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Papa F, Felici G, Franzetti M, Gandolfi A, Sinisgalli C. Impact of ART-induced viral suppression on the HIV epidemic in Italy. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2021; 37:183-211. [PMID: 31162541 DOI: 10.1093/imammb/dqz010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 04/04/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023]
Abstract
The present study aims to clarify the role of the fraction of patients under antiretroviral therapy (ART) achieving viral suppression (VS) (i.e. having plasma viral load below the detectability threshold) on the human immunodeficiency virus (HIV) epidemic in Italy. Based on the hypothesis that VS makes the virus untransmittable, we extend a previous model and we develop a time-varying ordinary differential equation model with immigration and treatment, where the naive and non-naive populations of infected are distinguished, and different compartments account for treated subjects virally suppressed and not suppressed. Moreover, naive and non-naive individuals with acquired immune deficiency syndrome (AIDS) are considered separately. Clinical data stored in the nationwide database Antiviral Response Cohort Analysis are used to reconstruct the history of the fraction of virally suppressed patients since highly active ART introduction, as well as to assess some model parameters. Other parameters are set according to the literature and the final model calibration is obtained by fitting epidemic data over the years 2003-2015. Predictions on the evolution of the HIV epidemic up to the end of 2035 are made assuming different future trends of the fraction of virally suppressed patients and different eligibility criteria for treatment. Increasing the VS fraction is found to reduce the incidence, the new cases of AIDS and the deaths from AIDS per year, especially in combination with early ART initiation. The asymptotic properties of a time-invariant formulation of the model are studied, and the existence and global asymptotic stability of a unique positive equilibrium are proved.
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Affiliation(s)
- Federico Papa
- Istituto di Analisi dei Sistemi ed Informatica 'A. Ruberti' - CNR, Via dei Taurini, Roma, Italy
| | - Giovanni Felici
- Istituto di Analisi dei Sistemi ed Informatica 'A. Ruberti' - CNR, Via dei Taurini, Roma, Italy
| | - Marco Franzetti
- Infectious Diseases Unit, 'A. Manzoni' Hospital, Via dell'Eremo, 9/11, Lecco, Italy
| | - Alberto Gandolfi
- Istituto di Analisi dei Sistemi ed Informatica 'A. Ruberti' - CNR, Via dei Taurini, Roma, Italy
| | - Carmela Sinisgalli
- Istituto di Analisi dei Sistemi ed Informatica 'A. Ruberti' - CNR, Via dei Taurini, Roma, Italy
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Nationwide Study of Drug Resistance Mutations in HIV-1 Infected Individuals under Antiretroviral Therapy in Brazil. Int J Mol Sci 2021; 22:ijms22105304. [PMID: 34069929 PMCID: PMC8157590 DOI: 10.3390/ijms22105304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/02/2022] Open
Abstract
The success of antiretroviral treatment (ART) is threatened by the emergence of drug resistance mutations (DRM). Since Brazil presents the largest number of people living with HIV (PLWH) in South America we aimed at understanding the dynamics of DRM in this country. We analyzed a total of 20,226 HIV-1 sequences collected from PLWH undergoing ART between 2008–2017. Results show a mild decline of DRM over the years but an increase of the K65R reverse transcriptase mutation from 2.23% to 12.11%. This increase gradually occurred following alterations in the ART regimens replacing zidovudine (AZT) with tenofovir (TDF). PLWH harboring the K65R had significantly higher viral loads than those without this mutation (p < 0.001). Among the two most prevalent HIV-1 subtypes (B and C) there was a significant (p < 0.001) association of K65R with subtype C (11.26%) when compared with subtype B (9.27%). Nonetheless, evidence for K65R transmission in Brazil was found both for C and B subtypes. Additionally, artificial neural network-based immunoinformatic predictions suggest that K65R could enhance viral recognition by HLA-B27 that has relatively low prevalence in the Brazilian population. Overall, the results suggest that tenofovir-based regimens need to be carefully monitored particularly in settings with subtype C and specific HLA profiles.
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Lombardi F, Giacomelli A, Armenia D, Lai A, Dusina A, Bezenchek A, Timelli L, Saladini F, Vichi F, Corsi P, Colao G, Bruzzone B, Gagliardini R, Callegaro A, Castagna A, Santoro MM. Prevalence and factors associated with HIV-1 multi-drug resistance over the past two decades in the Italian ARCA database. Int J Antimicrob Agents 2020; 57:106252. [PMID: 33259914 DOI: 10.1016/j.ijantimicag.2020.106252] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/30/2020] [Accepted: 11/22/2020] [Indexed: 12/27/2022]
Abstract
Despite successful antiretroviral therapy (ART), patients infected with human immunodeficiency virus (HIV) can develop multi-class drug resistance (MDR). This retrospective study aimed to explore the prevalence of HIV-1 drug resistance over the past two decades by focusing on HIV-MDR and its predictors. ART-experienced patients with HIV with results from at least one plasma genotypic resistance test (GRT) from 1998 to 2018, from the Antiviral Response Cohort Analysis database, were included in this study. The temporal trend of resistance to any drug class was evaluated by considering all GRTs. Prevalence and predictors of HIV-MDR were analysed by consideration of cumulative GRTs. Among 15 628 isolates from 6802 patients, resistance to at least one drug class decreased sharply from 1998 to 2010 (1998-2001: 78%; 2008-2010: 59%; P<0.001) and then remained relatively constant at approximately 50% from 2011 to 2018, with the proportion of isolates with HIV-MDR also stable (approximately 9%). By evaluating factors associated with cumulative HIV-MDR, the following factors were found to be associated with increased risk of HIV-MDR on multi-variate analysis: male gender; sexual and vertical transmission; number of previous protease inhibitors, nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and non-NRTIs; previous exposure to integrase strand transfer inhibitors, enfuvirtide and maraviroc; and co-infection with hepatitis B virus. In contrast, a nadir CD4 cell count ≥200 cells/mm3, starting first-line ART in 2008 or later and co-infection with hepatitis C virus were associated with lower risk of HIV-MDR. In conclusion, this study revealed that HIV-1 drug resistance has been stable since 2011 despite its dramatic decrease over the past two decades. HIV-MDR is still present, although at a lower rate, suggesting the need for continuous surveillance and accurate management of ART-experienced patients with HIV.
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Affiliation(s)
- Francesca Lombardi
- Università Cattolica del Sacro Cuore, Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Rome, Italy
| | - Andrea Giacomelli
- III Infectious Diseases Unit, ASST-FBF-Sacco, Milan, Italy; Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Daniele Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy; Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Alex Dusina
- Università Cattolica del Sacro Cuore, Dipartimento di Sicurezza e Bioetica Sezione Malattie Infettive, Rome, Italy
| | | | | | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Paola Corsi
- Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Grazia Colao
- Laboratory of Virology, Careggi Hospital, Florence, Italy
| | - Bianca Bruzzone
- Hygiene Unit, Ospedale Policlinico San Martino, Genoa, Italy
| | - Roberta Gagliardini
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | - Antonella Castagna
- Clinic of Infectious Diseases, Vita-Salute San Raffaele University, San Raffaele Scientific Institute, Milan, Italy
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Pingarilho M, Pimentel V, Diogo I, Fernandes S, Miranda M, Pineda-Pena A, Libin P, Theys K, O. Martins MR, Vandamme AM, Camacho R, Gomes P, Abecasis A. Increasing Prevalence of HIV-1 Transmitted Drug Resistance in Portugal: Implications for First Line Treatment Recommendations. Viruses 2020; 12:E1238. [PMID: 33143301 PMCID: PMC7693025 DOI: 10.3390/v12111238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Treatment for All recommendations have allowed access to antiretroviral (ARV) treatment for an increasing number of patients. This minimizes the transmission of infection but can potentiate the risk of transmitted (TDR) and acquired drug resistance (ADR). OBJECTIVE To study the trends of TDR and ADR in patients followed up in Portuguese hospitals between 2001 and 2017. METHODS In total, 11,911 patients of the Portuguese REGA database were included. TDR was defined as the presence of one or more surveillance drug resistance mutation according to the WHO surveillance list. Genotypic resistance to ARV was evaluated with Stanford HIVdb v7.0. Patterns of TDR, ADR and the prevalence of mutations over time were analyzed using logistic regression. RESULTS AND DISCUSSION The prevalence of TDR increased from 7.9% in 2003 to 13.1% in 2017 (p < 0.001). This was due to a significant increase in both resistance to nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleotide reverse transcriptase inhibitors (NNRTIs), from 5.6% to 6.7% (p = 0.002) and 2.9% to 8.9% (p < 0.001), respectively. TDR was associated with infection with subtype B, and with lower viral load levels (p < 0.05). The prevalence of ADR declined from 86.6% in 2001 to 51.0% in 2017 (p < 0.001), caused by decreasing drug resistance to all antiretroviral (ARV) classes (p < 0.001). CONCLUSIONS While ADR has been decreasing since 2001, TDR has been increasing, reaching a value of 13.1% by the end of 2017. It is urgently necessary to develop public health programs to monitor the levels and patterns of TDR in newly diagnosed patients.
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Affiliation(s)
- Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Isabel Diogo
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
| | - Sandra Fernandes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
| | - Mafalda Miranda
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Andrea Pineda-Pena
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Pieter Libin
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
- Artificial Intelligence Lab, Department of computer science, Vrije Universiteit Brussel, 1000 Brussels, Belgium
- Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, 3500 Hasselt, Belgium
| | - Kristof Theys
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - M. Rosário O. Martins
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
| | - Anne-Mieke Vandamme
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - Ricardo Camacho
- Department of Microbiology and Immunology, KU Leuven, Clinical and Epidemiological Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium; (P.L.); (K.T.); (R.C.)
| | - Perpétua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), 1349-019 Lisbon, Portugal; (I.D.); (S.F.); (P.G.)
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, 2829-511 Caparica, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), 1349–028 Lisbon, Portugal; (V.P.); (M.M.); (A.P.-P.); (M.R.O.M.); (A.-M.V.); (A.A.)
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Lai A, Franzetti M, Bergna A, Saladini F, Bruzzone B, Di Giambenedetto S, Di Biagio A, Lo Caputo S, Santoro MM, Maggiolo F, Parisi SG, Rusconi S, Gianotti N, Balotta C. Marked decrease in acquired resistance to antiretrovirals in latest years in Italy. Clin Microbiol Infect 2020; 27:1038.e1-1038.e6. [PMID: 32979570 DOI: 10.1016/j.cmi.2020.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate acquired drug resistance in Italy in the 2009-2018 period. METHODS We analysed 3094 patients from the Italian ARCA database who had failed antiretroviral treatment and who had received a genotypic test after 6 months of treatment. Drug resistance mutations were identified using International AIDS Society (IAS)-USA tables and the Stanford HIVdb algorithm. The global burden of acquired resistance was calculated among all subjects with antiretroviral failure. Time trends and correlates of resistance were analysed using standard statistical tests. RESULTS Patients of non-European origin and non-B subtypes increased significantly from 11.5% (103/896) to 19.2% (33/172) and from 13.1% (141/1079) to 23.8% (53/223), respectively, over time. Overall, 14.5% (448/3094), 12.1% (374/3094) and 37.8% (1169/3094) of patients failed first, second and later lines, respectively. According to both IAS and HIVdb, in the study period resistance to any class, nucleoside reverse inhibitor, non-nucleoside reverse inhibitor, and protease inhibitors (PIs) declined significantly. Integrase strand transfer inhibitor (INSTI) resistance declined significantly from 31% (36/116) to 20.8% (41/197) according to HIVdb but not to IAS. Divergent data were highlighted regarding the proportion of non-European patients carrying any, PI and INSTI resistance using IAS tables compared with the Stanford HIVdb algorithm, as the former failed to detect a decrease in resistance while the latter indicates a reduction of 1.6-, 5- and 1.8-fold resistance for such drug classes. In the multivariate analysis, the risk of resistance increased in patients with a larger number of treatment lines and higher viraemia and decreased in those starting therapy in the last biennium of the study. DISCUSSION A marked reduction in drug resistance was observed over 10 years, compatible with higher genetic barrier and potency of new antiretrovirals. Nonetheless, concerns remain for subjects with non-B subtypes when using mutation lists instead of interpretation systems because of the extensive polymorphism of the protease region.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
| | - Marco Franzetti
- Infectious Diseases Unit, 'A. Manzoni' Hospital, Lecco, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Bianca Bruzzone
- Hygiene Unit, Policlinico San Martino Hospital, Genoa, Italy
| | - Simona Di Giambenedetto
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart of Rome, Rome, Italy
| | - Antonio Di Biagio
- Infectious Diseases Clinic, Department of Health Sciences, University of Genoa, San Martino Hospital-IRCCS, Genoa, Italy
| | - Sergio Lo Caputo
- Clinic of Infectious Diseases, University Hospital Policlinico, University of Bari, Bari, Italy
| | | | - Franco Maggiolo
- Clinic of Infectious Diseases, Ospedali Riuniti, Bergamo, Italy
| | - Saverio G Parisi
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Stefano Rusconi
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | | | - Claudia Balotta
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
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Franzetti M, De Luca A, Ceccherini-Silberstein F, Spagnuolo V, Nicastri E, Mussini C, Antinori A, Monno L, Vecchiet J, Fanti I, d'Arminio Monforte A, Balotta C. Evolution of HIV-1 transmitted drug resistance in Italy in the 2007-2014 period: A weighted analysis. J Clin Virol 2018; 106:49-52. [PMID: 30075459 DOI: 10.1016/j.jcv.2018.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 06/06/2018] [Accepted: 07/25/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Recent studies suggest that transmitted drug resistance (TDR) may be decreasing in latest years, likely because of the reduced frequency of acquired resistance. However, specific risk factors, geographical areas and special HIV-infected populations may be disproportionally affected by TDR. OBJECTIVES Correlates of TDR and time trends were evaluated from 2007 to 2014. STUDY DESIGN We evaluated the genotypic results of 2155 naïve patients enrolled in the I.Co.N.A cohort at 23 clinical Centers in Italy between 2007 and 2014. A weighted analysis was performed to account for the patients enrolled in the cohort in each clinical Centre at each biennium (total number of patients: 3737). RESULTS Overall prevalence of TDR was 10.7%. Independent predictors of TDR were sexual risk factor (OR 2.315, p = 0.020) and non-Italian geographical origin (OR 1.57, p = 0.038). The weighted prevalence of TDR was 10.5% with a stable proportion over calendar years. Generally, TDR prevalence was numerically higher, although not significantly, in clinical Centers of metropolitan areas with more than 3 millions of residents as compared to others (11.3% vs. 9.2%). The difference in TDR prevalence between these Centers decreased in more recent years. CONCLUSIONS A stable frequency of TDR was observed during the most recent years in Italy, with opposite and converging trends in large metropolitan areas as compared to the rest of the country, suggesting a more homogeneous spread of TDR across the country in latest years. Concerns remain for sexual route of infection and non-Italian origin, reinforcing the need for specific prevention strategies prioritizing specific populations.
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Affiliation(s)
- M Franzetti
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
| | - A De Luca
- Siena University Hospital, Infectious Diseases Unit, Siena, Italy
| | | | - V Spagnuolo
- San Raffaele Scientific Institute, Infectious Diseases, Milan, Italy
| | - E Nicastri
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - C Mussini
- Clinic of Infectious Disease, University Hospital, Modena, Italy
| | - A Antinori
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - L Monno
- University of Bari, Department of Biomedical Science and Oncology, Bari, Italy
| | - J Vecchiet
- University of Chieti, Infectious Diseases Clinic, Italy
| | - I Fanti
- Catholic University of Sacred Heart, Clinical Infectious Diseases, Rome, Italy
| | - A d'Arminio Monforte
- San Paolo University Hospital Milan, Clinic of Infectious and Tropical Diseases, Milan, Italy
| | - C Balotta
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
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Papa F, Binda F, Felici G, Franzetti M, Gandolfi A, Sinisgalli C, Balotta C. A simple model of HIV epidemic in Italy: The role of the antiretroviral treatment. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2018; 15:181-207. [PMID: 29161832 DOI: 10.3934/mbe.2018008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In the present paper we propose a simple time-varying ODE model to describe the evolution of HIV epidemic in Italy. The model considers a single population of susceptibles, without distinction of high-risk groups within the general population, and accounts for the presence of immigration and emigration, modelling their effects on both the general demography and the dynamics of the infected subpopulations. To represent the intra-host disease progression, the untreated infected population is distributed over four compartments in cascade according to the CD4 counts. A further compartment is added to represent infected people under antiretroviral therapy. The per capita exit rate from treatment, due to voluntary interruption or failure of therapy, is assumed variable with time. The values of the model parameters not reported in the literature are assessed by fitting available epidemiological data over the decade 2003÷2012. Predictions until year 2025 are computed, enlightening the impact on the public health of the early initiation of the antiretroviral therapy. The benefits of this change in the treatment eligibility consist in reducing the HIV incidence rate, the rate of new AIDS cases, and the rate of death from AIDS. Analytical results about properties of the model in its time-invariant form are provided, in particular the global stability of the equilibrium points is established either in the absence and in the presence of infected among immigrants.
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Affiliation(s)
- Federico Papa
- Istituto di Analisi dei Sistemi ed Informatica 'A. Ruberti' - CNR, Roma, Italy
| | - Francesca Binda
- Dipartimento di Scienze Biomediche e Cliniche 'L. Sacco', Sezione di Malattie Infettive e Immunopatologia, Università degli Studi di Milano, Milano, Italy
| | - Giovanni Felici
- Istituto di Analisi dei Sistemi ed Informatica 'A. Ruberti' - CNR, Roma, Italy
| | - Marco Franzetti
- Dipartimento di Scienze Biomediche e Cliniche 'L. Sacco', Sezione di Malattie Infettive e Immunopatologia, Università degli Studi di Milano, Milano, Italy
| | - Alberto Gandolfi
- Istituto di Analisi dei Sistemi ed Informatica 'A. Ruberti' - CNR, Roma, Italy
| | - Carmela Sinisgalli
- Istituto di Analisi dei Sistemi ed Informatica 'A. Ruberti' - CNR, Roma, Italy
| | - Claudia Balotta
- Dipartimento di Scienze Biomediche e Cliniche 'L. Sacco', Sezione di Malattie Infettive e Immunopatologia, Università degli Studi di Milano, Milano, Italy
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Sepúlveda-Torres LDC, Rishishwar L, Rogers ML, Ríos-Olivares E, Boukli N, Jordan IK, Cubano LA. A decade of viral mutations and associated drug resistance in a population of HIV-1+ Puerto Ricans: 2002-2011. PLoS One 2017; 12:e0177452. [PMID: 28493944 PMCID: PMC5426751 DOI: 10.1371/journal.pone.0177452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Puerto Rico has one of the highest rates of HIV/AIDS seen for any US state or territory, and antiretroviral therapy has been a mainstay of efforts to mitigate the HIV/AIDS public health burden on the island. We studied the evolutionary dynamics of HIV-1 mutation and antiretroviral drug resistance in Puerto Rico by monitoring the population frequency of resistance-associated mutations from 2002 to 2011. Whole blood samples from 4,475 patients were analyzed using the TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System in the Immunoretrovirus Research Laboratory at Universidad Central del Caribe. Results show that 64.0% of female and 62.9% of male patients had HIV-1 mutations that confer resistance to at least one antiretroviral medication. L63P and M184V were the dominant mutations observed for the protease (PRO) and reverse transcriptase (RT) encoding genes, respectively. Specific resistance mutations, along with their associated drug resistance profiles, can be seen to form temporal clusters that reveal a steadily changing landscape of resistance trends over time. Both women and men showed resistance mutations for an average of 4.8 drugs over the 10-year period, further underscoring the strong selective pressure exerted by antiretrovirals along with the rapid adaptive response of HIV. Nevertheless, both female and male patients showed a precipitous decrease for overall drug resistance, and for PRO mutations in particular, over the entire course of the study, with the most rapid decrease in frequency seen after 2006. The reduced HIV-1 mutation and drug resistance trends that we observed are consistent with previous reports from multi-year studies conducted around the world. Reduced resistance can be attributed to the use of more efficacious antiretroviral drug therapy, including the introduction of multi-drug combination therapies, which limited the ability of the virus to mount rapid adaptive responses to antiretroviral selection pressure.
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Affiliation(s)
- Lycely del C. Sepúlveda-Torres
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
| | - Maria Luisa Rogers
- Natural Sciences Department, Sacred Heart University, San Juan, Puerto Rico, United States of America
| | - Eddy Ríos-Olivares
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - Nawal Boukli
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
| | - Luis A. Cubano
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
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Duani H, Aleixo AW, Tupinambás U. Trends and predictors of HIV-1 acquired drug resistance in Minas Gerais, Brazil: 2002-2012. Braz J Infect Dis 2016; 21:148-154. [PMID: 28017554 PMCID: PMC9427561 DOI: 10.1016/j.bjid.2016.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/01/2016] [Accepted: 11/30/2016] [Indexed: 10/26/2022] Open
Abstract
Several studies show that the prevalence of multidrug-resistant HIV-1 virus is declining over time. A retrospective cohort study was carried out to evaluate the trends of drug resistance in antiretroviral treatment-exposed individuals in a state of a middle-income country, Minas Gerais, southeast region of Brazil. We analyzed 2115 HIV-1 sequences from 2002 up to 2012, from 52 cities of Minas Gerais. The groups were analyzed according to the definitions: "IAS - 3 class mutations", if ≥1 drug resistance mutation from IAS 2015 list (DRM) was present in each class; "No fully susceptible drugs" as the absence of any fully susceptible drug in Stanford algorithm; and "GSS≥2″, when a maximum calculated GSS (genotypic susceptibility score) was ≥2 or ≥3, counting only drugs available in Brazil and USA at given calendar years. Time trends of resistance were analyzed by Cochran-Armitage test. We observed a decrease in the rate resistance mutations for PI, NRTI, "IAS - 3 class mutations", and "No fully susceptible drugs" over these 11 years, from 69.2% to 20.7%, 92.3% to 90.2%, 46.2% to 22.5%, and 12.8% to 5.7%, respectively (p<0.05). Resistance to NNRTI increased from 74.4% to 81.6%, mainly because of K103N mutation. The GSS score ≥2 increased during the years from 35.9% to 87.3% (p<0.001). We demonstrate that resistance to PI and to the three main classes simultaneously are declining, although the number of patients on of antiretroviral therapy has doubled in the last ten years in Brazil (125,000 in 2002 to 400,000 in 2014). Broader resistance testing and the availability of more therapeutic options might have influenced this decline. The increase in NNRTI resistance can limit this class as first line treatment in Brazil in the future.
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Affiliation(s)
- Helena Duani
- Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Departamento de Clínica Médica, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Pós-Graduação em Ciências da Saúde, Infectologia e Medicina Tropical, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Laboratório de Imunologia e Biologia Molecular (DIP-UFMG), Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Hospital das Clínicas, Belo Horizonte, MG, Brazil.
| | - Agdemir Waleria Aleixo
- Universidade Federal de Minas Gerais (UFMG), Laboratório de Imunologia e Biologia Molecular (DIP-UFMG), Belo Horizonte, MG, Brazil
| | - Unaí Tupinambás
- Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Departamento de Clínica Médica, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Faculdade de Medicina, Pós-Graduação em Ciências da Saúde, Infectologia e Medicina Tropical, Belo Horizonte, MG, Brazil
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10
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Tintori C, Brai A, Dasso Lang MC, Deodato D, Greco AM, Bizzarri BM, Cascone L, Casian A, Zamperini C, Dreassi E, Crespan E, Maga G, Vanham G, Ceresola E, Canducci F, Ariën KK, Botta M. Development and in Vitro Evaluation of a Microbicide Gel Formulation for a Novel Non-Nucleoside Reverse Transcriptase Inhibitor Belonging to the N-Dihydroalkyloxybenzyloxopyrimidines (N-DABOs) Family. J Med Chem 2016; 59:2747-59. [PMID: 26898379 DOI: 10.1021/acs.jmedchem.5b01979] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Preventing HIV transmission by the use of a vaginal microbicide is a topic of considerable interest in the fight against AIDS. Both a potent anti-HIV agent and an efficient formulation are required to develop a successful microbicide. In this regard, molecules able to inhibit the HIV replication before the integration of the viral DNA into the genetic material of the host cells, such as entry inhibitors or reverse transcriptase inhibitors (RTIs), are ideal candidates for prevention purpose. Among RTIs, S- and N-dihydroalkyloxybenzyloxopyrimidines (S-DABOs and N-DABOs) are interesting compounds active at nanomolar concentration against wild type of RT and with a very interesting activity against RT mutations. Herein, novel N-DABOs were synthesized and tested as anti-HIV agents. Furthermore, their mode of binding was studied by molecular modeling. At the same time, a vaginal microbicide gel formulation was developed and tested for one of the most promising candidates.
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Affiliation(s)
- Cristina Tintori
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Davide Deodato
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Antonia Michela Greco
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Bruno Mattia Bizzarri
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Lorena Cascone
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Alexandru Casian
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Claudio Zamperini
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Guido Vanham
- Virology Unit, Institute of Tropical Medicine , Nationalestraat 155, B-2000 Antwerpen, Belgium
| | - Elisa Ceresola
- Department of Biotechnology and Life Sciences, University of Insubria , Dunant 3, 21100, Varese, Italy
| | - Filippo Canducci
- Department of Biotechnology and Life Sciences, University of Insubria , Dunant 3, 21100, Varese, Italy
| | - Kevin K Ariën
- Virology Unit, Institute of Tropical Medicine , Nationalestraat 155, B-2000 Antwerpen, Belgium
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University , Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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11
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Identification of minority resistance mutations in the HIV-1 integrase coding region using next generation sequencing. J Clin Virol 2015; 73:95-100. [PMID: 26587787 DOI: 10.1016/j.jcv.2015.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/31/2015] [Accepted: 11/03/2015] [Indexed: 11/20/2022]
Abstract
BACKGROUND The current widely applied standard method to screen for HIV-1 genotypic resistance is based on Sanger population sequencing (Sseq), which does not allow for the identification of minority variants (MVs) below the limit of detection for the Sseq-method in patients receiving integrase strand-transfer inhibitors (INSTI). Next generation sequencing (NGS) has facilitated the detection of MVs at a much deeper level than Sseq. OBJECTIVES Here, we compared Illumina MiSeq and Sseq approaches to evaluate the detection of MVs involved in resistance to the three commonly used INSTI: raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG). STUDY DESIGN NGS and Sseq were used to analyze RT-PCR products of the HIV-1 integrase coding region from six patients and in serial samples from two patients. NGS sequences were assembled and analyzed using the low frequency variant detection (LFVDT) tool in CLC genomic workbench. RESULTS Sseq detected INSTI resistance and accessory mutations in three of the patients (called INSTI Res+), while no resistance or accessory mutations were detected in the remaining three patients (called INSTI Res-). Additional INSTI resistance and/or accessory mutations were detected by NGS analysis of integrase sequences from all three INSTI Res+ and one INSTI Res- patient. CONCLUSION Our observations suggested that NGS demonstrated a higher sensitivity than sSEQ in the identification of INSTI relevant MVs both in patients at treatment baseline and in patients receiving INSTI therapy. Thus NGS can be a valuable tool in monitoring of antiretroviral minority resistance in patients receiving INSTI therapy.
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