1
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Mainou E, Berendam SJ, Obregon-Perko V, Uffman EA, Phan CT, Shaw GM, Bar KJ, Kumar MR, Fray EJ, Siliciano JM, Siliciano RF, Silvestri G, Permar SR, Fouda GG, McCarthy J, Chahroudi A, Chan C, Conway JM. Comparative analysis of within-host dynamics of acute infection and viral rebound dynamics in postnatally SHIV-infected ART-treated infant rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595130. [PMID: 38826467 PMCID: PMC11142125 DOI: 10.1101/2024.05.21.595130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Viral dynamics of acute HIV infection and HIV rebound following suspension of antiretroviral therapy may be qualitatively similar but must differ given, for one, development of adaptive immune responses. Understanding the differences of acute HIV infection and viral rebound dynamics in pediatric populations may provide insights into the mechanisms of viral control with potential implications for vaccine design and the development of effective targeted therapeutics for infants and children. Mathematical models have been a crucial tool to elucidate the complex processes driving viral infections within the host. Traditionally, acute HIV infection has been modeled with a standard model of viral dynamics initially developed to explore viral decay during treatment, while viral rebound has necessitated extensions of that standard model to incorporate explicit immune responses. Previous efforts to fit these models to viral load data have underscored differences between the two infection stages, such as increased viral clearance rate and increased death rate of infected cells during rebound. However, these findings have been predicated on viral load measurements from disparate adult individuals. In this study, we aim to bridge this gap, in infants, by comparing the dynamics of acute infection and viral rebound within the same individuals by leveraging an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model. Ten infant Rhesus macaques (RMs) orally challenged with SHIV.C.CH505 375H dCT and given ART at 8 weeks post-infection. These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We use the HIV standard viral dynamics model fitted to viral load measurements in a nonlinear mixed effects framework. We find that the primary difference between acute infection and rebound is the increased death rate of infected cells during rebound. We use these findings to generate hypotheses on the effects of adaptive immune responses. We leverage these findings to formulate hypotheses to elucidate the observed results and provide arguments to support the notion that delayed viral rebound is characterized by a stronger CD8+ T cell response.
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Affiliation(s)
- Ellie Mainou
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Emilie A Uffman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Caroline T Phan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katharine J Bar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mithra R Kumar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily J Fray
- Department of Biochemistry and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | | | - Janice McCarthy
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Jessica M Conway
- Department of Mathematics, Pennsylvania State University, University Park, PA, USA
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2
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Phan T, Conway JM, Pagane N, Kreig J, Sambaturu N, Iyaniwura S, Li JZ, Ribeiro RM, Ke R, Perelson AS. Understanding early HIV-1 rebound dynamics following antiretroviral therapy interruption: The importance of effector cell expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592318. [PMID: 38746144 PMCID: PMC11092759 DOI: 10.1101/2024.05.03.592318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Most people living with HIV-1 experience rapid viral rebound once antiretroviral therapy is interrupted; however, a small fraction remain in viral remission for an extended duration. Understanding the factors that determine whether viral rebound is likely after treatment interruption can enable the development of optimal treatment regimens and therapeutic interventions to potentially achieve a functional cure for HIV-1. We built upon the theoretical framework proposed by Conway and Perelson to construct dynamic models of virus-immune interactions to study factors that influence viral rebound dynamics. We evaluated these models using viral load data from 24 individuals following antiretroviral therapy interruption. The best-performing model accurately captures the heterogeneity of viral dynamics and highlights the importance of the effector cell expansion rate. Our results show that post-treatment controllers and non-controllers can be distinguished based on the effector cell expansion rate in our models. Furthermore, these results demonstrate the potential of using dynamic models incorporating an effector cell response to understand early viral rebound dynamics post-antiretroviral therapy interruption.
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Affiliation(s)
- Tin Phan
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jessica M Conway
- Department of Mathematics, Pennsylvania State University, College Township, PA, USA
- Department of Biology, Pennsylvania State University, College Township, PA, USA
| | - Nicole Pagane
- Program in Computational and Systems Biology, Massachusetts Institute of Technology; Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
| | - Jasmine Kreig
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Narmada Sambaturu
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Sarafa Iyaniwura
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jonathan Z Li
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- Santa Fe Institute, Santa Fe, NM, USA
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Hayashi R, Hara A, Iwasa Y. Viral rebound occurrence immediately after drug discontinuation involving neither drug resistance nor latent reservoir. J Theor Biol 2024; 582:111767. [PMID: 38387506 DOI: 10.1016/j.jtbi.2024.111767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Some viruses exhibit "rebound" when the administration of antiviral drugs is discontinued. Viral rebound caused by resistance mutations or latent reservoirs has been studied mathematically. In this study, we investigated the viral rebound due to other causes. Since immunity is weaker during antiviral treatment than without the treatment, drug discontinuation may lead to an increase in the viral load. We analyzed the dynamics of the number of virus-infected cells, cytotoxic T lymphocytes, and memory cells and identified the conditions under which the viral load increased upon drug discontinuation. If drug is administered for an extended period, a viral rebound occurs when the ratio of viral growth rate in the absence to that in the presence of the antiviral drug exceeds the "rebound threshold." We analyzed how the rebound threshold depended on the patient's conditions and the type of treatment. Mathematical and numerical analyses revealed that rebound after discontinuation was more likely to occur when the drug effectively reduced viral proliferation, drug discontinuation was delayed, and the processes activating immune responses directly were stronger than those occurring indirectly through immune memory formation. We discussed additional reasons for drugs to cause viral rebound more likely.
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Affiliation(s)
- Rena Hayashi
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Akane Hara
- Laboratory of Pharmaceutical Quality Assurance and Assessment, School of Pharmacy and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoh Iwasa
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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Gobran ST, Pagliuzza A, Khedr O, Fert A, Chomont N, Bruneau J, Klein MB, Ancuta P, Shoukry NH. DAA-mediated HCV cure reduces HIV DNA levels in HCV/HIV coinfected people. J Virol 2023; 97:e0110523. [PMID: 38051044 PMCID: PMC10734513 DOI: 10.1128/jvi.01105-23] [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: 07/20/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Antiretroviral therapy (ART) for human immunodeficiency virus (HIV) can control virus replication and prolong the life of people living with HIV (PLWH). However, the virus remains dormant within immune cells in what is called the HIV reservoir. Furthermore, 2.3 million PLWH are also coinfected with hepatitis C virus (HCV) and are at risk of developing chronic liver disease and cancer. HCV treatment with direct acting antivirals (DAA) can completely cure the infection in more than 95% of treated individuals and improve their long-term health outcomes. In this study, we investigated how HCV treatment and cure affect the HIV reservoir. We demonstrate the beneficial impact of DAA treatment as it reduces the HIV reservoirs in particular in people infected with HCV before HIV. These results support the need for early ART and DAA treatment in HIV/HCV coinfections.
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Affiliation(s)
- Samaa T. Gobran
- Département de microbiologie, infectiologie, et immunologie, Université de Montréal, Faculté de médicine, Montréal, Québec, Canada
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Amélie Pagliuzza
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Omar Khedr
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Augustine Fert
- Département de microbiologie, infectiologie, et immunologie, Université de Montréal, Faculté de médicine, Montréal, Québec, Canada
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Nicolas Chomont
- Département de microbiologie, infectiologie, et immunologie, Université de Montréal, Faculté de médicine, Montréal, Québec, Canada
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Julie Bruneau
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Département de médecine de famille et de médecine d'urgence, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Marina B. Klein
- Department of Medicine, Faculty of Medicine and Health Sciences, McGill University, Montréal, Québec, Canada
- Department of Medicine, Division of Infectious Diseases, McGill University Health Center (MUHC), Montréal, Québec, Canada
| | - Petronela Ancuta
- Département de microbiologie, infectiologie, et immunologie, Université de Montréal, Faculté de médicine, Montréal, Québec, Canada
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Naglaa H. Shoukry
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Département de médecine, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
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5
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Mainou E, Berendam SJ, Obregon-Perko V, Uffman EA, Phan CT, Shaw GM, Bar KJ, Kumar MR, Fray EJ, Siliciano JM, Siliciano RF, Silvestri G, Permar SR, Fouda GG, McCarthy J, Chahroudi A, Conway JM, Chan C. Assessing the impact of autologous neutralizing antibodies on viral rebound in postnatally SHIV-infected ART-treated infant rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550159. [PMID: 37502921 PMCID: PMC10370170 DOI: 10.1101/2023.07.22.550159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
While the benefits of early antiretroviral therapy (ART) initiation in perinatally infected infants are well documented, early ART initiation is not always possible in postnatal pediatric HIV infections, which account for the majority of pediatric HIV cases worldwide. The timing of onset of ART initiation is likely to affect the size of the latent viral reservoir established, as well as the development of adaptive immune responses, such as the generation of neutralizing antibody responses against the virus. How these parameters impact the ability of infants to control viremia and the time to viral rebound after ART interruption is unclear. To gain insight into the dynamics, we utilized mathematical models to investigate the effect of time of ART initiation via latent reservoir size and autologous virus neutralizing antibody responses in delaying viral rebound when treatment is interrupted. We used an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model that mimics breast milk HIV transmission in human infants. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C.CH505 375H dCT and either given ART at 4-7 days post-infection (early ART condition), at 2 weeks post-infection (intermediate ART condition), or at 8 weeks post-infection (late ART condition). These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We develop a stochastic mathematical model to investigate the joint effect of latent reservoir size, the autologous neutralizing antibody potency, and CD4+ T cell levels on the time to viral rebound and control of post-rebound viral loads. We find that the latent reservoir size is an important determinant in explaining time to viral rebound by affecting the growth rate of the virus. The presence of neutralizing antibodies also can delay rebound, but we find this effect for high potency antibody responses only.
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Affiliation(s)
- Ellie Mainou
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Emilie A Uffman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - Caroline T Phan
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine J Bar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mithra R Kumar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily J Fray
- Department of Biochemistry and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | | | - Janice McCarthy
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jessica M Conway
- Department of Mathematics, Pennsylvania State University, University Park, PA, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
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6
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Duran-Castells C, Prats A, Oriol-Tordera B, Llano A, Galvez C, Martinez-Picado J, Ballana E, Garcia-Vidal E, Clotet B, Muñoz-Moreno JA, Hanke T, Moltó J, Mothe B, Brander C, Ruiz-Riol M. Plasma proteomic profiling identifies CD33 as a marker of HIV control in natural infection and after therapeutic vaccination. EBioMedicine 2023; 95:104732. [PMID: 37506557 PMCID: PMC10410179 DOI: 10.1016/j.ebiom.2023.104732] [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: 01/17/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Biomarkers predicting the outcome of HIV-1 virus control in natural infection and after therapeutic interventions in HIV-1 cure trials remain poorly defined. The BCN02 trial (NCT02616874), combined a T-cell vaccine with romidepsin (RMD), a cancer-drug that was used to promote HIV-1 latency reversal and which has also been shown to have beneficial effects on neurofunction. We conducted longitudinal plasma proteomics analyses in trial participants to define biomarkers associated with virus control during monitored antiretroviral pause (MAP) and to identify novel therapeutic targets that can improve future cure strategies. METHODS BCN02 was a phase I, open-label, single-arm clinical trial in early-treated, HIV infected individuals. Longitudinal plasma proteomes were analyzed in 11 BCN02 participants, including 8 participants that showed a rapid HIV-1 plasma rebound during a monitored antiretroviral pause (MAP-NC, 'non-controllers') and 3 that remained off ART with sustained plasma viremia <2000 copies/ml (MAP-C, 'controllers'). Inflammatory and neurological proteomes in plasma were evaluated and integration data analysis (viral and neurocognitive parameters) was performed. Validation studies were conducted in a cohort of untreated HIV-1+ individuals (n = 96) and in vitro viral replication assays using an anti-CD33 antibody were used for functional validation. FINDINGS Inflammatory plasma proteomes in BCN02 participants showed marked longitudinal alterations. Strong proteome differences were also observed between MAP-C and MAP-NC, including in baseline timepoints. CD33/Siglec-3 was the unique plasma marker with the ability to discriminate between MAPC-C and MAP-NC at all study timepoints and showed positive correlations with viral parameters. Analyses in an untreated cohort of PLWH confirmed the positive correlation between viral parameters and CD33 plasma levels, as well as PBMC gene expression. Finally, adding an anti-CD33 antibody to in vitro virus cultures significantly reduced HIV-1 replication and proviral levels in T cells and macrophages. INTERPRETATION This study indicates that CD33/Siglec-3 may serve as a predictor of HIV-1 control and as potential therapeutic tool to improve future cure strategies. FUNDING Spanish Science and Innovation Ministry (SAF2017-89726-R and PID2020-119710RB-I00), NIH (P01-AI131568), European Commission (GA101057548) and a Grifols research agreement.
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Affiliation(s)
- Clara Duran-Castells
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona, Spain
| | - Anna Prats
- Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Bruna Oriol-Tordera
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona, Spain
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Cristina Galvez
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain; Catalan Institution for Research Advanced Studies (ICREA), Barcelona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Ester Ballana
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Edurne Garcia-Vidal
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Jose A Muñoz-Moreno
- Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Faculty of Psychology and Education Sciences, Universitat Oberta de Catalunya (UOC), Barcelona, Spain
| | - Thomas Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - José Moltó
- Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Fight Infections Foundation and Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona, Spain; University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain; Catalan Institution for Research Advanced Studies (ICREA), Barcelona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute Badalona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.
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7
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Phan T, Brozak S, Pell B, Oghuan J, Gitter A, Hu T, Ribeiro RM, Ke R, Mena KD, Perelson AS, Kuang Y, Wu F. Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks. WATER RESEARCH 2023; 243:120372. [PMID: 37494742 DOI: 10.1016/j.watres.2023.120372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023]
Abstract
Wastewater surveillance has proved to be a valuable tool to track the COVID-19 pandemic. However, most studies using wastewater surveillance data revolve around establishing correlations and lead time relative to reported case data. In this perspective, we advocate for the integration of wastewater surveillance data with dynamic within-host and between-host models to better understand, monitor, and predict viral disease outbreaks. Dynamic models overcome emblematic difficulties of using wastewater surveillance data such as establishing the temporal viral shedding profile. Complementarily, wastewater surveillance data bypasses the issues of time lag and underreporting in clinical case report data, thus enhancing the utility and applicability of dynamic models. The integration of wastewater surveillance data with dynamic models can enhance real-time tracking and prevalence estimation, forecast viral transmission and intervention effectiveness, and most importantly, provide a mechanistic understanding of infectious disease dynamics and the driving factors. Dynamic modeling of wastewater surveillance data will advance the development of a predictive and responsive monitoring system to improve pandemic preparedness and population health.
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Affiliation(s)
- Tin Phan
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Samantha Brozak
- School of Mathematical and Statistical Sciences, Arizona State University, AZ 85281, USA
| | - Bruce Pell
- Department of Mathematics and Computer Science, Lawrence Technological University, MI 48075, USA
| | - Jeremiah Oghuan
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Anna Gitter
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Tao Hu
- Department of Geography, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Kristina D Mena
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Texas Epidemic Public Health Institute, Houston, TX 77030, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, AZ 85281, USA
| | - Fuqing Wu
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Texas Epidemic Public Health Institute, Houston, TX 77030, USA.
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8
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Rennie S, Henderson G, Phanuphak N, Kuczynski K, Colby D, Ormsby N, Kroon E, Hsu D, Likhitwonnawut U, Vasan S, Sacdalan C, Jupimai T, Butterworth O, Peay H. The Essential Need for Trust When Transmission Risk Cannot Be Eliminated in HIV-Remission Trials. Ethics Hum Res 2023; 45:2-15. [PMID: 37368521 DOI: 10.1002/eahr.500172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Analytic treatment interruption (ATI) is scientifically necessary in HIV-remission ("cure") studies to test the effects of new interventions. However, stopping antiretroviral treatment poses risks to research participants and their sexual partners. Ethical debate about whether and how to conduct such studies has largely centered on designing risk-mitigation strategies and identifying the responsibilities of research stakeholders. In this paper, we argue that because the possibility of HIV transmission from research participants to partners during ATI cannot practicably be eliminated-that is, it is ineliminable-the successful conduct of such trials ultimately depends on relationships of trust and trustworthiness. We describe our experiences with conducting and studying HIV-remission trials with ATI in Thailand to examine the strengths, complexities, and limitations of the risk-mitigation and responsibility approaches and to explore ways in which the building of trust-and trustworthiness-may help enhance the scientific, practical, and ethical dimensions of these trials.
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Affiliation(s)
- Stuart Rennie
- Professor at the Center for Bioethics in the Department of Social Medicine at the University of North Carolina at Chapel Hill
| | - Gail Henderson
- Professor in the Department of Social Medicine and the director of the Center for Genomics and Society at the University of North Carolina at Chapel Hill
| | - Nittaya Phanuphak
- Executive director of the Institute of HIV Research and Innovation in Bangkok
| | - Kristine Kuczynski
- Program manager at the Center for Genomics and Society and PPMH Precision Genomic Screening Program in the School of Medicine at the University of North Carolina at Chapel Hill
| | - Donn Colby
- Senior research physician at the Henry M. Jackson Foundation for the Advancement of Military Medicine at the U.S. Military HIV Research Program at the Walter Reed Army Institute of Research
| | - Nuchanart Ormsby
- Research assistant and an administrative support associate in the Computational Medicine Program in the School of Medicine at the University of North Carolina at Chapel Hill
| | - Eugene Kroon
- Senior research physician at the Institute of HIV Research and Innovation in Bangkok
| | - Denise Hsu
- Associate director of therapeutics at the Henry M. Jackson Foundation for the Advancement of Military Medicine at the U.S. Military HIV Research Program at the Walter Reed Army Institute of Research
| | | | - Sandhya Vasan
- Vice president of Global Infectious Diseases Research and the director of the Henry M. Jackson Foundation for the Advancement of Military Medicine at the U.S. Military HIV Research Program at the Walter Reed Army Institute of Research
| | - Carlo Sacdalan
- Research physician at the SEARCH Research Foundation in Bangkok
| | - Thidarat Jupimai
- Clinical research assistant at the Center of Excellence in Pediatric Infectious Diseases and Vaccines Faculty of Medicine at the Chulalongkorn University in Bangkok
| | - Oratai Butterworth
- Clinical project manager at the Henry M. Jackson Foundation for the Advancement of Military Medicine at the U.S. Military HIV Research Program at the Walter Reed Army Institute of Research
| | - Holly Peay
- Senior research public health analyst at RTI International
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9
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Tettamanti Boshier FA, Reeves DB, Duke ER, Swan DA, Prlic M, Cardozo-Ojeda EF, Schiffer JT. Substantial uneven proliferation of CD4 + T cells during recovery from acute HIV infection is sufficient to explain the observed expanded clones in the HIV reservoir. J Virus Erad 2022; 8:100091. [PMID: 36582473 PMCID: PMC9792356 DOI: 10.1016/j.jve.2022.100091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/08/2022] [Accepted: 10/10/2022] [Indexed: 12/03/2022] Open
Abstract
The HIV reservoir is a population of 1-10 million anatomically dispersed, latently infected memory CD4+ T cells in which HIV DNA is quiescently integrated into human chromosomal DNA. When antiretroviral therapy (ART) is stopped and HIV replication initiates in one of these cells, systemic viral spread resumes, rekindling progression to AIDS. Therefore, HIV latency prevents cure. The detection of many populations of identical HIV sequences at unique integration sites implicates CD4+ T cell proliferation as the critical driver of reservoir sustainment after a prolonged period of effective ART. Initial reservoir formation occurs during the first week of primary infection usually before ART is started. While empirical data indicates that both de novo infection and cellular proliferation generate latently infected cells during early untreated infection, it is not known which of these mechanisms is predominant. We developed a mathematical model that recapitulates the profound depletion and brisk recovery of CD4+ T cells, reservoir creation, and viral load trajectory during primary HIV infection. We extended the model to stochastically simulate individual HIV reservoir clones. This model predicts the first detection of HIV infected clones approximately 5 weeks after infection as has recently been shown in vivo and suggests that substantial, uneven proliferation among clones during the recovery from CD4+ lymphopenia is the most plausible explanation for the observed clonal reservoir distribution during the first year of infection.
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Affiliation(s)
- Florencia A. Tettamanti Boshier
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
| | - Elizabeth R. Duke
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
- Department of Medicine, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - David A. Swan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
| | - Martin Prlic
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
- Department of Global Health, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - E. Fabian Cardozo-Ojeda
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., Seattle, WA, 98122, USA
- Department of Medicine, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
- Clinical Research Division, University of Washington, 1959 NE Pacific St., Seattle, WA, USA
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10
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Hendricks CM, Cash MN, Tagliamonte MS, Riva A, Brander C, Llano A, Salemi M, Stevenson M, Mavian C. Discordance between HIV-1 Population in Plasma at Rebound after Structured Treatment Interruption and Archived Provirus Population in Peripheral Blood Mononuclear Cells. Microbiol Spectr 2022; 10:e0135322. [PMID: 35699458 PMCID: PMC9431602 DOI: 10.1128/spectrum.01353-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/07/2022] [Indexed: 11/20/2022] Open
Abstract
Antiretroviral therapy (ART) can sustain the suppression of plasma viremia to below detection levels. Infected individuals undergoing a treatment interruption exhibit rapid viral rebound in plasma viremia which is fueled by cellular reservoirs such as CD4+ T cells, myeloid cells, and potentially uncharacterized cellular sources. Interrogating the populations of viruses found during analytical treatment interruption (ATI) can give insights into the biologically competent reservoirs that persist under effective ART as well as the nature of the cellular reservoirs that enable viral persistence under ART. We interrogated plasma viremia from four rare cases of individuals undergoing sequential ATIs. We performed next-generation sequencing (NGS) on cell-associated viral DNA and cell-free virus to understand the interrelationship between sequential ATIs as well as the relationship between viral genomes in circulating peripheral blood mononuclear cells (PBMCs) and RNA from rebound plasma. We observed population differences between viral populations recrudescing at sequential ATIs as well as divergence between viral sequences in plasma and those in PBMCs. This indicated that viruses in PBMCs were not a major source of post-ATI viremia and highlights the role of anatomic reservoirs in post-ATI viremia and viral persistence. IMPORTANCE Even with effective ART, HIV-1 persists at undetectable levels and rebounds in individuals who stop treatment. Cellular and anatomical reservoirs ignite viral rebound upon treatment interruption, remaining one of the key obstacles for HIV-1 cure. To further examine HIV-1 persistence, a better understanding of the distinct populations that fuel viral rebound is necessary to identify and target reservoirs and the eradication of HIV-1. This study investigates the populations of viruses found from proviral genomes from PBMCs and plasma at rebound from a unique cohort of individuals who underwent multiple rounds of treatment interruption. Using NGS, we characterized the subtypes of viral sequences and found divergence in viral populations between plasma and PBMCs at each rebound, suggesting that distinct viral populations appear at each treatment interruption.
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Affiliation(s)
- Chynna M. Hendricks
- Department of Microbiology and Immunology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Melanie N. Cash
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Massimiliano S. Tagliamonte
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | | | - Anuska Llano
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Division of Infectious Diseases, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
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11
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Porter AM, Baker CR, Fulco PP. Administration of Crushed Doravirine via Nasojejunal Feeding Tube in a Patient With Treatment-Experienced Human Immunodeficiency Virus. J Pharm Pract 2022:8971900221104258. [PMID: 35610547 DOI: 10.1177/08971900221104258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Allison M Porter
- Clinical Pharmacy Manager, 23726Fairview Park Hospital, Dublin, GA, USA
| | - Cassandra R Baker
- Department of Pharmacy, 6887Virginia Commonwealth University Health, Richmond, VA, USA
| | - Patricia P Fulco
- Department of Pharmacy, 6887Virginia Commonwealth University Health, Richmond, VA, USA.,Division of Infectious Diseases, 6887Virginia Commonwealth University Health, Richmond, VA, USA
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12
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Bazié WW, Boucher J, Traoré IT, Kania D, Somé DY, Alary M, Gilbert C. Vesicular MicroRNA as Potential Biomarkers of Viral Rebound. Cells 2022; 11:cells11050859. [PMID: 35269481 PMCID: PMC8909274 DOI: 10.3390/cells11050859] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
Changes in the cellular microRNA (miRNA) expression profile in response to HIV infection, replication or latency have been reported. Nevertheless, little is known concerning the abundance of miRNA in extracellular vesicles (EVs). In the search for a reliable predictor of viral rebound, we quantified the amount of miR-29a, miR-146a, and miR-155 in two types of plasma extracellular vesicles. Venous blood was collected from 235 ART-treated and ART-naive persons living with HIV (85 with ongoing viral replication, ≥20 copies/mL) and 60 HIV-negative participants at five HIV testing or treatment centers in Burkina Faso. Large and small plasma EVs were purified and counted, and mature miRNA miR-29a, miR-146a, and miR-155 were measured by RT-qPCR. Diagnostic performance of miRNA levels in large and small EVs was evaluated by a receiver operating characteristic curve analysis. The median duration of HIV infection was 36 months (IQR 14-117). The median duration of ART was 34 months (IQR 13-85). The virus was undetectable in 63.8% of these persons. In the others, viral load ranged from 108 to 33,978 copies/mL (median = 30,032). Large EVs were more abundant in viremic participants than aviremic. All three miRNAs were significantly more abundant in small EVs in persons with detectable HIV RNA, and their expression levels in copies per vesicle were a more reliable indicator of viral replication in ART-treated patients with low viremia (20-1000 copies/mL). HIV replication increased the production of large EVs more than small EVs. Combined with viral load measurement, quantifying EV-associated miRNA abundance relative to the number of vesicles provides a more reliable marker of the viral status. The expression level as copies per small vesicle could predict the viral rebound in ART-treated patients with undetectable viral loads.
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Affiliation(s)
- Wilfried Wenceslas Bazié
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
- Correspondence: (W.W.B.); (C.G.); Tel.: +1-(418)-525-4444 (ext. 44104) (W.W.B.); +1-(418)-525-4444 (ext. 46107) (C.G.); Fax: +1-(418)-654-2765 (C.G.)
| | - Julien Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
| | - Isidore Tiandiogo Traoré
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
- Département de Santé Publique, Institut Supérieur des Sciences de la Santé, Université Nazi Boni, Bobo-Dioulasso 01 BP 1091, Burkina Faso
| | - Dramane Kania
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
| | - Diane Yirgnur Somé
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso; (I.T.T.); (D.K.); (D.Y.S.)
| | - Michel Alary
- Axe de Recherche Santé des Populations et Pratiques Optimales en Santé, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1S 4L8, Canada;
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut National de Santé Publique du Québec, Quebec City, QC G1V 5B3, Canada
| | - Caroline Gilbert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada;
- Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Correspondence: (W.W.B.); (C.G.); Tel.: +1-(418)-525-4444 (ext. 44104) (W.W.B.); +1-(418)-525-4444 (ext. 46107) (C.G.); Fax: +1-(418)-654-2765 (C.G.)
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13
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Zacharopoulou P, Marchi E, Ogbe A, Robinson N, Brown H, Jones M, Parolini L, Pace M, Grayson N, Kaleebu P, Rees H, Fidler S, Goulder P, Klenerman P, Frater J. Expression of type I interferon-associated genes at antiretroviral therapy interruption predicts HIV virological rebound. Sci Rep 2022; 12:462. [PMID: 35013427 PMCID: PMC8748440 DOI: 10.1038/s41598-021-04212-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/08/2021] [Indexed: 12/25/2022] Open
Abstract
Although certain individuals with HIV infection can stop antiretroviral therapy (ART) without viral load rebound, the mechanisms under-pinning 'post-treatment control' remain unclear. Using RNA-Seq we explored CD4 T cell gene expression to identify evidence of a mechanism that might underpin virological rebound and lead to discovery of associated biomarkers. Fourteen female participants who received 12 months of ART starting from primary HIV infection were sampled at the time of stopping therapy. Two analysis methods (Differential Gene Expression with Gene Set Enrichment Analysis, and Weighted Gene Co-expression Network Analysis) were employed to interrogate CD4+ T cell gene expression data and study pathways enriched in post-treatment controllers versus early rebounders. Using independent analysis tools, expression of genes associated with type I interferon responses were associated with a delayed time to viral rebound following treatment interruption (TI). Expression of four genes identified by Cox-Lasso (ISG15, XAF1, TRIM25 and USP18) was converted to a Risk Score, which associated with rebound (p < 0.01). These data link transcriptomic signatures associated with innate immunity with control following stopping ART. The results from this small sample need to be confirmed in larger trials, but could help define strategies for new therapies and identify new biomarkers for remission.
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Affiliation(s)
- P Zacharopoulou
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - E Marchi
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - A Ogbe
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - N Robinson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Jones
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - L Parolini
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Pace
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - N Grayson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - P Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Entebbe, Uganda
| | - H Rees
- Wits Reproductive Health and HIV Institute of the University of the Witwatersrand in Johannesburg, Johannesburg, South Africa
| | - S Fidler
- Division of Medicine, Wright Fleming Institute, Imperial College, London, UK
- Imperial College NIHR Biomedical Research Centre, London, UK
| | - P Goulder
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - P Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Biomedical Research Centre, Oxford, UK
| | - J Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- National Institute of Health Research Biomedical Research Centre, Oxford, UK.
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14
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Abstract
The introduction of antiretroviral therapy (ART) and highly active antiretroviral therapy (HAART) has transformed human immunodeficiency virus (HIV)-1 into a chronic, well-managed disease. However, these therapies do not eliminate all infected cells from the body despite suppressing viral load. Viral rebound is largely due to the presence of cellular reservoirs which support long-term persistence of HIV-1. A thorough understanding of the HIV-1 reservoir will facilitate the development of new strategies leading to its detection, reduction, and elimination, ultimately leading to curative therapies for HIV-1. Although immune cells derived from lymphoid and myeloid progenitors have been thoroughly studied as HIV-1 reservoirs, few studies have examined whether mesenchymal stromal/stem cells (MSCs) can assume this function. In this review, we evaluate published studies which have assessed whether MSCs contribute to the HIV-1 reservoir. MSCs have been found to express the receptors and co-receptors required for HIV-1 entry, albeit at levels of expression and receptor localisation that vary considerably between studies. Exposure to HIV-1 and HIV-1 proteins alters MSC properties in vitro, including their proliferation capacity and differentiation potential. However, in vitro and in vivo experiments investigating whether MSCs can become infected with and harbour latent integrated proviral DNA are lacking. In conclusion, MSCs appear to have the potential to contribute to the HIV-1 reservoir. However, further studies are needed using techniques such as those used to prove that cluster of differentiation (CD)4+ T cells constitute an HIV-1 reservoir before a reservoir function can definitively be ascribed to MSCs.
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15
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Gao S, Wu L, Yu T, Kouyos R, Günthard HF, Wang R. Nonlinear mixed-effects models for HIV viral load trajectories before and after antiretroviral therapy interruption, incorporating left censoring. STATISTICAL COMMUNICATIONS IN INFECTIOUS DISEASES 2022; 14:20210001. [PMID: 35880974 PMCID: PMC9204768 DOI: 10.1515/scid-2021-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 01/28/2022] [Accepted: 02/28/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES Characterizing features of the viral rebound trajectories and identifying host, virological, and immunological factors that are predictive of the viral rebound trajectories are central to HIV cure research. We investigate if key features of HIV viral decay and CD4 trajectories during antiretroviral therapy (ART) are associated with characteristics of HIV viral rebound following ART interruption. METHODS Nonlinear mixed effect (NLME) models are used to model viral load trajectories before and following ART interruption, incorporating left censoring due to lower detection limits of viral load assays. A stochastic approximation EM (SAEM) algorithm is used for parameter estimation and inference. To circumvent the computational intensity associated with maximizing the joint likelihood, we propose an easy-to-implement three-step method. RESULTS We evaluate the performance of the proposed method through simulation studies and apply it to data from the Zurich Primary HIV Infection Study. We find that some key features of viral load during ART (e.g., viral decay rate) are significantly associated with important characteristics of viral rebound following ART interruption (e.g., viral set point). CONCLUSIONS The proposed three-step method works well. We have shown that key features of viral decay during ART may be associated with important features of viral rebound following ART interruption.
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Affiliation(s)
- Sihaoyu Gao
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
| | - Lang Wu
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
| | - Tingting Yu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
| | - Roger Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Rui Wang
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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16
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Lau JSY, Cromer D, Pinkevych M, Lewin SR, Rasmussen TA, McMahon JH, Davenport MP. OUP accepted manuscript. J Infect Dis 2022; 226:236-245. [PMID: 35104873 PMCID: PMC9400422 DOI: 10.1093/infdis/jiac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/30/2022] [Indexed: 11/14/2022] Open
Abstract
Background Methods Results Conclusions
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Affiliation(s)
- Jillian S Y Lau
- Correspondence: Jillian Lau, MBBS, FRACP, PhD, Department of Infectious Diseases, The Alfred Hospital, 85 Commercial Road, Prahran, 3181 Victoria, Australia ()
| | | | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute, University of New South Wales, Sydney, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, Alfred Hospital, Prahran, Australia
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Thomas A Rasmussen
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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17
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Rahman SA, Yagnik B, Bally AP, Morrow KN, Wang S, Vanderford TH, Freeman GJ, Ahmed R, Amara RR. PD-1 blockade and vaccination provide therapeutic benefit against SIV by inducing broad and functional CD8 + T cells in lymphoid tissue. Sci Immunol 2021; 6:eabh3034. [PMID: 34516743 DOI: 10.1126/sciimmunol.abh3034] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Sheikh Abdul Rahman
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Bhrugu Yagnik
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Alexander P Bally
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Kristen N Morrow
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Shelly Wang
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gordon J Freeman
- Department of Medical Oncology and Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Rafi Ahmed
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Rama Rao Amara
- Division of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
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18
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Tebas P, Jadlowsky JK, Shaw PA, Tian L, Esparza E, Brennan AL, Kim S, Naing SY, Richardson MW, Vogel AN, Maldini CR, Kong H, Liu X, Lacey SF, Bauer AM, Mampe F, Richman LP, Lee G, Ando D, Levine BL, Porter DL, Zhao Y, Siegel DL, Bar KJ, June CH, Riley JL. CCR5-edited CD4+ T cells augment HIV-specific immunity to enable post-rebound control of HIV replication. J Clin Invest 2021; 131:144486. [PMID: 33571163 PMCID: PMC8011906 DOI: 10.1172/jci144486] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/03/2021] [Indexed: 12/15/2022] Open
Abstract
BackgroundWe conducted a phase I clinical trial that infused CCR5 gene-edited CD4+ T cells to determine how these T cells can better enable HIV cure strategies.MethodsThe aim of trial was to develop RNA-based approaches to deliver zinc finger nuclease (ZFN), evaluate the effect of CCR5 gene-edited CD4+ T cells on the HIV-specific T cell response, test the ability of infused CCR5 gene-edited T cells to delay viral rebound during analytical treatment interruption, and determine whether individuals heterozygous for CCR5 Δ32 preferentially benefit. We enrolled 14 individuals living with HIV whose viral load was well controlled by antiretroviral therapy (ART). We measured the time to viral rebound after ART withdrawal, the persistence of CCR5-edited CD4+ T cells, and whether infusion of 10 billion CCR5-edited CD4+ T cells augmented the HIV-specific immune response.ResultsInfusion of the CD4+ T cells was well tolerated, with no serious adverse events. We observed a modest delay in the time to viral rebound relative to historical controls; however, 3 of the 14 individuals, 2 of whom were heterozygous for CCR5 Δ32, showed post-viral rebound control of viremia, before ultimately losing control of viral replication. Interestingly, only these individuals had substantial restoration of HIV-specific CD8+ T cell responses. We observed immune escape for 1 of these reinvigorated responses at viral recrudescence, illustrating a direct link between viral control and enhanced CD8+ T cell responses.ConclusionThese findings demonstrate how CCR5 gene-edited CD4+ T cell infusion could aid HIV cure strategies by augmenting preexisting HIV-specific immune responses.REGISTRATIONClinicalTrials.gov NCT02388594.FundingNIH funding (R01AI104400, UM1AI126620, U19AI149680, T32AI007632) was provided by the National Institute of Allergy and Infectious Diseases (NIAID), the National Institute on Drug Abuse (NIDA), the National Institute of Mental Health (NIMH), and the National Institute of Neurological Disorders and Stroke (NINDS). Sangamo Therapeutics also provided funding for these studies.
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Affiliation(s)
| | | | - Pamela A. Shaw
- Department of Biostatistics, Epidemiology and Informatics, and
| | - Lifeng Tian
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erin Esparza
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrea L. Brennan
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Ashley N. Vogel
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Colby R. Maldini
- Department of Microbiology and Center for Cellular Immunotherapies
| | - Hong Kong
- Department of Microbiology and Center for Cellular Immunotherapies
| | - Xiaojun Liu
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Simon F. Lacey
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | - Gary Lee
- Sangamo Therapeutics Inc., Richmond, California, USA
| | - Dale Ando
- Sangamo Therapeutics Inc., Richmond, California, USA
| | - Bruce L. Levine
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Yangbing Zhao
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Don L. Siegel
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Carl H. June
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James L. Riley
- Department of Microbiology and Center for Cellular Immunotherapies
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19
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Conway JM, Meily P, Li JZ, Perelson AS. Unified model of short- and long-term HIV viral rebound for clinical trial planning. J R Soc Interface 2021; 18:20201015. [PMID: 33849338 PMCID: PMC8086917 DOI: 10.1098/rsif.2020.1015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/23/2021] [Indexed: 11/12/2022] Open
Abstract
Antiretroviral therapy (ART) effectively controls HIV infection, suppressing HIV viral loads. Typically suspension of therapy is rapidly followed by rebound of viral loads to high, pre-therapy levels. Indeed, a recent study showed that approximately 90% of treatment interruption study participants show viral rebound within at most a few months of therapy suspension, but the remaining 10%, showed viral rebound some months, or years, after ART suspension. Some may even never rebound. We investigate and compare branching process models aimed at gaining insight into these viral dynamics. Specifically, we provide a theory that explains both short- and long-term viral rebounds, and post-treatment control, via a multitype branching process with time-inhomogeneous rates, validated with data from Li et al. (Li et al. 2016 AIDS30, 343-353. (doi:10.1097/QAD.0000000000000953)). We discuss the associated biological interpretation and implications of our best-fit model. To test the effectiveness of an experimental intervention in delaying or preventing rebound, the standard practice is to suspend therapy and monitor the study participants for rebound. We close with a discussion of an important application of our modelling in the design of such clinical trials.
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Affiliation(s)
- Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Paige Meily
- University of Pennsylvania School of Arts and Sciences, Philadephia, PA, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
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20
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Kim Y, Mensah GA, Al Sharif S, Pinto DO, Branscome H, Yelamanchili SV, Cowen M, Erickson J, Khatkar P, Mahieux R, Kashanchi F. Extracellular Vesicles from Infected Cells Are Released Prior to Virion Release. Cells 2021; 10:cells10040781. [PMID: 33916140 PMCID: PMC8066806 DOI: 10.3390/cells10040781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/29/2022] Open
Abstract
Here, we have attempted to address the timing of EV and virion release from virally infected cells. Uninfected (CEM), HIV-1-infected (J1.1), and human T cell leukemia virus-1 (HTLV-1)-infected (HUT102) cells were synchronized in G0. Viral latency was reversed by increasing gene expression with the addition of serum-rich media and inducers. Supernatants and cell pellets were collected post-induction at different timepoints and assayed for extracellular vesicle (EV) and autophagy markers; and for viral proteins and RNAs. Tetraspanins and autophagy-related proteins were found to be differentially secreted in HIV-1- and HTLV-1-infected cells when compared with uninfected controls. HIV-1 proteins were present at 6 h and their production increased up to 24 h. HTLV-1 proteins peaked at 6 h and plateaued. HIV-1 and HTLV-1 RNA production correlated with viral protein expression. Nanoparticle tracking analysis (NTA) showed increase of EV concentration over time in both uninfected and infected samples. Finally, the HIV-1 supernatant from the 6-h samples was found not to be infectious; however, the virus from the 24-h samples was successfully rescued and infectious. Overall, our data indicate that EV release may occur prior to viral release from infected cells, thereby implicating a potentially significant effect of EVs on uninfected recipient cells prior to subsequent viral infection and spread.
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Affiliation(s)
- Yuriy Kim
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Gifty A. Mensah
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Sarah Al Sharif
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Daniel O. Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Heather Branscome
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Sowmya V. Yelamanchili
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - James Erickson
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Pooja Khatkar
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Renaud Mahieux
- International Center for Research in Infectiology, Retroviral Oncogenesis Laboratory, INSERM U1111-Université Claude Bernard Lyon 1, Ecole Normale Superieure de Lyon, Université de Lyon, Fondation Pour La Recherche Médicale, Labex Ecofect, 69007 Lyon, France;
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
- Correspondence: ; Tel.: +703-993-9160; Fax: +703-993-7022
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21
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Cardozo-Ojeda EF, Duke ER, Peterson CW, Reeves DB, Mayer BT, Kiem HP, Schiffer JT. Thresholds for post-rebound SHIV control after CCR5 gene-edited autologous hematopoietic cell transplantation. eLife 2021; 10:57646. [PMID: 33432929 PMCID: PMC7803377 DOI: 10.7554/elife.57646] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 12/27/2020] [Indexed: 01/10/2023] Open
Abstract
Autologous, CCR5 gene-edited hematopoietic stem and progenitor cell (HSPC) transplantation is a promising strategy for achieving HIV remission. However, only a fraction of HSPCs can be edited ex vivo to provide protection against infection. To project the thresholds of CCR5-edition necessary for HIV remission, we developed a mathematical model that recapitulates blood T cell reconstitution and plasma simian-HIV (SHIV) dynamics from SHIV-1157ipd3N4-infected pig-tailed macaques that underwent autologous transplantation with CCR5 gene editing. The model predicts that viral control can be obtained following analytical treatment interruption (ATI) when: (1) transplanted HSPCs are at least fivefold higher than residual endogenous HSPCs after total body irradiation and (2) the fraction of protected HSPCs in the transplant achieves a threshold (76–94%) sufficient to overcome transplantation-dependent loss of SHIV immunity. Under these conditions, if ATI is withheld until transplanted gene-modified cells engraft and reconstitute to a steady state, spontaneous viral control is projected to occur.
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Affiliation(s)
- E Fabian Cardozo-Ojeda
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States
| | - Elizabeth R Duke
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States.,Department of Medicine, University of Washington, Seattle, United States
| | - Christopher W Peterson
- Department of Medicine, University of Washington, Seattle, United States.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Daniel B Reeves
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States
| | - Bryan T Mayer
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States
| | - Hans-Peter Kiem
- Department of Medicine, University of Washington, Seattle, United States.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Pathology, University of Washington, Seattle, United States
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, University of Washington, Seattle, United States.,Department of Medicine, University of Washington, Seattle, United States.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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22
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Saha A, Dixit NM. Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection. PLoS Comput Biol 2020; 16:e1008434. [PMID: 33253162 PMCID: PMC7728175 DOI: 10.1371/journal.pcbi.1008434] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 12/10/2020] [Accepted: 10/11/2020] [Indexed: 01/26/2023] Open
Abstract
Passive immunization with broadly neutralizing antibodies (bNAbs) of HIV-1 appears a promising strategy for eliciting long-term HIV-1 remission. When administered concomitantly with the cessation of antiretroviral therapy (ART) to patients with established viremic control, bNAb therapy is expected to prolong remission. Surprisingly, in clinical trials on chronic HIV-1 patients, the bNAb VRC01 failed to prolong remission substantially. Identifying the cause of this failure is important for improving VRC01-based therapies and unraveling potential vulnerabilities of other bNAbs. In the trials, viremia resurged rapidly in most patients despite suppressive VRC01 concentrations in circulation, suggesting that VRC01 resistance was the likely cause of failure. ART swiftly halts viral replication, precluding the development of resistance during ART. If resistance were to emerge post ART, virological breakthrough would have taken longer than without VRC01 therapy. We hypothesized therefore that VRC01-resistant strains must have been formed before ART initiation, survived ART in latently infected cells, and been activated during VRC01 therapy, causing treatment failure. Current assays preclude testing this hypothesis experimentally. We developed a mathematical model based on the hypothesis and challenged it with available clinical data. The model integrated within-host HIV-1 evolution, stochastic latency reactivation, and viral dynamics with multiple-dose VRC01 pharmacokinetics. The model predicted that single but not higher VRC01-resistant mutants would pre-exist in the latent reservoir. We constructed a virtual patient population that parsimoniously recapitulated inter-patient variations. Model predictions with this population quantitatively captured data of VRC01 failure from clinical trials, presenting strong evidence supporting the hypothesis. We attributed VRC01 failure to single-mutant VRC01-resistant proviruses in the latent reservoir triggering viral recrudescence, particularly when VRC01 was at trough levels. Pre-existing resistant proviruses in the latent reservoir may similarly compromise other bNAbs. Our study provides a framework for designing bNAb-based therapeutic protocols that would avert such failure and maximize HIV-1 remission. Antiretroviral therapy (ART) can control but not eradicate HIV-1. Stopping ART leads to rapid viral resurgence and progressive disease. ART is therefore administered lifelong. Tremendous efforts are ongoing to devise strategies that will enable stopping ART and yet prevent viral resurgence. One such strategy involves the administration of broadly neutralizing antibodies (bNAbs) of HIV-1 at the time of stopping ART. This strategy is expected to delay if not prevent viral resurgence. Surprisingly, treatment with VRC01, a potent bNAb, resulted in hardly any improvement in viral remission. In this study, we elucidate the cause of this failure. We hypothesized that VRC01-resistant strains may pre-exist in latently infected cells, which are unaffected by ART. They can thus outlast ART and get reactivated, triggering VRC01 failure. We built a detailed mathematical model based on this hypothesis and showed that it quantitatively captured observations of VRC01 failure in clinical trials on chronic HIV-1 patients. Our study thus identifies a potential vulnerability of bNAbs, namely, bNAb-resistant strains pre-existing in latently infected cells. Our model offers a framework for predicting bNAb-based treatment protocols that would preclude failure due to pre-existing resistance and maximally prolong remission.
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Affiliation(s)
- Ananya Saha
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
- * E-mail:
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23
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van Dorp CH, Conway JM, Barouch DH, Whitney JB, Perelson AS. Models of SIV rebound after treatment interruption that involve multiple reactivation events. PLoS Comput Biol 2020; 16:e1008241. [PMID: 33001979 PMCID: PMC7529301 DOI: 10.1371/journal.pcbi.1008241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023] Open
Abstract
In order to assess the efficacy of novel HIV-1 treatments leading to a functional cure, the time to viral rebound is frequently used as a surrogate endpoint. The longer the time to viral rebound, the more efficacious the therapy. In support of such an approach, mathematical models serve as a connection between the size of the latent reservoir and the time to HIV-1 rebound after treatment interruption. The simplest of such models assumes that a single successful latent cell reactivation event leads to observable viremia after a period of exponential viral growth. Here we consider a generalization developed by Pinkevych et al. and Hill et al. of this simple model in which multiple reactivation events can occur, each contributing to the exponential growth of the viral load. We formalize and improve the previous derivation of the dynamics predicted by this model, and use the model to estimate relevant biological parameters from SIV rebound data. We confirm a previously described effect of very early antiretroviral therapy (ART) initiation on the rate of recrudescence and the viral load growth rate after treatment interruption. We find that every day ART initiation is delayed results in a 39% increase in the recrudescence rate (95% credible interval: [18%, 62%]), and a 11% decrease of the viral growth rate (95% credible interval: [4%, 20%]). We show that when viral rebound occurs early relative to the viral load doubling time, a model with multiple successful reactivation events fits the data better than a model with only a single successful reactivation event.
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Affiliation(s)
- Christiaan H. van Dorp
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - James B. Whitney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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24
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Wu Y, Pinkevych M, Xu Z, Keele BF, Davenport MP, Cromer D. Impact of fluctuation in frequency of human immunodeficiency virus/simian immunodeficiency virus reactivation during antiretroviral therapy interruption. Proc Biol Sci 2020; 287:20200354. [PMID: 32811309 PMCID: PMC7482276 DOI: 10.1098/rspb.2020.0354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
Antiretroviral therapy (ART) provides effective control of human immunodeficiency virus (HIV) replication and maintains viral loads of HIV at undetectable levels. Interruption of ART causes rapid recrudescence of HIV plasma viremia due to reactivation of latently HIV-infected cells. Here, we characterize the timing of both the initial and subsequent successful viral reactivations following ART interruption in macaques infected with simian immunodeficiency virus (SIV). We compare these to previous results from HIV-infected patients. We find that on average the time until the first successful viral reactivation event is longer than the time between subsequent reactivations. Based on this result, we hypothesize that the reactivation frequency of both HIV and SIV may fluctuate over time, and that this may impact the treatment of HIV. We develop a stochastic model incorporating fluctuations in the frequency of viral reactivation following ART interruption that shows behaviours consistent with the observed data. Furthermore, we show that one of the impacts of a fluctuating reactivation frequency would be to significantly reduce the efficacy of 'anti-latency' interventions for HIV that aim to reduce the frequency of reactivation. It is therefore essential to consider the possibility of a fluctuating reactivation frequency when assessing the impact of such intervention strategies.
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Affiliation(s)
- Yuhuang Wu
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
| | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
| | - Zhuang Xu
- School of Physics, University of New South Wales, Sydney, NSW, Australia
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
| | - Deborah Cromer
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
- School of Mathematics and Statistics, University of New South Wales, Sydney, NSW, Australia
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25
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Bing A, Hu Y, Prague M, Hill AL, Li JZ, Bosch RJ, De Gruttola V, Wang R. Comparison of empirical and dynamic models for HIV viral load rebound after treatment interruption. STATISTICAL COMMUNICATIONS IN INFECTIOUS DISEASES 2020; 12:20190021. [PMID: 34158910 PMCID: PMC8216669 DOI: 10.1515/scid-2019-0021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE To compare empirical and mechanistic modeling approaches for describing HIV-1 RNA viral load trajectories after antiretroviral treatment interruption and for identifying factors that predict features of viral rebound process. METHODS We apply and compare two modeling approaches in analysis of data from 346 participants in six AIDS Clinical Trial Group studies. From each separate analysis, we identify predictors for viral set points and delay in rebound. Our empirical model postulates a parametric functional form whose parameters represent different features of the viral rebound process, such as rate of rise and viral load set point. The viral dynamics model augments standard HIV dynamics models-a class of mathematical models based on differential equations describing biological mechanisms-by including reactivation of latently infected cells and adaptive immune response. We use Monolix, which makes use of a Stochastic Approximation of the Expectation-Maximization algorithm, to fit non-linear mixed effects models incorporating observations that were below the assay limit of quantification. RESULTS Among the 346 participants, the median age at treatment interruption was 42. Ninety-three percent of participants were male and sixty-five percent, white non-Hispanic. Both models provided a reasonable fit to the data and can accommodate atypical viral load trajectories. The median set points obtained from two approaches were similar: 4.44 log10 copies/mL from the empirical model and 4.59 log10 copies/mL from the viral dynamics model. Both models revealed that higher nadir CD4 cell counts and ART initiation during acute/recent phase were associated with lower viral set points and identified receiving a non-nucleoside reverse transcriptase inhibitor (NNRTI)-based pre-ATI regimen as a predictor for a delay in rebound. CONCLUSION Although based on different sets of assumptions, both models lead to similar conclusions regarding features of viral rebound process.
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Affiliation(s)
- Ante Bing
- Department of Mathematics and Statistics, Boston University, Boston, MA, 02215, USA
| | - Yuchen Hu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Melanie Prague
- University of Bordeaux, Inria Bordeaux Sud-Ouest, Inserm, Bordeaux Population Health Research Center, SISTM Team, UMR 1219, F-33000 Bordeaux, France
| | - Alison L Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston MA 02215, USA
| | - Ronald J Bosch
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Victor De Gruttola
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Rui Wang
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
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26
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Wang R, Bing A, Wang C, Hu Y, Bosch RJ, DeGruttola V. A flexible nonlinear mixed effects model for HIV viral load rebound after treatment interruption. Stat Med 2020; 39:2051-2066. [PMID: 32293756 PMCID: PMC8081565 DOI: 10.1002/sim.8529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 01/14/2020] [Accepted: 02/27/2020] [Indexed: 12/30/2022]
Abstract
Characterization of HIV viral rebound after the discontinuation of antiretroviral therapy is central to HIV cure research. We propose a parametric nonlinear mixed effects model for the viral rebound trajectory, which often has a rapid rise to a peak value followed by a decrease to a viral load set point. We choose a flexible functional form that captures the shapes of viral rebound trajectories and can also provide biological insights regarding the rebound process. Each parameter can incorporate a random effect to allow for variation in parameters across individuals. Key features of viral rebound trajectories such as viral set points are represented by the parameters in the model, which facilitates assessment of intervention effects and identification of important pretreatment interruption predictors for these features. We employ a stochastic expectation-maximization (StEM) algorithm to incorporate HIV-1 RNA values that are below the lower limit of assay quantification. We evaluate the performance of our model in simulation studies and apply the proposed model to longitudinal HIV-1 viral load data from five AIDS Clinical Trials Group treatment interruption studies.
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Affiliation(s)
- Rui Wang
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ante Bing
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Cathy Wang
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yuchen Hu
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ronald J. Bosch
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Victor DeGruttola
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
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27
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Dessie ZG, Zewotir T, Mwambi H, North D. Modeling Viral Suppression, Viral Rebound and State-Specific Duration of HIV Patients with CD4 Count Adjustment: Parametric Multistate Frailty Model Approach. Infect Dis Ther 2020; 9:367-388. [PMID: 32318999 PMCID: PMC7237593 DOI: 10.1007/s40121-020-00296-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Combination antiretroviral therapy has become the standard care of human immunodeficiency virus (HIV)-infected patients and has further led to a dramatically decreased progression probability to acquired immune deficiency syndrome (AIDS) for patients under such a therapy. However, responses of the patients to this therapy have recorded heterogeneous complexity and high dynamism. In this paper, we simultaneously model long-term viral suppression, viral rebound, and state-specific duration of HIV-infected patients. METHODS Full-parametric and semi-parametric Markov multistate models were applied to assess the effects of covariates namely TB co-infection, educational status, marital status, age, quality of life (QoL) scores, white and red blood cell parameters, and liver enzyme abnormality on long-term viral suppression, viral rebound and state-specific duration for HIV-infected individuals before and after treatment. Furthermore, two models, one including and another excluding the effect of the frailty, were presented and compared in this study. RESULTS Results from the diagnostic plots, Akaike information criterion (AIC) and likelihood ratio test showed that the Weibull multistate frailty model fitted significantly better than the exponential and semi-parametric multistate models. Viral rebound was found to be significantly associated with many sex partners, higher eosinophils count, younger age, lower educational level, higher monocyte counts, having abnormal neutrophils count, and higher liver enzyme abnormality. Furthermore, viral suppression was also found to be significantly associated with higher QoL scores, and having a stable sex partner. The analysis result also showed that patients with a stable sex partner, higher educational levels, higher QoL scores, lower eosinophils count, lower monocyte counts, and higher RBC indices were more likely to spend more time in undetectable viral load state. CONCLUSIONS To achieve and maintain the UNAIDS 90% suppression targets, additional interventions are required to optimize antiretroviral therapy outcomes, specifically targeting those with poor clinical characteristics, lower education, younger age, and those with many sex partners. From a methodological perspective, the parametric multistate approach with frailty is a flexible approach for modeling time-varying variables, allowing for dealing with heterogeneity between the sequence of transitions, as well as allowing for a reasonable degree of flexibility with a few additional parameters, which then aids in gaining a better insight into how factors change over time.
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Affiliation(s)
- Zelalem G Dessie
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa.
- College of Science, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Temesgen Zewotir
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
| | - Henry Mwambi
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
| | - Delia North
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Durban, South Africa
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