered HIV-1 drug resistant variants resulting from APOBEC3-induced mutagenesis, but these variants were less able to replicate than drug resistant viruses derived from RT-induced mutations alone. The data support a model in which APOBEC3 enzymes cooperate to restrict HIV-1, promoting viral inactivation over evolution to drug resistance.
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18
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Gopalan BP, D'Souza RR, Rajnala N, Arumugam K, Dias M, Ranga U, Shet A. Viral evolution in the cell-associated HIV-1 DNA during early ART can lead to drug resistance and virological failure in children. J Med Virol 2019; 91:1036-1047. [PMID: 30695102 DOI: 10.1002/jmv.25413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/08/2019] [Accepted: 01/24/2019] [Indexed: 11/07/2022]
Abstract
Using cell-associated DNA and cell-free RNA of human immunodeficiency virus type-1 (HIV-1), we investigated the role of drug-resistant viral variants that emerged during early antiretroviral therapy (ART) in determining virological outcome. This case-control study compared virologic nonresponder children (two viral loads [VLs] ≥ 200 copies/mL within 2 years of ART) and responder children (two VLs < 200 copies/mL after six months of ART) infected with HIV-1 initiated on nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based ART. The partial reverse-transcriptase gene of HIV-1 in cell-associated DNA was genotyped using next-generation sequencing (NGS; Illumina; threshold 0.5%; at baseline and month six of ART) and in cell-free RNA (concurrently and at virological failure; VL > 1000 copies/mL at ≥ 12 months of ART) using the Sanger method. Among 30 nonresponders and 37 responders, baseline differences were insignificant while adherence, VL, and drug resistance mutations (DRMs) observed at month six differed significantly ( P ≥ 0.05). At month six, NGS estimated a higher number of DRMs compared with Sanger (50% vs 33%; P = 0.001). Among the nonresponders carrying a resistant virus (86.6%) at virological failure, 26% harbored clinically relevant low-frequency DRMs in the cell-associated DNA at month six (0.5%-20%; K103N, G190A, Y181C, and M184I). Plasma VL of > 3 log 10 copies/mL (AOR, 30.4; 95% CI, 3.3-281; P = 0.003) and treatment-relevant DRMs detected in the cell-associated DNA at month six (AOR, 24.2; 95% CI, 2.6-221; P = 0.005) were independently associated with increased risk for early virological failure. Our findings suggest that treatment-relevant DRMs acquired in cell-associated DNA during the first six months of ART can predict virological failure in children initiated on NNRTI-based ART.
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Affiliation(s)
- Bindu Parachalil Gopalan
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,School of Integrative Health Sciences, University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Reena R D'Souza
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Niharika Rajnala
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Karthika Arumugam
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Udaykumar Ranga
- Molecular Biology and Genetics Unit, HIV/AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Anita Shet
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India.,International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Silver N, Paynter M, McAllister G, Atchley M, Sayir C, Short J, Winner D, Alouani DJ, Sharkey FH, Bergefall K, Templeton K, Carrington D, Quiñones-Mateu ME. Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay. AIDS Res Ther 2018; 15:18. [PMID: 30409215 PMCID: PMC6223033 DOI: 10.1186/s12981-018-0206-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The widespread global access to antiretroviral drugs has led to considerable reductions in morbidity and mortality but, unfortunately, the risk of virologic failure increases with the emergence, and potential transmission, of drug resistant viruses. Detecting and quantifying HIV-1 drug resistance has therefore become the standard of care when designing new antiretroviral regimens. The sensitivity of Sanger sequencing-based HIV-1 genotypic assays is limited by its inability to identify minority members of the quasispecies, i.e., it only detects variants present above ~ 20% of the viral population, thus, failing to detect minority variants below this threshold. It is clear that deep sequencing-based HIV-1 genotyping assays are an important step change towards accurately monitoring HIV-infected individuals. METHODS We implemented and verified a clinically validated HIV-1 genotyping assay based on deep sequencing (DEEPGEN™) in two clinical laboratories in the United Kingdom: St. George's University Hospitals Healthcare NHS Foundation Trust (London) and at NHS Lothian (Edinburgh), to characterize minority HIV-1 variants in 109 plasma samples from ART-naïve or -experienced individuals. RESULTS Although subtype B HIV-1 strains were highly prevalent (44%, 48/109), most individuals were infected with non-B subtype viruses (i.e., A1, A2, C, D, F1, G, CRF02_AG, and CRF01_AE). DEEPGEN™ was able to accurately detect drug resistance-associated mutations not identified using standard Sanger sequencing-based tests, which correlated significantly with patient's antiretroviral treatment histories. A higher proportion of minority PI-, NRTI-, and NNRTI-resistance mutations was detected in NHS Lothian patients compared to individuals from St. George's, mainly M46I/L and I50 V (associated with PIs), D67 N, K65R, L74I, M184 V/I, and K219Q (NRTIs), and L100I (NNRTIs). Interestingly, we observed an inverse correlation between intra-patient HIV-1 diversity and CD4+ T cell counts in the NHS Lothian patients. CONCLUSIONS This is the first study evaluating the transition, training, and implementation of DEEPGEN™ between three clinical laboratories in two different countries. More importantly, we were able to characterize the HIV-1 drug resistance profile (including minority variants), coreceptor tropism, subtyping, and intra-patient viral diversity in patients from the United Kingdom, providing a rigorous foundation for basing clinical decisions on highly sensitive and cost-effective deep sequencing-based HIV-1 genotyping assays in the country.
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Ji H, Enns E, Brumme CJ, Parkin N, Howison M, Lee ER, Capina R, Marinier E, Avila‐Rios S, Sandstrom P, Van Domselaar G, Harrigan R, Paredes R, Kantor R, Noguera‐Julian M. Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus. J Int AIDS Soc 2018; 21:e25193. [PMID: 30350345 PMCID: PMC6198166 DOI: 10.1002/jia2.25193] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/26/2018] [Indexed: 11/14/2022] Open
Abstract
INTRODUCTION Next-generation sequencing (NGS) has several advantages over conventional Sanger sequencing for HIV drug resistance (HIVDR) genotyping, including detection and quantitation of low-abundance variants bearing drug resistance mutations (DRMs). However, the high HIV genomic diversity, unprecedented large volume of data, complexity of analysis and potential for error pose significant challenges for data processing. Several NGS analysis pipelines have been developed and used in HIVDR research; however, the absence of uniformity in data processing strategies results in lack of consistency and comparability of outputs from different pipelines. To fill this gap, an international symposium on bioinformatic strategies for NGS-based HIVDR testing was held in February 2018 in Winnipeg, Canada, convening laboratory scientists, bioinformaticians and clinicians involved in four recently developed, publicly available NGS HIVDR pipelines. The goal of this symposium was to establish a consensus on effective bioinformatic strategies for NGS data management and its use for HIVDR reporting. DISCUSSION Essential functionalities of an NGS HIVDR pipeline were divided into five analytic blocks: (1) NGS read quality control (QC)/quality assurance (QA); (2) NGS read alignment and reference mapping; (3) HIV variant calling and variant QC; (4) NGS HIVDR reporting; and (5) extended data applications and additional considerations for data management. The consensuses reached among the participants on all major aspects of these blocks are summarized here. They encompass not only recommended data management and analysis strategies, but also detailed bioinformatic approaches that help ensure accuracy of the derived HIVDR analysis outputs for both research and potential clinical use. CONCLUSIONS While NGS is being adopted more broadly in HIVDR testing laboratories, data processing is often a bottleneck hindering its generalized application. The proposed standardization of NGS read QC/QA, read alignment and reference mapping, variant calling and QC, HIVDR reporting and relevant data management strategies in this "Winnipeg Consensus" may serve as a starting guideline for NGS HIVDR data processing that informs the refinement of existing pipelines and those yet to be developed. Moreover, the bioinformatic strategies presented here may apply more broadly to NGS data analysis of microbes harbouring significant genomic diversity.
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Affiliation(s)
- Hezhao Ji
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
| | - Eric Enns
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | | | | | - Mark Howison
- Watson Institute for International and Public AffairsBrown UniversityProvidenceRIUSA
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
| | - Rupert Capina
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
| | - Eric Marinier
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | - Santiago Avila‐Rios
- Centre for Research in Infectious DiseasesNational Institute of Respiratory DiseasesMexico CityMexico
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research CentrePublic Health Agency of CanadaWinnipegMBCanada
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
| | - Gary Van Domselaar
- Department of Medical Microbiology and Infectious DiseasesUniversity of ManitobaWinnipegMBCanada
- Bioinformatics Core at the National Microbiology LaboratoryPublic Health Agency of CanadaWinnipegMBCanada
| | - Richard Harrigan
- Division of AIDSDepartment of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Roger Paredes
- IrsiCaixa AIDS Research InstituteBadalonaCataloniaSpain
| | - Rami Kantor
- Division of Infectious DiseasesBrown University Alpert Medical SchoolProvidenceRIUSA
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Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing. J Clin Microbiol 2018; 56:JCM.00105-18. [PMID: 29618499 DOI: 10.1128/jcm.00105-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/20/2018] [Indexed: 11/20/2022] Open
Abstract
The ability of next-generation sequencing (NGS) technologies to detect low frequency HIV-1 drug resistance mutations (DRMs) not detected by dideoxynucleotide Sanger sequencing has potential advantages for improved patient outcomes. We compared the performance of an in vitro diagnostic (IVD) NGS assay, the Sentosa SQ HIV genotyping assay for HIV-1 genotypic resistance testing, with Sanger sequencing on 138 protease/reverse transcriptase (RT) and 39 integrase sequences. The NGS assay used a 5% threshold for reporting low-frequency variants. The level of complete plus partial nucleotide sequence concordance between Sanger sequencing and NGS was 99.9%. Among the 138 protease/RT sequences, a mean of 6.4 DRMs was identified by both Sanger and NGS, a mean of 0.5 DRM was detected by NGS alone, and a mean of 0.1 DRM was detected by Sanger sequencing alone. Among the 39 integrase sequences, a mean of 1.6 DRMs was detected by both Sanger sequencing and NGS and a mean of 0.15 DRM was detected by NGS alone. Compared with Sanger sequencing, NGS estimated higher levels of resistance to one or more antiretroviral drugs for 18.2% of protease/RT sequences and 5.1% of integrase sequences. There was little evidence for technical artifacts in the NGS sequences, but the G-to-A hypermutation was detected in three samples. In conclusion, the IVD NGS assay evaluated in this study was highly concordant with Sanger sequencing. At the 5% threshold for reporting minority variants, NGS appeared to attain a modestly increased sensitivity for detecting low-frequency DRMs without compromising sequence accuracy.
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The Perils of Multiplex Gastrointestinal Pathogen Panels: Pseudo-outbreaks of Salmonellae and Entamoeba histolytica in Immunocompromised Hosts. Infect Control Hosp Epidemiol 2018; 39:867-870. [PMID: 29743127 DOI: 10.1017/ice.2018.95] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Two distinct clusters of gastroenteritis due to Salmonellae and Entamoeba histolytica (EH) were identified using a multiplex gastrointestinal pathogen panel (GPP) at a tertiary-care cancer center. Despite temporo-spatial overlap, our investigation did not corroborate transmission or true infection. In clinical practice, GPPs may render false-positive results.Infect Control Hosp Epidemiol 2018;867-870.
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Borzooee F, Asgharpour M, Quinlan E, Grant MD, Larijani M. Viral subversion of APOBEC3s: Lessons for anti-tumor immunity and tumor immunotherapy. Int Rev Immunol 2018; 37:151-164. [PMID: 29211501 DOI: 10.1080/08830185.2017.1403596] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
APOBEC3s (A3) are endogenous DNA-editing enzymes that are expressed in immune cells including T lymphocytes. A3s target and mutate the genomes of retroviruses that infect immune tissues such as the human immunodeficiency virus (HIV). Therefore, A3s were classically defined as host anti-viral innate immune factors. In contrast, we and others showed that A3s can also benefit the virus by mediating escape from adaptive immune recognition and drugs. Crucially, whether A3-mediated mutations help or hinder HIV, is not up to chance. Rather, the virus has evolved multiple mechanisms to actively and maximally subvert A3 activity. More recently, extensive A3 mutational footprints in tumor genomes have been observed in many different cancers. This suggests a role for A3s in cancer initiation and progression. On the other hand, multiple anti-tumor activities of A3s have also come to light, including impact on immune checkpoint molecules and possible generation of tumor neo-antigens. Here, we review the studies that reshaped the view of A3s from anti-viral innate immune agents to host factors exploited by HIV to escape from immune recognition. Viruses and tumors share many attributes, including rapid evolution and adeptness at exploiting mutations. Given this parallel, we then discuss the pro- and anti-tumor roles of A3s, and suggest that lessons learned from studying A3s in the context of anti-viral immunity can be applied to tumor immunotherapy.
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Affiliation(s)
- Faezeh Borzooee
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mahdi Asgharpour
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Emma Quinlan
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Michael D Grant
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mani Larijani
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
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Darcissac E, Nacher M, Adriouch L, Berlioz-Arthaud A, Boukhari R, Couppié P, Djossou F, Donato D, El Guedj M, Lavergne A, Papot E, Pouliquen JF, Tanguy E, Vantilcke V, Lacoste V. HIV-1 Pol Gene Polymorphism and Antiretroviral Resistance Mutations in Treatment-Naive Adult Patients in French Guiana Between 2006 and 2012. AIDS Res Hum Retroviruses 2016; 32:801-11. [PMID: 27009561 DOI: 10.1089/aid.2016.0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Little information is available on the molecular epidemiologic profile of HIV-1 in French Guiana, the French department with the highest HIV/AIDS incidence. To follow the evolution of HIV-1 diversity, we carried out a molecular analysis of HIV-1 isolates from 305 treatment-naive patients between 2006 and 2012. Protease and reverse-transcriptase sequences were obtained for subtype characterization, polymorphism analysis, and identification of drug resistance mutations. Of 305 HIV-1 strains, 95.1% were subtype B viruses. The overall prevalence of transmitted drug-resistance mutations (TDRMs) was 4.6% (14/305), ranging from 1.9% to 7.1% depending on the year. This study shows a low level of HIV-1 genetic diversity and a moderate prevalence of TDRMs with no evidence of an increasing trend over the study period. Nevertheless, the strong genetic polymorphism observed on both genes may be of concern for long-term treatment of people living with HIV-1 and thus deserves continuous monitoring.
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Affiliation(s)
- Edith Darcissac
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Mathieu Nacher
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
- Centre d'Investigation Clinique—Epidemiologie Clinique (CIC-EC) Antilles Guyane, INSERM CIE 802, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Leila Adriouch
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Alain Berlioz-Arthaud
- Laboratoire de Biologie Médicale, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Rachida Boukhari
- Service de Biologie Médicale, Centre Hospitalier de l'Ouest Guyanais “Franck Joly,” Saint Laurent du Maroni, Guyane Française
| | - Pierre Couppié
- Service de Dermatologie, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Felix Djossou
- Unité des Maladies Infectieuses et Tropicales, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Damien Donato
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Myriam El Guedj
- Hôpital de Jour Adultes, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Emmanuelle Papot
- Service de Dermatologie, Centre Hospitalier de Cayenne “Andrée Rosemon,” Cayenne Cedex, Guyane Française
| | - Jean-François Pouliquen
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Edouard Tanguy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
| | - Vincent Vantilcke
- Hôpital de Jour Adultes, Centre Hospitalier de l'Ouest Guyanais “Franck Joly,” Saint Laurent du Maroni, Guyane Française
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne Cedex, Guyane Française
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Delviks-Frankenberry KA, Nikolaitchik OA, Burdick RC, Gorelick RJ, Keele BF, Hu WS, Pathak VK. Minimal Contribution of APOBEC3-Induced G-to-A Hypermutation to HIV-1 Recombination and Genetic Variation. PLoS Pathog 2016; 12:e1005646. [PMID: 27186986 PMCID: PMC4871359 DOI: 10.1371/journal.ppat.1005646] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/28/2016] [Indexed: 11/19/2022] Open
Abstract
Although the predominant effect of host restriction APOBEC3 proteins on HIV-1 infection is to block viral replication, they might inadvertently increase retroviral genetic variation by inducing G-to-A hypermutation. Numerous studies have disagreed on the contribution of hypermutation to viral genetic diversity and evolution. Confounding factors contributing to the debate include the extent of lethal (stop codon) and sublethal hypermutation induced by different APOBEC3 proteins, the inability to distinguish between G-to-A mutations induced by APOBEC3 proteins and error-prone viral replication, the potential impact of hypermutation on the frequency of retroviral recombination, and the extent to which viral recombination occurs in vivo, which can reassort mutations in hypermutated genomes. Here, we determined the effects of hypermutation on the HIV-1 recombination rate and its contribution to genetic variation through recombination to generate progeny genomes containing portions of hypermutated genomes without lethal mutations. We found that hypermutation did not significantly affect the rate of recombination, and recombination between hypermutated and wild-type genomes only increased the viral mutation rate by 3.9 × 10-5 mutations/bp/replication cycle in heterozygous virions, which is similar to the HIV-1 mutation rate. Since copackaging of hypermutated and wild-type genomes occurs very rarely in vivo, recombination between hypermutated and wild-type genomes does not significantly contribute to the genetic variation of replicating HIV-1. We also analyzed previously reported hypermutated sequences from infected patients and determined that the frequency of sublethal mutagenesis for A3G and A3F is negligible (4 × 10-21 and1 × 10-11, respectively) and its contribution to viral mutations is far below mutations generated during error-prone reverse transcription. Taken together, we conclude that the contribution of APOBEC3-induced hypermutation to HIV-1 genetic variation is substantially lower than that from mutations during error-prone replication.
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Affiliation(s)
- Krista A. Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Olga A. Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, Maryland, United States of America
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, Maryland, United States of America
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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