1
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Phan T, Zitzmann C, Chew KW, Smith DM, Daar ES, Wohl DA, Eron JJ, Currier JS, Hughes MD, Choudhary MC, Deo R, Li JZ, Ribeiro RM, Ke R, Perelson AS. Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody. PLoS Pathog 2024; 20:e1011680. [PMID: 38635853 DOI: 10.1371/journal.ppat.1011680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/18/2024] [Indexed: 04/20/2024] Open
Abstract
To mitigate the loss of lives during the COVID-19 pandemic, emergency use authorization was given to several anti-SARS-CoV-2 monoclonal antibody (mAb) therapies for the treatment of mild-to-moderate COVID-19 in patients with a high risk of progressing to severe disease. Monoclonal antibodies used to treat SARS-CoV-2 target the spike protein of the virus and block its ability to enter and infect target cells. Monoclonal antibody therapy can thus accelerate the decline in viral load and lower hospitalization rates among high-risk patients with variants susceptible to mAb therapy. However, viral resistance has been observed, in some cases leading to a transient viral rebound that can be as large as 3-4 orders of magnitude. As mAbs represent a proven treatment choice for SARS-CoV-2 and other viral infections, evaluation of treatment-emergent mAb resistance can help uncover underlying pathobiology of SARS-CoV-2 infection and may also help in the development of the next generation of mAb therapies. Although resistance can be expected, the large rebounds observed are much more difficult to explain. We hypothesize replenishment of target cells is necessary to generate the high transient viral rebound. Thus, we formulated two models with different mechanisms for target cell replenishment (homeostatic proliferation and return from an innate immune response antiviral state) and fit them to data from persons with SARS-CoV-2 treated with a mAb. We showed that both models can explain the emergence of resistant virus associated with high transient viral rebounds. We found that variations in the target cell supply rate and adaptive immunity parameters have a strong impact on the magnitude or observability of the viral rebound associated with the emergence of resistant virus. Both variations in target cell supply rate and adaptive immunity parameters may explain why only some individuals develop observable transient resistant viral rebound. Our study highlights the conditions that can lead to resistance and subsequent viral rebound in mAb treatments during acute infection.
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Affiliation(s)
- Tin Phan
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Carolin Zitzmann
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Kara W Chew
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Davey M Smith
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Judith S Currier
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Michael D Hughes
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Manish C Choudhary
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rinki Deo
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan Z Li
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruy M Ribeiro
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ruian Ke
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S Perelson
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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2
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Zitzmann C, Ke R, Ribeiro RM, Perelson AS. How robust are estimates of key parameters in standard viral dynamic models? PLoS Comput Biol 2024; 20:e1011437. [PMID: 38626190 PMCID: PMC11051641 DOI: 10.1371/journal.pcbi.1011437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 04/26/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Mathematical models of viral infection have been developed, fitted to data, and provide insight into disease pathogenesis for multiple agents that cause chronic infection, including HIV, hepatitis C, and B virus. However, for agents that cause acute infections or during the acute stage of agents that cause chronic infections, viral load data are often collected after symptoms develop, usually around or after the peak viral load. Consequently, we frequently lack data in the initial phase of viral growth, i.e., when pre-symptomatic transmission events occur. Missing data may make estimating the time of infection, the infectious period, and parameters in viral dynamic models, such as the cell infection rate, difficult. However, having extra information, such as the average time to peak viral load, may improve the robustness of the estimation. Here, we evaluated the robustness of estimates of key model parameters when viral load data prior to the viral load peak is missing, when we know the values of some parameters and/or the time from infection to peak viral load. Although estimates of the time of infection are sensitive to the quality and amount of available data, particularly pre-peak, other parameters important in understanding disease pathogenesis, such as the loss rate of infected cells, are less sensitive. Viral infectivity and the viral production rate are key parameters affecting the robustness of data fits. Fixing their values to literature values can help estimate the remaining model parameters when pre-peak data is missing or limited. We find a lack of data in the pre-peak growth phase underestimates the time to peak viral load by several days, leading to a shorter predicted growth phase. On the other hand, knowing the time of infection (e.g., from epidemiological data) and fixing it results in good estimates of dynamical parameters even in the absence of early data. While we provide ways to approximate model parameters in the absence of early viral load data, our results also suggest that these data, when available, are needed to estimate model parameters more precisely.
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Affiliation(s)
- Carolin Zitzmann
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ruian Ke
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Alan S. Perelson
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico
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3
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Dhaubhadel S, Ganguly K, Ribeiro RM, Cohn JD, Hyman JM, Hengartner NW, Kolade B, Singley A, Bhattacharya T, Finley P, Levin D, Thelen H, Cho K, Costa L, Ho YL, Justice AC, Pestian J, Santel D, Zamora-Resendiz R, Crivelli S, Tamang S, Martins S, Trafton J, Oslin DW, Beckham JC, Kimbrel NA, McMahon BH. High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning. Sci Rep 2024; 14:1793. [PMID: 38245528 PMCID: PMC10799879 DOI: 10.1038/s41598-024-51762-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
We present an ensemble transfer learning method to predict suicide from Veterans Affairs (VA) electronic medical records (EMR). A diverse set of base models was trained to predict a binary outcome constructed from reported suicide, suicide attempt, and overdose diagnoses with varying choices of study design and prediction methodology. Each model used twenty cross-sectional and 190 longitudinal variables observed in eight time intervals covering 7.5 years prior to the time of prediction. Ensembles of seven base models were created and fine-tuned with ten variables expected to change with study design and outcome definition in order to predict suicide and combined outcome in a prospective cohort. The ensemble models achieved c-statistics of 0.73 on 2-year suicide risk and 0.83 on the combined outcome when predicting on a prospective cohort of [Formula: see text] 4.2 M veterans. The ensembles rely on nonlinear base models trained using a matched retrospective nested case-control (Rcc) study cohort and show good calibration across a diversity of subgroups, including risk strata, age, sex, race, and level of healthcare utilization. In addition, a linear Rcc base model provided a rich set of biological predictors, including indicators of suicide, substance use disorder, mental health diagnoses and treatments, hypoxia and vascular damage, and demographics.
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Affiliation(s)
| | - Kumkum Ganguly
- Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Ruy M Ribeiro
- Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Judith D Cohn
- Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - James M Hyman
- Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | | | - Beauty Kolade
- Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Anna Singley
- Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | | | | | - Drew Levin
- Sandia National Laboratory, Albuquerque, NM, 87123, USA
| | - Haedi Thelen
- Sandia National Laboratory, Albuquerque, NM, 87123, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology and Research Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Lauren Costa
- Massachusetts Veterans Epidemiology and Research Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology and Research Information Center (MAVERIC), VA Boston Healthcare System, Boston, USA
| | - Amy C Justice
- VA Connecticut Healthcare System, Yale Schools of Medicine and Public Health, Yale University, West Haven, CT, USA
| | - John Pestian
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Daniel Santel
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Rafael Zamora-Resendiz
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Silvia Crivelli
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Suzanne Tamang
- Program Evaluation and Resource Center, Office of Mental Health and Suicide Prevention, Veterans Affairs Palo Alto Health Care System, Menlo Park, CA, USA
- Department of Medicine, Stanford University, Stanford, California, USA
| | - Susana Martins
- Program Evaluation and Resource Center, Office of Mental Health and Suicide Prevention, Veterans Affairs Palo Alto Health Care System, Menlo Park, CA, USA
| | - Jodie Trafton
- Program Evaluation and Resource Center, Office of Mental Health and Suicide Prevention, Veterans Affairs Palo Alto Health Care System, Menlo Park, CA, USA
| | - David W Oslin
- Cpl Michael J Crescenz VA Medical Center, VISN 4 Mental Illness Research, Education, and Clinical Center; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, 3535 Market Street, Philadelphia, PA, 19104, USA
| | - Jean C Beckham
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, USA
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Nathan A Kimbrel
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, USA
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham, NC, USA
- VA Health Services Research and Development Center of Innovation to Accelerate Discovery and Practice Transformation, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
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4
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Williams B, Carruthers J, Gillard JJ, Lythe G, Perelson AS, Ribeiro RM, Molina-París C, López-García M. The reproduction number and its probability distribution for stochastic viral dynamics. J R Soc Interface 2024; 21:20230400. [PMID: 38264928 PMCID: PMC10806437 DOI: 10.1098/rsif.2023.0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
We consider stochastic models of individual infected cells. The reproduction number, R, is understood as a random variable representing the number of new cells infected by one initial infected cell in an otherwise susceptible (target cell) population. Variability in R results partly from heterogeneity in the viral burst size (the number of viral progeny generated from an infected cell during its lifetime), which depends on the distribution of cellular lifetimes and on the mechanism of virion release. We analyse viral dynamics models with an eclipse phase: the period of time after a cell is infected but before it is capable of releasing virions. The duration of the eclipse, or the subsequent infectious, phase is non-exponential, but composed of stages. We derive the probability distribution of the reproduction number for these viral dynamics models, and show it is a negative binomial distribution in the case of constant viral release from infectious cells, and under the assumption of an excess of target cells. In a deterministic model, the ultimate in-host establishment or extinction of the viral infection depends entirely on whether the mean reproduction number is greater than, or less than, one, respectively. Here, the probability of extinction is determined by the probability distribution of R, not simply its mean value. In particular, we show that in some cases the probability of infection is not an increasing function of the mean reproduction number.
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Affiliation(s)
- Bevelynn Williams
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | | | - Joseph J. Gillard
- CBR Division, Defence Science and Technology Laboratory, Salisbury, UK
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | - Alan S. Perelson
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ruy M. Ribeiro
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Carmen Molina-París
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
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5
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Sambaturu N, Fray EJ, Wu F, Zitzmann C, Simonetti FR, Barouch DH, Siliciano JD, Siliciano RF, Ribeiro RM, Perelson AS, Molina-París C, Leitner T. Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4 + T cells. bioRxiv 2023:2023.11.03.565539. [PMID: 37961482 PMCID: PMC10635124 DOI: 10.1101/2023.11.03.565539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
HIV can persist in a latent form as integrated DNA (provirus) in resting CD4+ T cells of infected individuals and as such is unaffected by antiretroviral therapy (ART). Despite being a major obstacle for eradication efforts, the genetic variation and timing of formation of this latent reservoir remains poorly understood. Previous studies on when virus is deposited in the latent reservoir have come to contradictory conclusions. To reexamine the genetic variation of HIV in CD4+ T cells during ART, we determined the divergence in envelope sequences collected from 10 SIV infected rhesus macaques. We found that the macaques displayed a biphasic decline of the viral divergence over time, where the first phase lasted for an average of 11.6 weeks (range 4-28 weeks). Motivated by recent observations that the HIV-infected CD4+ T cell population is composed of short- and long-lived subsets, we developed a model to study the divergence dynamics. We found that SIV in short-lived cells was on average more diverged, while long-lived cells harbored less diverged virus. This suggests that the long-lived cells harbor virus deposited starting earlier in infection and continuing throughout infection, while short-lived cells predominantly harbor more recent virus. As these cell populations decayed, the overall proviral divergence decline matched that observed in the empirical data. This model explains previous seemingly contradictory results on the timing of virus deposition into the latent reservoir, and should provide guidance for future eradication efforts.
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Affiliation(s)
- Narmada Sambaturu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Carolin Zitzmann
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Carmen Molina-París
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
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Thio CL, Taddese M, Saad Y, Zambo K, Ribeiro RM, Grudda T, Sulkowski MS, Sterling RK, Zhang Y, Young ED, Hwang HS, Balagopal A. Hepatitis B e Antigen-Negative Single Hepatocyte Analysis Shows Transcriptional Silencing and Slow Decay of Infected Cells With Treatment. J Infect Dis 2023; 228:1219-1226. [PMID: 37129258 PMCID: PMC10629706 DOI: 10.1093/infdis/jiad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Nucleos(t)ide analogues (NUCs) rarely cure chronic hepatitis B (CHB) because they do not eliminate covalently closed circular deoxyribonucleic acid, the stable replication template. In hepatitis B e antigen (HBeAg)-positive CHB during NUCs, HBV-infected cells decline slowly and are transcriptionally silenced. Whether these occur in HBeAg-negative CHB is unknown. METHODS Using paired liver biopsies separated by 2.7-3.7 years in 4 males with HIV and HBeAg-negative CHB at both biopsies and 1 male with HIV who underwent HBeAg seroconversion between biopsies, we quantified amounts of viral nucleic acids in hundreds of individual hepatocytes. RESULTS In the 4 persistently HBeAg-negative participants, HBV-infected hepatocytes ranged from 6.2% to 17.7% (biopsy 1) and significantly declined in 3 of 4 by biopsy 2. In the HBeAg seroconverter, the proportion was 97.4% (biopsy 1) and declined to 81.9% at biopsy 2 (P < .05). We extrapolated that HBV eradication with NUCs would take >100 years. At biopsy 1 in the persistently HBeAg-negative participants, 23%-56.8% of infected hepatocytes were transcriptionally inactive-higher than we observed in HBeAg-positive CHB-and significantly declined in 1 of 4 at biopsy 2. CONCLUSIONS In HBeAg-negative CHB on NUCs, the negligible decline in infected hepatocytes is similar to HBeAg-positive CHB, supporting the need for more potent therapeutics to achieve functional cure.
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Affiliation(s)
- Chloe L Thio
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MarylandUSA
| | - Maraake Taddese
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yasmeen Saad
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kristina Zambo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ruy M Ribeiro
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Tanner Grudda
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MarylandUSA
| | - Mark S Sulkowski
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard K Sterling
- Divison of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yang Zhang
- Division of Gastrointestinal and Hepatic Pathology, Joint Pathology Center, Silver Spring, Maryland, USA
| | - Eric D Young
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hyon S Hwang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ashwin Balagopal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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7
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Kumar MR, Fray EJ, Bender AM, Zitzmann C, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir. Proc Natl Acad Sci U S A 2023; 120:e2313209120. [PMID: 37844236 PMCID: PMC10614214 DOI: 10.1073/pnas.2313209120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy (ART) and precludes cure. Reservoir-targeting interventions are evaluated in ART-treated macaques infected with simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV). Efficacy is determined by reservoir measurements before and after the intervention. However, most proviruses persisting in the setting of ART are defective. In addition, intact HIV-1 and SIV genomes undergo complex, multiphasic decay observable when new infection events are blocked by ART. Intervention-induced elimination of latently infected cells must be distinguished from natural decay. Here, we address these issues for SHIV. We describe an intact proviral DNA assay that allows digital counting of SHIV genomes lacking common fatal defects. We show that intact SHIV genomes in circulating CD4+ T cells undergo biphasic decay during the first year of ART, with a rapid first phase (t1/2 = 30.1 d) and a slower second phase (t1/2 = 8.1 mo) that is still more rapid that the slow decay observed in people with HIV-1 on long-term ART (t1/2 = 3.7 y). In SHIV models, most interventions are tested during 2nd phase decay. Natural 2nd phase decay must be considered in evaluating interventions as most infected cells present at this time do not become part of the stable reservoir. In addition, for interventions tested during 2nd phase decay, a caveat is that the intervention may not be equally effective in people with HIV on long-term ART whose reservoirs are dominated by latently infected cells with a slower decay rate.
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Affiliation(s)
- Mithra R. Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Emily J. Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Alexandra M. Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | | | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA02215
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Baltimore, MD21205
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8
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Policicchio BB, Cardozo-Ojeda EF, Xu C, Ma D, He T, Raehtz KD, Sivanandham R, Kleinman AJ, Perelson AS, Apetrei C, Pandrea I, Ribeiro RM. CD8 + T cells control SIV infection using both cytolytic effects and non-cytolytic suppression of virus production. Nat Commun 2023; 14:6657. [PMID: 37863982 PMCID: PMC10589330 DOI: 10.1038/s41467-023-42435-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Whether CD8+ T lymphocytes control human immunodeficiency virus infection by cytopathic or non-cytopathic mechanisms is not fully understood. Multiple studies highlighted non-cytopathic effects, but one hypothesis is that cytopathic effects of CD8+ T cells occur before viral production. Here, to examine the role of CD8+ T cells prior to virus production, we treated SIVmac251-infected macaques with an integrase inhibitor combined with a CD8-depleting antibody, or with either reagent alone. We analyzed the ensuing viral dynamics using a mathematical model that included infected cells pre- and post- viral DNA integration to compare different immune effector mechanisms. Macaques receiving the integrase inhibitor alone experienced greater viral load decays, reaching lower nadirs on treatment, than those treated also with the CD8-depleting antibody. Models including CD8+ cell-mediated reduction of viral production (non-cytolytic) were found to best explain the viral profiles across all macaques, in addition an effect in killing infected cells pre-integration (cytolytic) was supported in some of the best models. Our results suggest that CD8+ T cells have both a cytolytic effect on infected cells before viral integration, and a direct, non-cytolytic effect by suppressing viral production.
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Affiliation(s)
- Benjamin B Policicchio
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | | | - Cuiling Xu
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Dongzhu Ma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Tianyu He
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Kevin D Raehtz
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Ranjit Sivanandham
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Adam J Kleinman
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Cristian Apetrei
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Ivona Pandrea
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
- Laboratório de Biomatemática, Faculdade de Medicina da Universidade de Lisboa (previous address), Lisboa, Portugal.
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9
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Phan T, Zitzmann C, Chew KW, Smith DM, Daar ES, Wohl DA, Eron JJ, Currier JS, Hughes MD, Choudhary MC, Deo R, Li JZ, Ribeiro RM, Ke R, Perelson AS. Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody. bioRxiv 2023:2023.09.14.557679. [PMID: 37745410 PMCID: PMC10515893 DOI: 10.1101/2023.09.14.557679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The COVID-19 pandemic has led to over 760 million cases and 6.9 million deaths worldwide. To mitigate the loss of lives, emergency use authorization was given to several anti-SARS-CoV-2 monoclonal antibody (mAb) therapies for the treatment of mild-to-moderate COVID-19 in patients with a high risk of progressing to severe disease. Monoclonal antibodies used to treat SARS-CoV-2 target the spike protein of the virus and block its ability to enter and infect target cells. Monoclonal antibody therapy can thus accelerate the decline in viral load and lower hospitalization rates among high-risk patients with susceptible variants. However, viral resistance has been observed, in some cases leading to a transient viral rebound that can be as large as 3-4 orders of magnitude. As mAbs represent a proven treatment choice for SARS-CoV-2 and other viral infections, evaluation of treatment-emergent mAb resistance can help uncover underlying pathobiology of SARS-CoV-2 infection and may also help in the development of the next generation of mAb therapies. Although resistance can be expected, the large rebounds observed are much more difficult to explain. We hypothesize replenishment of target cells is necessary to generate the high transient viral rebound. Thus, we formulated two models with different mechanisms for target cell replenishment (homeostatic proliferation and return from an innate immune response anti-viral state) and fit them to data from persons with SARS-CoV-2 treated with a mAb. We showed that both models can explain the emergence of resistant virus associated with high transient viral rebounds. We found that variations in the target cell supply rate and adaptive immunity parameters have a strong impact on the magnitude or observability of the viral rebound associated with the emergence of resistant virus. Both variations in target cell supply rate and adaptive immunity parameters may explain why only some individuals develop observable transient resistant viral rebound. Our study highlights the conditions that can lead to resistance and subsequent viral rebound in mAb treatments during acute infection.
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Affiliation(s)
- Tin Phan
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Carolin Zitzmann
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kara W. Chew
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Davey M. Smith
- Department of Medicine, University of California, San Diego, CA, USA
| | - Eric S. Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David A. Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Joseph J. Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Judith S. Currier
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Manish C. Choudhary
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rinki Deo
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 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 & Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ruian Ke
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Alan S. Perelson
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- Santa Fe Institute, Santa Fe, NM, USA
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10
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McMyn NF, Varriale J, Fray EJ, Zitzmann C, MacLeod H, Lai J, Singhal A, Moskovljevic M, Garcia MA, Lopez BM, Hariharan V, Rhodehouse K, Lynn K, Tebas P, Mounzer K, Montaner LJ, Benko E, Kovacs C, Hoh R, Simonetti FR, Laird GM, Deeks SG, Ribeiro RM, Perelson AS, Siliciano RF, Siliciano JM. The latent reservoir of inducible, infectious HIV-1 does not decrease despite decades of antiretroviral therapy. J Clin Invest 2023; 133:e171554. [PMID: 37463049 PMCID: PMC10471168 DOI: 10.1172/jci171554] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/11/2023] [Indexed: 09/02/2023] Open
Abstract
HIV-1 persists in a latent reservoir in resting CD4+ T cells despite antiretroviral therapy (ART). The reservoir decays slowly over the first 7 years of ART (t1/2 = 44 months). However, whether decay continues with long-term ART is unclear. Recent integration site studies indicate gradual selection against inducible, intact proviruses, raising speculation that decades of ART might allow treatment interruption without viral rebound. Therefore, we measured the reservoir in 42 people on long-term ART (mean 22 years) using a quantitative viral outgrowth assay. After 7 years of ART, there was no long-term decrease in the frequency of inducible, replication-competent proviruses but rather an increase with an estimated doubling time of 23 years. Another reservoir assay, the intact proviral DNA assay, confirmed that reservoir decay with t1/2 of 44 months did not continue with long-term ART. The lack of decay reflected proliferation of infected cells. Most inducible, replication-competent viruses (79.8%) had env sequences identical to those of other isolates from the same sample. Thus, although integration site analysis indicates changes in reservoir composition, the proliferation of CD4+ T cells counteracts decay, maintaining the frequency of inducible, replication-competent proviruses at roughly constant levels over the long term. These results reinforce the need for lifelong ART.
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Affiliation(s)
- Natalie F. McMyn
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph Varriale
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emily J. Fray
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Jun Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anushka Singhal
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mauro A. Garcia
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brianna M. Lopez
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vivek Hariharan
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenneth Lynn
- The Wistar Institute, Philadelphia, Pennsylvania, USA
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pablo Tebas
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karam Mounzer
- Philadelphia Field Initiating Group for HIV-1 Trials, Philadelphia, Pennsylvania, USA
| | | | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Colin Kovacs
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | | | | | | | | | - Ruy M. Ribeiro
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Robert F. Siliciano
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
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11
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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 Res 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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Ribeiro RM, Choudhary MC, Deo R, Giganti MJ, Moser C, Ritz J, Greninger AL, Regan J, Flynn JP, Wohl DA, Currier JS, Eron JJ, Hughes MD, Smith DM, Chew KW, Daar ES, Perelson AS, Li JZ. Variant-Specific Viral Kinetics in Acute COVID-19. J Infect Dis 2023; 228:S136-S143. [PMID: 37650233 PMCID: PMC10469346 DOI: 10.1093/infdis/jiad314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Understanding variant-specific differences in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral kinetics may explain differences in transmission efficiency and provide insights on pathogenesis and prevention. We evaluated SARS-CoV-2 kinetics from nasal swabs across multiple variants (Alpha, Delta, Epsilon, Gamma) in placebo recipients of the ACTIV-2/A5401 trial. Delta variant infection led to the highest maximum viral load and shortest time from symptom onset to viral load peak. There were no significant differences in time to viral clearance across the variants. Viral decline was biphasic with first- and second-phase decays having half-lives of 11 hours and 2.5 days, respectively, with differences among variants, especially in the second phase. These results suggest that while variant-specific differences in viral kinetics exist, post-peak viral load all variants appeared to be efficiently cleared by the host. Clinical Trials Registration. NCT04518410.
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Affiliation(s)
- Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico
| | - Manish C Choudhary
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Rinki Deo
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Mark J Giganti
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Carlee Moser
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Justin Ritz
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | - James Regan
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - James P Flynn
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - David A Wohl
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill
| | - Judith S Currier
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Joseph J Eron
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill
| | - Michael D Hughes
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California
| | - Kara W Chew
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Eric S Daar
- Lundquist Institute, Harbor-UCLA Medical Center, Torrance, California
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham & Women's Hospital, Harvard Medical School, Cambridge, Massachusetts
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13
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Sachithanandham J, Balagopal A, Leep-Lazar J, Quinn J, Bowden K, Ward K, Ribeiro RM, Sulkowski MS. Second-Phase Hepatitis C Plasma Viral Kinetics Directly Reflects Reduced Intrahepatic Burden of Hepatitis C Virus. J Infect Dis 2023; 228:311-320. [PMID: 36722133 PMCID: PMC10420397 DOI: 10.1093/infdis/jiad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Mathematical models explain how antivirals control viral infections. Hepatitis C virus (HCV) treatment results in at least 2 phases of decline in viremia. The first phase reflects clearance of rapidly produced virions. The second phase is hypothesized to derive from loss of infected cells but has been challenging to prove. METHODS Using single-cell methods, we quantified the number of hepatitis C virus (HCV)-infected hepatocytes in liver biopsies taken before and within 7 days of initiating direct-acting antivirals (DAAs) in a double-blinded randomized controlled trial testing 2 (sofosbuvir-velpatasvir) versus 3 (sofosbuvir-velpatasvir-voxilaprevir) DAAs. RESULTS We employed thousands of intrahepatic measurements in 10 persons with chronic genotype 1a HCV infection: median proportion of infected hepatocytes declined from 11.3% (range, 1.3%-59%) to 0.6% (range, <0.3%-5.8%), a loss of 75%-95% infected hepatocytes. Plasma viremia correlated with numbers of HCV-infected hepatocytes (r = 0.77; P < .0001). Second-phase plasma dynamics and changes in infected hepatocytes were indistinct (P = .16), demonstrating that second-phase viral dynamics derive from loss of infected cells. DAAs led to a decline in intracellular HCV RNA and interferon-stimulated gene expression (P < .05 for both). CONCLUSIONS We proved that second-phase viral dynamics reflect decay of intrahepatic burden of HCV, partly due to clearance of HCV RNA from hepatocytes. CLINICAL TRIALS REGISTRATION NCT02938013.
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Affiliation(s)
- Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
| | - Ashwin Balagopal
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julia Leep-Lazar
- Lewis Katz School of Medicine, Temple University,Philadelphia, Pennsylvania, USA
| | - Jeffrey Quinn
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenneth Bowden
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland, USA
| | - Kathleen Ward
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ruy M Ribeiro
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Mark S Sulkowski
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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14
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Apetrei C, Gaufin T, Brocca-Cofano E, Sivanandham R, Sette P, He T, Sivanandham S, Martinez Sosa N, Martin KJ, Raehtz KD, Kleinman AJ, Valentine A, Krampe N, Gautam R, Lackner AA, Landay AL, Ribeiro RM, Pandrea I. T cell activation is insufficient to drive SIV disease progression. JCI Insight 2023; 8:e161111. [PMID: 37485874 PMCID: PMC10443804 DOI: 10.1172/jci.insight.161111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/31/2023] [Indexed: 07/25/2023] Open
Abstract
Resolution of T cell activation and inflammation is a key determinant of the lack of SIV disease progression in African green monkeys (AGMs). Although frequently considered together, T cell activation occurs in response to viral stimulation of acquired immunity, while inflammation reflects innate immune responses to mucosal injury. We dissociated T cell activation from inflammation through regulatory T cell (Treg) depletion with Ontak (interleukin-2 coupled with diphtheria toxin) during early SIV infection of AGMs. This intervention abolished control of T cell immune activation beyond the transition from acute to chronic infection. Ontak had no effect on gut barrier integrity, microbial translocation, inflammation, and hypercoagulation, despite increasing T cell activation. Ontak administration increased macrophage counts yet decreased their activation. Persistent T cell activation influenced SIV pathogenesis, shifting the ramp-up in viral replication to earlier time points, prolonging the high levels of replication, and delaying CD4+ T cell restoration yet without any clinical or biological sign of disease progression in Treg-depleted AGMs. Thus, by inducing T cell activation without damaging mucosal barrier integrity, we showed that systemic T cell activation per se is not sufficient to drive disease progression, which suggests that control of systemic inflammation (likely through maintenance of gut integrity) is the key determinant of lack of disease progression in natural hosts of SIVs.
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Affiliation(s)
- Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, and
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, USA
| | - Thaidra Gaufin
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, USA
| | - Egidio Brocca-Cofano
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ranjit Sivanandham
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Paola Sette
- Division of Infectious Diseases, Department of Medicine, and
| | - Tianyu He
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sindhuja Sivanandham
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | - Kevin D. Raehtz
- Division of Infectious Diseases, Department of Medicine, and
| | | | - Audrey Valentine
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Noah Krampe
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rajeev Gautam
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, USA
| | - Andrew A. Lackner
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, USA
| | - Alan L. Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Ruy M. Ribeiro
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Ivona Pandrea
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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15
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Phan T, Brozak S, Pell B, Ciupe SM, Ke R, Ribeiro RM, Gitter A, Mena KD, Perelson AS, Kuang Y, Wu F. Prolonged viral shedding from noninfectious individuals confounds wastewater-based epidemiology. medRxiv 2023:2023.06.08.23291144. [PMID: 37333173 PMCID: PMC10274979 DOI: 10.1101/2023.06.08.23291144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Wastewater surveillance has been widely used to track and estimate SARS-CoV-2 incidence. While both infectious and recovered individuals shed virus into wastewater, epidemiological inferences using wastewater often only consider the viral contribution from the former group. Yet, the persistent shedding in the latter group could confound wastewater-based epidemiological inference, especially during the late stage of an outbreak when the recovered population outnumbers the infectious population. To determine the impact of recovered individuals' viral shedding on the utility of wastewater surveillance, we develop a quantitative framework that incorporates population-level viral shedding dynamics, measured viral RNA in wastewater, and an epidemic dynamic model. We find that the viral shedding from the recovered population can become higher than the infectious population after the transmission peak, which leads to a decrease in the correlation between wastewater viral RNA and case report data. Furthermore, the inclusion of recovered individuals' viral shedding into the model predicts earlier transmission dynamics and slower decreasing trends in wastewater viral RNA. The prolonged viral shedding also induces a potential delay in the detection of new variants due to the time needed to generate enough new cases for a significant viral signal in an environment dominated by virus shed by the recovered population. This effect is most prominent toward the end of an outbreak and is greatly affected by both the recovered individuals' shedding rate and shedding duration. Our results suggest that the inclusion of viral shedding from non-infectious recovered individuals into wastewater surveillance research is important for precision epidemiology.
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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
| | - Stanca M. Ciupe
- Department of Mathematics, Virginia Tech, Blacksburg, VA 24060, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Anna Gitter
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Epidemic Public Health Institute, TX, 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, TX, 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, TX, USA
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16
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Perelson AS, Ribeiro RM, Phan T. An explanation for SARS-CoV-2 rebound after Paxlovid treatment. medRxiv 2023:2023.05.30.23290747. [PMID: 37398088 PMCID: PMC10312846 DOI: 10.1101/2023.05.30.23290747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
In a fraction of SARS-CoV-2 infected individuals treated with the oral antiviral Paxlovid, the virus rebounds following treatment. The mechanism driving rebound is not understood. Here, we show that viral dynamic models based on the hypothesis that Paxlovid treatment near the time of symptom onset halts the depletion of target cells, but may not fully eliminate the virus, which can lead to viral rebound. We also show that the occurrence of viral rebound is sensitive to model parameters, and the time treatment is initiated, which may explain why only a fraction of individuals develop viral rebound. Finally, the models are used to test the therapeutic effects of two alternative treatment schemes. These findings also provide a possible explanation for rebounds following other antiviral treatments for SARS-CoV-2.
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Affiliation(s)
- Alan S. Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544 USA
- Santa Fe Institute, Santa Fe, NM 87501 USA
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544 USA
| | - Tin Phan
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544 USA
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17
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Graca L, Faria AC, Ribeiro RM. Illuminating a blind spot in SARS-CoV-2 immunity. Nat Immunol 2023; 24:889-890. [PMID: 37248418 DOI: 10.1038/s41590-023-01518-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Luis Graca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Lisbon Academic Medical Center, Universidade de Lisboa, Lisboa, Portugal.
| | - Ana Caetano Faria
- Departamento de Bioquímica e Imunologia, Insituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
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18
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Nair MS, Ribeiro RM, Wang M, Bowen AD, Liu L, Guo Y, Chang JY, Wang P, Sheng Z, Sobieszczyk ME, Perelson AS, Huang Y, Ho DD. Changes in serum-neutralizing antibody potency and breadth post-SARS-CoV-2 mRNA vaccine boost. iScience 2023; 26:106345. [PMID: 36925721 PMCID: PMC9987605 DOI: 10.1016/j.isci.2023.106345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
A better understanding of the durability and breadth of serum-neutralizing antibody responses against multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants elicited by COVID-19 vaccines is crucial in addressing the current pandemic. In this study, we quantified the decay of serum neutralization antibodies (nAbs) after second and third doses of the original COVID-19 mRNA vaccine. Using an authentic virus-neutralization assay, we found that decay half-lives of WA1- and Delta-nAbs were both ∼60 days after second and third vaccine dose. Unexpectedly, the durability of serum antibodies that neutralize three different Omicron subvariants (BA.1.1, BA.5, BA.2.12.1) was substantially better, with half-lives of ≥6 months. A booster dose of the original COVID-19 vaccine was also found to broaden antibody responses against SARS-CoV and four other sarbecoviruses, in addition to multiple SARS-CoV-2 strains. These findings suggest that repeated vaccinations with the COVID-19 vaccine may confer a degree of protection against future spillover of sarbecoviruses from animal reservoirs.
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Affiliation(s)
- Manoj S. Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Anthony D. Bowen
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jennifer Y. Chang
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Magdalena E. Sobieszczyk
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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19
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Henriques AR, Gromicho M, Grosskreutz J, Kuzma-Kozakiewicz M, Petri S, Uysal H, Pinto S, Antunes M, De Carvalho M, Ribeiro RM. Association of the practice of contact sports with the development of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2023:1-8. [PMID: 36992635 DOI: 10.1080/21678421.2023.2189911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Objectives: High-intensity physical activity and sports prone to repetitive injuries of the cervical spine and head (when associated with vigorous practice) have been suggested as possible risk factors for amyotrophic lateral sclerosis (ALS). Our objective was to evaluate the relationship between the practice of contact sports (boxing, hockey, football, rugby) and ALS. Methods: The study included 2247 individuals, 1326 patients and 921 controls from several European countries. Analysis of the effect of contact sports on ALS was conducted in male participants only, as very few women practiced contact sports. Logistic regression models were used with the response variable as the presence or absence of ALS, with α = 0.05 significance level. Results: A relationship between the practice of contact sports and ALS was found, with those practicing contact sports having 76% higher odds of an ALS diagnosis (OR = 1.76, p = 0.001). In addition, univariate analyses for age (higher risk for older people, p < 0.001), smoking status (higher risk for ex-smokers, p = 0.022) and tobacco exposure (higher risk for more exposure, p = 0.038) also indicated that these variables are risk factors for ALS. In multivariate models, in addition to age, the interaction term between practice of contact sports and tobacco exposure was still significant (p = 0.03). Conclusions: This is one of the largest studies on the role of contact sport in ALS development. Our results support the existence of a relationship between the practice of sports with repetitive trauma at the level of the cervical spine and head, and ALS. This risk appears to be enhanced by tobacco exposure.
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Affiliation(s)
- Ana Rita Henriques
- CEAUL - Centro de Estatística e Aplicações, Departamento de Estatística e Investigação Operacional, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Comprehensive Health Research Centre (CHRC) and EpiDoC Unit, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Marta Gromicho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | | | - Susanne Petri
- Department of Neurology, Hannover Medical School, Germany
| | - Hilmi Uysal
- Department of Neurology, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Marília Antunes
- CEAUL - Centro de Estatística e Aplicações, Departamento de Estatística e Investigação Operacional, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Mamede De Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Neurociências e Saúde Mental, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal, and
| | - Ruy M Ribeiro
- Laboratório de Biomatemática, Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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20
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Fray EJ, Wu F, Simonetti FR, Zitzmann C, Sambaturu N, Molina-Paris C, Bender AM, Liu PT, Ventura JD, Wiseman RW, O'Connor DH, Geleziunas R, Leitner T, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants. Cell Host Microbe 2023; 31:356-372.e5. [PMID: 36809762 PMCID: PMC10583177 DOI: 10.1016/j.chom.2023.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/02/2022] [Accepted: 01/24/2023] [Indexed: 02/22/2023]
Abstract
The decay kinetics of HIV-1-infected cells are critical to understand virus persistence. We evaluated the frequency of simian immunodeficiency virus (SIV)-infected cells for 4 years of antiretroviral therapy (ART). The intact proviral DNA assay (IPDA) and an assay for hypermutated proviruses revealed short- and long-term infected cell dynamics in macaques starting ART ∼1 year after infection. Intact SIV genomes in circulating CD4+T cells showed triphasic decay with an initial phase slower than the decay of the plasma virus, a second phase faster than the second phase decay of intact HIV-1, and a stable third phase reached after 1.6-2.9 years. Hypermutated proviruses showed bi- or mono-phasic decay, reflecting different selective pressures. Viruses replicating at ART initiation had mutations conferring antibody escape. With time on ART, viruses with fewer mutations became more prominent, reflecting decay of variants replicating at ART initiation. Collectively, these findings confirm ART efficacy and indicate that cells enter the reservoir throughout untreated infection.
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Affiliation(s)
- Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | - Alexandra M Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Po-Ting Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | | | - Thomas Leitner
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ruy M Ribeiro
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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21
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Malato J, Ribeiro RM, Fernandes E, Leite PP, Casaca P, Antunes C, Fonseca VR, Gomes MC, Graca L. Stability of hybrid versus vaccine immunity against BA.5 infection over 8 months. Lancet Infect Dis 2023; 23:148-150. [PMID: 36620968 PMCID: PMC9815828 DOI: 10.1016/s1473-3099(22)00833-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 01/07/2023]
Affiliation(s)
- João Malato
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, Lisboa, 1649-028, Portugal,CEAUL - Centro de Estatística e Aplicações da Universidade de Lisboa, Lisboa, Portugal
| | - Ruy M Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, Lisboa, 1649-028, Portugal,Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Eugénia Fernandes
- Direção de Serviços de Informação e Análise, Direção Geral da Saúde, Lisboa, Portugal
| | - Pedro Pinto Leite
- Direção de Serviços de Informação e Análise, Direção Geral da Saúde, Lisboa, Portugal
| | - Pedro Casaca
- Direção de Serviços de Informação e Análise, Direção Geral da Saúde, Lisboa, Portugal
| | - Carlos Antunes
- Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal,Instituto Dom Luiz, Universidade de Lisboa, Portugal
| | - Válter R Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, Lisboa, 1649-028, Portugal,Comissão Técnica de Vacinação contra a COVID-19, Direção Geral de Saúde, Lisboa, Portugal
| | - Manuel Carmo Gomes
- Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal,Comissão Técnica de Vacinação contra a COVID-19, Direção Geral de Saúde, Lisboa, Portugal
| | - Luis Graca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Centro Académico de Medicina de Lisboa, Universidade de Lisboa, Lisboa, 1649-028, Portugal,Comissão Técnica de Vacinação contra a COVID-19, Direção Geral de Saúde, Lisboa, Portugal
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22
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Chew KW, Moser C, Daar ES, Wohl DA, Li JZ, Coombs RW, Ritz J, Giganti M, Javan AC, Li Y, Choudhary MC, Deo R, Malvestutto C, Klekotka P, Price K, Nirula A, Fischer W, Bala V, Ribeiro RM, Perelson AS, Fletcher CV, Eron JJ, Currier JS, Hughes MD, Smith DM. Publisher Correction: Antiviral and clinical activity of bamlanivimab in a randomized trial of non-hospitalized adults with COVID-19. Nat Commun 2023; 14:333. [PMID: 36658128 PMCID: PMC9851732 DOI: 10.1038/s41467-023-35835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Kara W Chew
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA.
| | - Carlee Moser
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jonathan Z Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert W Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Justin Ritz
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark Giganti
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Yijia Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Manish C Choudhary
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rinki Deo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - William Fischer
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Veenu Bala
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, NE, USA
- Clinical Pharmacology & Pharmacometrics, Jounce Therapeutics, Cambridge, MA, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Courtney V Fletcher
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Judith S Currier
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Davey M Smith
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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23
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Choudhary MC, Chew KW, Deo R, Flynn JP, Regan J, Crain CR, Moser C, Hughes MD, Ritz J, Ribeiro RM, Ke R, Dragavon JA, Javan AC, Nirula A, Klekotka P, Greninger AL, Fletcher CV, Daar ES, Wohl DA, Eron JJ, Currier JS, Parikh UM, Sieg SF, Perelson AS, Coombs RW, Smith DM, Li JZ. Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial. Nat Microbiol 2022; 7:1906-1917. [PMID: 36289399 PMCID: PMC9675946 DOI: 10.1038/s41564-022-01254-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 09/19/2022] [Indexed: 11/08/2022]
Abstract
SARS-CoV-2 mutations that cause resistance to monoclonal antibody (mAb) therapy have been reported. However, it remains unclear whether in vivo emergence of SARS-CoV-2 resistance mutations alters viral replication dynamics or therapeutic efficacy in the immune-competent population. As part of the ACTIV-2/A5401 randomized clinical trial (NCT04518410), non-hospitalized participants with symptomatic SARS-CoV-2 infection were given bamlanivimab (700 mg or 7,000 mg) or placebo treatment. Here¸ we report that treatment-emergent resistance mutations [detected through targeted Spike (S) gene next-generation sequencing] were significantly more likely to be detected after bamlanivimab 700 mg treatment compared with the placebo group (7% of 111 vs 0% of 112 participants, P = 0.003). No treatment-emergent resistance mutations among the 48 participants who received 7,000 mg bamlanivimab were recorded. Participants in which emerging mAb resistant virus mutations were identified showed significantly higher pretreatment nasopharyngeal and anterior nasal viral loads. Daily respiratory tract viral sampling through study day 14 showed the dynamic nature of in vivo SARS-CoV-2 infection and indicated a rapid and sustained viral rebound after the emergence of resistance mutations. Participants with emerging bamlanivimab resistance often accumulated additional polymorphisms found in current variants of concern/interest that are associated with immune escape. These results highlight the potential for rapid emergence of resistance during mAb monotherapy treatment that results in prolonged high-level respiratory tract viral loads. Assessment of viral resistance should be prioritized during the development and clinical implementation of antiviral treatments for COVID-19.
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Affiliation(s)
- Manish C Choudhary
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kara W Chew
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Rinki Deo
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James P Flynn
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James Regan
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charles R Crain
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlee Moser
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Justin Ritz
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Joan A Dragavon
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Ajay Nirula
- Lilly Research Laboratories, San Diego, CA, USA
| | | | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Courtney V Fletcher
- Center for Drug Discovery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Judith S Currier
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Urvi M Parikh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Scott F Sieg
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Robert W Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Davey M Smith
- Department of Medicine, University of California, San Diego, CA, USA.
| | - Jonathan Z Li
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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24
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Pessoa FMCP, Machado CB, Barreto IV, Gadelha RB, Ribeiro RM, Oliveira DS, Filho MOM, Montenegro RC, Moraes MEA, Moreira-Nunes CA. EPIDEMIOLOGICAL AND MOLECULAR PROFILE OF PATIENTS WITH ACUTE MIELOID LEUKEMIA IN CEARÁ. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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Pessoa FMCP, Machado CB, Barreto IV, Gadelha RB, Ribeiro RM, Oliveira DS, Filho MOM, Montenegro RC, Moraes MEA, Moreira-Nunes CA. EPIDEMIOLOGICAL AND MOLECULAR PROFILE OF ADULT PATIENTS WITH ACUTE LYMPHOBLASTIC LEUKEMIA IN CEARÁ. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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26
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Malato J, Ribeiro RM, Leite PP, Casaca P, Fernandes E, Antunes C, Fonseca VR, Gomes MC, Graca L. Risk of BA.5 Infection among Persons Exposed to Previous SARS-CoV-2 Variants. N Engl J Med 2022; 387:953-954. [PMID: 36044619 PMCID: PMC9454644 DOI: 10.1056/nejmc2209479] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- João Malato
- Instituto de Medicina Molecular João Lobo Antunes, Lisbon, Portugal
| | | | | | | | | | | | | | | | - Luis Graca
- Instituto de Medicina Molecular João Lobo Antunes, Lisbon, Portugal
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27
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Chew KW, Moser C, Daar ES, Wohl DA, Li JZ, Coombs RW, Ritz J, Giganti M, Javan AC, Li Y, Choudhary MC, Deo R, Malvestutto C, Klekotka P, Price K, Nirula A, Fischer W, Bala V, Ribeiro RM, Perelson AS, Fletcher CV, Eron JJ, Currier JS, Hughes MD, Smith DM. Antiviral and clinical activity of bamlanivimab in a randomized trial of non-hospitalized adults with COVID-19. Nat Commun 2022; 13:4931. [PMID: 35995785 PMCID: PMC9395368 DOI: 10.1038/s41467-022-32551-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/04/2022] [Indexed: 01/25/2023] Open
Abstract
Anti-SARS-CoV-2 monoclonal antibodies are mainstay COVID-19 therapeutics. Safety, antiviral, and clinical efficacy of bamlanivimab were evaluated in the randomized controlled trial ACTIV-2/A5401. Non-hospitalized adults were randomized 1:1 within 10 days of COVID-19 symptoms to bamlanivimab or blinded-placebo in two dose-cohorts (7000 mg, n = 94; 700 mg, n = 223). No differences in bamlanivimab vs placebo were observed in the primary outcomes: proportion with undetectable nasopharyngeal SARS-CoV-2 RNA at days 3, 7, 14, 21, and 28 (risk ratio = 0.82-1.05 for 7000 mg [p(overall) = 0.88] and 0.81-1.21 for 700 mg [p(overall) = 0.49]), time to symptom improvement (median 21 vs 18.5 days [p = 0.97], 7000 mg; 24 vs 20.5 days [p = 0.08], 700 mg), or grade 3+ adverse events. However, bamlanivimab was associated with lower day 3 nasopharyngeal viral levels and faster reductions in inflammatory markers and viral decay by modeling. This study provides evidence of faster reductions in nasopharyngeal SARS-CoV-2 RNA levels but not shorter symptom durations in non-hospitalized adults with early variants of SARS-CoV-2.
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Affiliation(s)
- Kara W Chew
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA.
| | - Carlee Moser
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jonathan Z Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert W Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Justin Ritz
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark Giganti
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Yijia Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Manish C Choudhary
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rinki Deo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - William Fischer
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Veenu Bala
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, NE, USA
- Clinical Pharmacology & Pharmacometrics, Jounce Therapeutics, Cambridge, MA, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Courtney V Fletcher
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Judith S Currier
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Davey M Smith
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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Sanche S, Cassidy T, Chu P, Perelson AS, Ribeiro RM, Ke R. A simple model of COVID-19 explains disease severity and the effect of treatments. Sci Rep 2022; 12:14210. [PMID: 35988008 PMCID: PMC9392071 DOI: 10.1038/s41598-022-18244-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/08/2022] [Indexed: 12/23/2022] Open
Abstract
Considerable effort has been made to better understand why some people suffer from severe COVID-19 while others remain asymptomatic. This has led to important clinical findings; people with severe COVID-19 generally experience persistently high levels of inflammation, slower viral load decay, display a dysregulated type-I interferon response, have less active natural killer cells and increased levels of neutrophil extracellular traps. How these findings are connected to the pathogenesis of COVID-19 remains unclear. We propose a mathematical model that sheds light on this issue by focusing on cells that trigger inflammation through molecular patterns: infected cells carrying pathogen-associated molecular patterns (PAMPs) and damaged cells producing damage-associated molecular patterns (DAMPs). The former signals the presence of pathogens while the latter signals danger such as hypoxia or lack of nutrients. Analyses show that SARS-CoV-2 infections can lead to a self-perpetuating feedback loop between DAMP expressing cells and inflammation, identifying the inability to quickly clear PAMPs and DAMPs as the main contributor to hyperinflammation. The model explains clinical findings and reveal conditions that can increase the likelihood of desired clinical outcome from treatment administration. In particular, the analysis suggest that antivirals need to be administered early during infection to have an impact on disease severity. The simplicity of the model and its high level of consistency with clinical findings motivate its use for the formulation of new treatment strategies.
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Malato J, Ribeiro RM, Fernandes E, Leite PP, Casaca P, Antunes C, Fonseca VR, Gomes MC, Graca L. Rapid waning of protection induced by prior BA.1/BA.2 infection against BA.5 infection. medRxiv 2022:2022.08.16.22278820. [PMID: 36032977 PMCID: PMC9413713 DOI: 10.1101/2022.08.16.22278820] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
SARS-CoV-2 omicron subvariants BA.1 and BA.2 became dominant in many countries in early 2022. These subvariants are now being displaced by BA.4 and BA.5. While natural infection with BA.1/BA.2 provides some protection against BA.4/BA.5 infection, the duration of this protection remains unknown. We used the national Portuguese COVID-19 registry to investigate the waning of protective immunity conferred by prior BA.1/BA.2 infection towards BA.5. We divided the individuals infected during the period of BA.1/BA.2 dominance (>90% of sample isolates) in successive 15-day intervals and determined the risk of subsequent infection with BA.5 over a fixed period. Compared with uninfected people, one previous infection conferred substantial protection against BA.5 re-infection at 3 months (RR=0.12; 95% CI: 0.11-0.12). However, although still significant, the protection was reduced by two-fold at 5 months post-infection (RR=0.24; 0.23-0.24). These results should be interpreted in the context of vaccine breakthrough infections, as the vaccination coverage in the individuals included in the analyses is >98% since the end of 2021. This waning of protection following BA.1/BA.2 infection highlights the need to assess the stability and durability of immune protection induced with the adapted vaccines (based on BA.1) over time.
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Quinn JR, Goyal A, Ribeiro RM, Massaccesi G, Bailey JR, Thomas DL, Balagopal A. Antiretroviral therapy for HIV and intrahepatic hepatitis C virus replication. AIDS 2022; 36:337-346. [PMID: 34690280 PMCID: PMC9296270 DOI: 10.1097/qad.0000000000003116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE HIV alters host responses to hepatitis C virus (HCV). However, the impact of antiretroviral therapy (ART) on HCV is rarely understood in relevant tissues and never before within individual hepatocytes. DESIGN HIV and HCV kinetics were studied before and after ART initiation among 19 HIV/HCV co-infected persons. From five persons with the largest decline in plasma HCV RNA, liver tissues collected before and during ART, when plasma HIV RNA was undetectable, were studied. METHODS We used single-cell laser capture microdissection and quantitative PCR to assess intrahepatic HCV. Immunohistochemistry was performed to characterize intrahepatic immune cell populations. RESULTS Plasma HCV RNA declined by 0.81 (0.52-1.60) log10 IU/ml from a median (range) 7.26 (6.05-7.29) log10 IU/ml and correlated with proportions of HCV-infected hepatocytes (r = 0.89, P = 2 × 10-5), which declined from median (range) of 37% (6-49%) to 23% (0.5-52%) after plasma HIV clearance. Median (range) HCV RNA abundance within cells was unchanged in four of five participants. Liver T-cell abundance unexpectedly decreased, whereas natural killer (NK) and NK T-cell infiltration increased, correlating with changes in proportions of HCV-infected hepatocytes (r = -0.82 and r = -0.73, respectively). Hepatocyte expression of HLA-E, an NK cell restriction marker, correlated with proportions of HCV-infected hepatocytes (r = 0.79). CONCLUSION These are the first data to show that ART control of HIV reduces the intrahepatic burden of HCV. Furthermore, our data suggest that HIV affects the pathogenesis of HCV infection by an NK/NK T-cell-mediated mechanism that may involve HLA-E and can be rescued, at least in part, by ART.
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Affiliation(s)
| | - Ashish Goyal
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Ruy M Ribeiro
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | | | - David L Thomas
- The Johns Hopkins Medical Institutions, Baltimore, Maryland
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White JA, Simonetti FR, Beg S, McMyn NF, Dai W, Bachmann N, Lai J, Ford WC, Bunch C, Jones JL, Ribeiro RM, Perelson AS, Siliciano JD, Siliciano RF. Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy. Proc Natl Acad Sci U S A 2022; 119:e2120326119. [PMID: 35110411 PMCID: PMC8833145 DOI: 10.1073/pnas.2120326119] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023] Open
Abstract
In persons living with HIV-1 (PLWH) who start antiretroviral therapy (ART), plasma virus decays in a biphasic fashion to below the detection limit. The first phase reflects the short half-life (<1 d) of cells that produce most of the plasma virus. The second phase represents the slower turnover (t1/2 = 14 d) of another infected cell population, whose identity is unclear. Using the intact proviral DNA assay (IPDA) to distinguish intact and defective proviruses, we analyzed viral decay in 17 PLWH initiating ART. Circulating CD4+ T cells with intact proviruses include few of the rapidly decaying first-phase cells. Instead, this population initially decays more slowly (t1/2 = 12.9 d) in a process that largely represents death or exit from the circulation rather than transition to latency. This more protracted decay potentially allows for immune selection. After ∼3 mo, the decay slope changes, and CD4+ T cells with intact proviruses decay with a half-life of 19 mo, which is still shorter than that of the latently infected cells that persist on long-term ART. Two-long-terminal repeat (2LTR) circles decay with fast and slow phases paralleling intact proviruses, a finding that precludes their use as a simple marker of ongoing viral replication. Proviruses with defects at the 5' or 3' end of the genome show equivalent monophasic decay at rates that vary among individuals. Understanding these complex early decay processes is important for correct use of reservoir assays and may provide insights into properties of surviving cells that can constitute the stable latent reservoir.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie F McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas Bachmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - William C Ford
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christina Bunch
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Joyce L Jones
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ruy M Ribeiro
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
- HHMI, Baltimore, MD 21205
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Canto e Castro L, Gomes A, Serrano M, Pereira AHG, Ribeiro R, Napoleão P, Domingues I, Silva C, Fanczal J, Afonso Â, Lopes A, Toader I, de Sousa MJR, de Sousa JGR, de Sousa G, Mota MM, Silva‐Santos B, Veldhoen M, Ribeiro RM. Longitudinal SARS-CoV-2 seroprevalence in Portugal and antibody maintenance 12 months after infection. Eur J Immunol 2022; 52:149-160. [PMID: 34695227 PMCID: PMC8646574 DOI: 10.1002/eji.202149619] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/01/2021] [Accepted: 10/22/2021] [Indexed: 11/10/2022]
Abstract
During the COVID-19 pandemic, Portugal has experienced three distinct SARS-CoV-2 infection waves. We previously documented the prevalence of SARS-CoV-2 immunity, measured by specific antibodies, in September 2020, 6 months after the initial moderate wave. Here, we show the seroprevalence changes 6 months later, up to the second week of March 2021, shortly following the third wave, which was one of the most severe in the world, and 2 months following the start of the vaccination campaign. A longitudinal epidemiological study was conducted, with a stratified quota sample of the Portuguese population. Serological testing was performed, including ELISA determination of antibody class and titers. The proportion of seropositives, which was 2.2% in September 2020, rose sharply to 17.3% (95% CI: 15.8-18.8%) in March 2021. Importantly, circulating IgG and IgA antibody levels were very stable 6 months after the initial determination and up to a year after initial infection, indicating long-lasting infection immunity against SARS-CoV-2. Moreover, vaccinated people had higher IgG levels from 3 weeks post-vaccination when compared with previously infected people at the same time post-infection.
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Affiliation(s)
- Luísa Canto e Castro
- Faculdade de Ciências, Centro de Estatística e Aplicações e Fundação Francisco Manuel dos SantosUniversidade de LisboaLisbonPortugal
| | - Andreia Gomes
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Marta Serrano
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | | | - Rita Ribeiro
- Centro de Medicina Laboratorial Germano de SousaLisbonPortugal
| | - Patrícia Napoleão
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Inês Domingues
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Cláudia Silva
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Júlia Fanczal
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Ângela Afonso
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Andreia Lopes
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Ionela Toader
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | | | | | | | - Maria M. Mota
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Bruno Silva‐Santos
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Marc Veldhoen
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
| | - Ruy M. Ribeiro
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
- Laboratório de Biomatemática, Instituto de Saúde AmbientalFaculdade de MedicinaUniversidade de LisboaLisbonPortugal
- Theoretical Biology and BiophysicsLos Alamos National LaboratoryNew MexicoUSA
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Chew KW, Moser C, Daar ES, Wohl DA, Li JZ, Coombs R, Ritz J, Giganti M, Javan AC, Li Y, Malvestutto C, Klekotka P, Price K, Nirula A, Fischer W, Bala V, Ribeiro RM, Perelson AS, Fletcher CV, Eron JJ, Currier JS, Hughes MD, Smith DM. Bamlanivimab reduces nasopharyngeal SARS-CoV-2 RNA levels but not symptom duration in non-hospitalized adults with COVID-19: A Phase 2 Randomized Clinical Trial. medRxiv 2021:2021.12.17.21268009. [PMID: 34981077 PMCID: PMC8722620 DOI: 10.1101/2021.12.17.21268009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Importance The antiviral activity and efficacy of anti-SARS-CoV-2 monoclonal antibody (mAb) therapies to accelerate recovery from COVID-19 is important to define. Objective To determine safety and efficacy of the mAb bamlanivimab to reduce nasopharyngeal (NP) SARS-CoV-2 RNA levels and symptom duration. Design ACTIV-2/A5401 is a randomized, blinded, placebo-controlled platform trial. Two dose cohorts were enrolled between August 19 and November 17, 2020 for phase 2 evaluation: in the first, participants were randomized 1:1 to bamlanivimab 7000 mg versus placebo, and in the second to bamlanivimab 700 mg versus placebo. Randomization was stratified by time from symptom onset (≤ or >5 days) and risk of progression to severe COVID-19 ("higher" vs "lower"). Setting Multicenter trial conducted at U.S. sites. Participants Non-hospitalized adults ≥18 years of age with positive SARS-CoV-2 antigen or nucleic acid test within 7 days, ≤10 days of COVID-19 symptoms, and with oxygen saturation ≥92% within 48 hours prior to study entry. Intervention Single infusion of bamlanivimab (7000 or 700 mg) or placebo. Main Outcomes and Measures Detection of NP SARS-CoV-2 RNA at days 3, 7, 14, 21, and 28, time to improvement of all of 13 targeted COVID-19 symptoms by daily self-assessment through day 28, and grade 3 or higher treatment emergent adverse events (TEAEs) through day 28. Secondary measures included quantitative NP SARS-CoV-2 RNA, all-cause hospitalizations and deaths (composite), area under the curve of symptom scores from day 0 through day 28, plasma bamlanivimab concentrations, plasma and serum inflammatory biomarkers, and safety through week 24. Results Ninety-four participants were enrolled to the 7000 mg cohort and 223 to the 700 mg cohort and initiated study intervention. The proportion meeting protocol criteria for "higher" risk for COVID-19 progression was 42% and 51% for the 7000 and 700 mg cohort, respectively. Median time from symptom onset at study entry for both cohorts was 6 days. There was no difference in the proportion with undetectable NP SARS-CoV-2 RNA at any post-treatment timepoints (risk ratio compared to placebo, 0.82-1.05 for 7000 mg dose [overall p=0.88] and 0.81-1.21 for 700 mg dose [overall p=0.49]), time to symptom improvement (median of 21 vs 18.5 days, p=0.97, for 7000 mg bamlanivimab vs placebo and 24 vs 20.5 days, p=0.08, for 700 mg bamlanivimab vs placebo), or grade 3+ TEAEs with either dose compared to placebo. Median NP SARS-CoV-2 RNA levels were lower at day 3 and C-reactive protein, ferritin, and fibrinogen levels significantly reduced at days 7 and 14 for bamlanivimab 700 mg compared to placebo, with similar trends observed for bamlanivimab 7000 mg. Viral decay modeling supported more rapid decay with bamlanivimab compared to placebo. Conclusions and Relevance Treatment with bamlanivimab 7000 mg and 700 mg was safe and compared to placebo led to more rapid reductions in NP SARS-CoV-2 RNA and inflammatory biomarkers, but did not decrease time to symptom improvement. The clinical utility of mAbs for outcomes other than hospitalizations and deaths is uncertain. Trial Registration ClinicalTrials.gov Identifier: NCT04518410.
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Affiliation(s)
- Kara W Chew
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Carlee Moser
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill NC, USA
| | - Jonathan Z Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Robert Coombs
- Departments of Laboratory Medicine and and Pathology; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Justin Ritz
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark Giganti
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Yijia Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA
| | | | | | - Karen Price
- Eli Lilly and Company, Indianapolis, IN, USA
| | | | - William Fischer
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill NC, USA
| | - Veenu Bala
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Courtney V Fletcher
- UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill NC, USA
| | - Judith S Currier
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Davey M Smith
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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Ke R, Zitzmann C, Ho DD, Ribeiro RM, Perelson AS. In vivo kinetics of SARS-CoV-2 infection and its relationship with a person's infectiousness. Proc Natl Acad Sci U S A 2021; 118:e2111477118. [PMID: 34857628 PMCID: PMC8670484 DOI: 10.1073/pnas.2111477118] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 01/11/2023] Open
Abstract
The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person's infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop viral dynamic models of SARS-CoV-2 infection and fit them to data to estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking viral load (VL) to infectiousness and show a person's infectiousness increases sublinearly with VL and that the logarithm of the VL in the upper respiratory tract is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and RT-PCR tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.
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Affiliation(s)
- Ruian Ke
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
- New Mexico Consortium, Los Alamos, NM 87544
| | - Carolin Zitzmann
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545;
- New Mexico Consortium, Los Alamos, NM 87544
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35
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De Sousa C, Ribeiro RM, Pinto FJ. Infective Endocarditis as the Cause of Death: A Populationbased Study in Portugal, from 2002 to 2018. ACTA MEDICA PORT 2021; 34:833-841. [PMID: 33687320 DOI: 10.20344/amp.14609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/02/2021] [Accepted: 01/24/2021] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Infective endocarditis presents a high rate of morbidity and mortality. Population-based studies addressing mortality caused by infective endocarditis in Portugal are scarce. We aimed to study deaths caused by Infective endocarditis, as well as corresponding demographics and temporal trends. MATERIAL AND METHODS Retrospective cohort study of all patients whose main cause of death was Infective endocarditis in Portugal from 2002 to 2018. The data was obtained from the national death certificate information system. RESULTS In Portugal, 3634 people died from infective endocarditis throughout the 17-year study period - infective endocarditis specific mortality rate of 2.1 per 100 000 habitants. Of all deceased, 89% were at least 60 years old, and most were women (55%). Overall, 72% died in a healthcare institution. An annual 9% increase in the incidence death rate from Infective endocarditis was observed, with a significant upward trend during the colder months. DISCUSSION In Portugal, mortality by infective endocarditis increased, mainly affecting older patients and women, and which can partially be explained by factors such as ageing of the population. The management of older patients with infective endocarditis is challenging as they present a higher number of comorbidities, more valvular heart disease and valve implants, invasive medical procedures and are less likely to undergo cardiac surgery. CONCLUSION In addition to data on the evolution of demographics in Portugal, it is crucial to study the incidence of infective endocarditis over time to help explain these findings. The identification of factors that can be used to better model national health policies to improve clinical outcomes of infective endocarditis in Portugal is also required.
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Affiliation(s)
- Catarina De Sousa
- Centro Cardiovascular da Universidade de Lisboa (CCUL). Faculdade de Medicina. Universidade de Lisboa. Lisboa; Serviço de Cardiologia. Centro Hospitalar Barreiro/Montijo (CHBM). Barreiro. Portugal
| | - Ruy M Ribeiro
- Laboratório de Biomatemática. Instituto de Saúde Ambiental. Faculdade de Medicina. Universidade de Lisboa. Lisboa. Portugal
| | - Fausto J Pinto
- Centro Cardiovascular da Universidade de Lisboa (CCUL). Faculdade de Medicina. Universidade de Lisboa. Lisboa. Departamento Coração e Vasos. Centro Hospitalar e Universitário Lisboa Norte (CHULN). Lisboa. Portugal
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Garrido MM, Marta JC, Ribeiro RM, Pinheiro LC, Holdenrieder S, Guimarães JT. Comparison of Three Assays for Total and Free PSA Using Hybritech and WHO Calibrations. In Vivo 2021; 35:3431-3439. [PMID: 34697179 DOI: 10.21873/invivo.12643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/29/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Lack of interchangeability between prostate-specific antigen (PSA) assays could have a clinical impact. We compared PSA assays from different manufacturers and calibrations. PATIENTS AND METHODS A total of 233 men who underwent prostate biopsy (PSA: 2-10 ng/ml; Beckman Coulter Access® Hybritech® as reference) were enrolled. Total (tPSA) and free PSA (fPSA) were also measured using the Roche cobas® and the Abbott Architect® methods. RESULTS Roche tPSA values were ≈1% higher than Beckman, while Abbott values were ≈5% lower. Roche had the highest diagnostic sensitivity (92%) compared to Beckman Coulter (87%) and Abbott (85%). Roche fPSA was ≈3% lower and Abbott ≈17% higher than that of Beckman. For the percentage of fPSA, Roche had the highest sensitivity (98%). CONCLUSION Roche cobas® and Beckman Coulter Access® Hybritech® tPSA were almost interchangeable. While the agreement was acceptable for tPSA, this did not happen with fPSA and greater efforts for harmonization are required.
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Affiliation(s)
- Manuel M Garrido
- Department of Clinical Pathology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal; .,Department of Laboratory Medicine, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - José C Marta
- Department of Clinical Pathology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Ruy M Ribeiro
- Biomathematics Laboratory, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Luís C Pinheiro
- Department of Urology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal.,Department of Urology, Faculdade de Ciências Médicas da Universidade Nova de Lisboa, Lisbon, Portugal
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - João T Guimarães
- Department of Clinical Pathology, Centro Hospitalar Universitário de São João, Porto, Portugal.,Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Porto, Portugal.,EPIUnit, Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
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Choudhary MC, Chew KW, Deo R, Flynn JP, Regan J, Crain CR, Moser C, Hughes M, Ritz J, Ribeiro RM, Ke R, Dragavon JA, Javan AC, Nirula A, Klekotka P, Greninger AL, Fletcher CV, Daar ES, Wohl DA, Eron JJ, Currier JS, Parikh UM, Sieg SF, Perelson AS, Coombs RW, Smith DM, Li JZ. Emergence of SARS-CoV-2 Resistance with Monoclonal Antibody Therapy. medRxiv 2021:2021.09.03.21263105. [PMID: 34545376 PMCID: PMC8452115 DOI: 10.1101/2021.09.03.21263105] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Resistance mutations to monoclonal antibody (mAb) therapy has been reported, but in the non-immunosuppressed population, it is unclear if in vivo emergence of SARS-CoV-2 resistance mutations alters either viral replication dynamics or therapeutic efficacy. In ACTIV-2/A5401, non-hospitalized participants with symptomatic SARS-CoV-2 infection were randomized to bamlanivimab (700mg or 7000mg) or placebo. Treatment-emergent resistance mutations were significantly more likely detected after bamlanivimab 700mg treatment than placebo (7% of 111 vs 0% of 112 participants, P=0.003). There were no treatment-emergent resistance mutations among the 48 participants who received bamlanivimab 7000mg. Participants with emerging mAb resistant virus had significantly higher pre-treatment nasopharyngeal and anterior nasal viral load. Intensive respiratory tract viral sampling revealed the dynamic nature of SARS-CoV-2 evolution, with evidence of rapid and sustained viral rebound after emergence of resistance mutations, and worsened symptom severity. Participants with emerging bamlanivimab resistance often accumulated additional polymorphisms found in current variants of concern/interest and associated with immune escape. These results highlight the potential for rapid emergence of resistance during mAb monotherapy treatment, resulting in prolonged high level respiratory tract viral loads and clinical worsening. Careful virologic assessment should be prioritized during the development and clinical implementation of antiviral treatments for COVID-19.
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Canto e Castro L, Pereira AHG, Ribeiro R, Alves C, Veloso L, Vicente V, Alves D, Domingues I, Silva C, Gomes A, Serrano M, Afonso Â, Veldhoen M, de Sousa MJR, de Sousa JGR, de Sousa G, Mota MM, Silva-Santos B, Ribeiro RM. Prevalence of SARS-CoV-2 Antibodies after First 6 Months of COVID-19 Pandemic, Portugal. Emerg Infect Dis 2021; 27:2878-2881. [PMID: 34437830 PMCID: PMC8544986 DOI: 10.3201/eid2711.210636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In September 2020, we tested 13,398 persons in Portugal for antibodies against severe acute respiratory syndrome coronavirus 2 by using a quota sample stratified by age and population density. We found a seroprevalence of 2.2%, 3-4 times larger than the official number of cases at the end of the first wave of the pandemic.
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Regan J, Flynn JP, Rosenthal A, Jordan H, Li Y, Chishti R, Giguel F, Corry H, Coxen K, Fajnzylber J, Gillespie E, Kuritzkes DR, Hacohen N, Goldberg MB, Filbin MR, Yu XG, Baden L, Ribeiro RM, Perelson AS, Conway JM, Li JZ. Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019. Open Forum Infect Dis 2021; 8:ofab153. [PMID: 34430669 PMCID: PMC8083268 DOI: 10.1093/ofid/ofab153] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/23/2021] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kinetics remain understudied, including the impact of remdesivir. In hospitalized individuals, peak sputum viral load occurred in week 2 of symptoms, whereas viremia peaked within 1 week of symptom-onset, suggesting early systemic seeding of SARS-CoV-2. Remdesivir treatment was associated with faster viral decay.
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Affiliation(s)
- James Regan
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - James P Flynn
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alexandra Rosenthal
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hannah Jordan
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rida Chishti
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Francoise Giguel
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heather Corry
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kendyll Coxen
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jesse Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth Gillespie
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel R Kuritzkes
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nir Hacohen
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Marcia B Goldberg
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael R Filbin
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Xu G Yu
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts, USA
| | - Lindsey Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.,New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Jessica M Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Santos CD, Santos AF, das Neves RC, Ribeiro RM, Rodrigues F, Caneiras C, Spruit MA, Bárbara C. Telemonitoring of daily activities compared to the six-minute walk test further completes the puzzle of oximetry-guided interventions. Sci Rep 2021; 11:16600. [PMID: 34400715 PMCID: PMC8367992 DOI: 10.1038/s41598-021-96060-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/04/2021] [Indexed: 01/15/2023] Open
Abstract
Pulmonary rehabilitation is based on a thorough patient assessment, including peripheral oxygen saturation (SpO2) and heart rate (HR) at rest and on exertion. To understand whether exercise-field tests identify patients who desaturate (SpO2 < 90%) during physical activities, this study compared the six-minute walk test (6MWT) and daily-life telemonitoring. Cross-sectional study including 100 patients referred for pulmonary rehabilitation. The 6MWT was performed in hospital with continuous assessment of SpO2, HR, walked distance and calculated metabolic equivalent of tasks (METs). Patients were also evaluated in real-life by SMARTREAB telemonitoring, a combined oximetry-accelerometery with remote continuous assessment of SpO2, HR and METs. SMARTREAB telemonitoring identified 24% more desaturators compared with the 6MWT. Moreover, there were significant mean differences between 6MWT and SMARTREAB in lowest SpO2 of 7.2 ± 8.4% (P < 0.0005), in peak HR of - 9.3 ± 15.5% (P < 0.0005) and also in activity intensity of - 0.3 ± 0.8 METs (P < 0.0005). The 6MWT underestimates the proportion of patients with exercise-induced oxygen desaturation compared to real-life telemonitoring. These results help defining oximetry-guided interventions, such as telemedicine algorithms, oxygen therapy titration and regular physical activity assessment in pulmonary rehabilitation.
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Affiliation(s)
- Catarina Duarte Santos
- Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Unidade de Reabilitação Respiratória, Hospital Pulido Valente, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal.
| | - Ana Filipe Santos
- Unidade de Reabilitação Respiratória, Hospital Pulido Valente, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Rui César das Neves
- CAST - Consultoria e Aplicações em Sistemas e Tecnologia, Lda., Lisbon, Portugal
| | - Ruy M Ribeiro
- Laboratório de Biomatemática, Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Fátima Rodrigues
- Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Unidade de Reabilitação Respiratória, Hospital Pulido Valente, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Cátia Caneiras
- Laboratório de Microbiologia na Saúde Ambiental (EnviHealthMicroLab), Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Instituto de Medicina Preventiva e Saúde Pública, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Healthcare Department, Nippon Gases, Maia, Portugal
| | - Martijn A Spruit
- Department of Research and Development, CIRO, 6085 NM, Horn, The Netherlands.,Department of Respiratory Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Centre, 6229 HX, Maastricht, The Netherlands
| | - Cristina Bárbara
- Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Serviço de Pneumologia, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
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41
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Garrido MM, Ribeiro RM, Krüger K, Pinheiro LC, Guimarães JT, Holdenrieder S. Relevance of Circulating Nucleosomes, HMGB1 and sRAGE for Prostate Cancer Diagnosis. In Vivo 2021; 35:2207-2212. [PMID: 34182498 DOI: 10.21873/invivo.12492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Evasion from cell death occurs in prostate cancer (PCa). We verified whether serum levels of cell death markers can have diagnostic value in PCa. PATIENTS AND METHODS A total of 233 men scheduled for prostate biopsy [prostate specific antigen (PSA) level: 2-10 ng/ml] were enrolled. Serum nucleosomes, nucleosomes containing the H3 histone (H3), high mobility group box 1 (HMGB1), and soluble receptor for advanced glycation end products (sRAGE) were analyzed by enzyme immunoassays. RESULTS There were no differences (p>0.05) in nucleosomes, H3, and sRAGE levels between patients with and without PCa or clinically significant PCa (csPCa). HMGB1 had lower levels in PCa patients (p=0.023) and was a predictor of PCa (p=0.047), but not of csPCa (p=0.180). CONCLUSION In patients with critical PSA levels between 2-10 ng/ml, HMGB1 had some diagnostic value for overall PCa detection, but it was not predictive of csPCa. Nucleosomes, H3 and sRAGE did not discriminate between PCa or csPCa and controls.
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Affiliation(s)
- Manuel M Garrido
- Department of Clinical Pathology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal; .,Department of Laboratory Medicine, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Ruy M Ribeiro
- Biomathematics Laboratory, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Kimberly Krüger
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Luís C Pinheiro
- Department of Urology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal.,Department of Urology, Faculdade de Ciências Médicas da Universidade Nova de Lisboa, Lisbon, Portugal
| | - João T Guimarães
- Department of Clinical Pathology, Centro Hospitalar Universitário de São João, Porto, Portugal.,Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Porto, Portugal.,EPIUnit, Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
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42
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Ke R, Zitzmann C, Ho DD, Ribeiro RM, Perelson AS. In vivo kinetics of SARS-CoV-2 infection and its relationship with a person's infectiousness. medRxiv 2021:2021.06.26.21259581. [PMID: 34230935 PMCID: PMC8259912 DOI: 10.1101/2021.06.26.21259581] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person's infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop data-driven viral dynamic models of SARS-CoV-2 infection and estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking VL to infectiousness, showing that a person's infectiousness increases sub-linearly with VL. We show that the logarithm of the VL in the upper respiratory tract (URT) is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and reverse transcription polymerase chain reaction (RT-PCR) tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost, but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies. SIGNIFICANCE Quantifying the kinetics of SARS-CoV-2 infection and individual infectiousness is key to quantitatively understanding SARS-CoV-2 transmission and evaluating intervention strategies. Here we developed data-driven within-host models of SARS-CoV-2 infection and by fitting them to clinical data we estimated key within-host viral dynamic parameters. We also developed a mechanistic model for viral transmission and show that the logarithm of the viral load in the upper respiratory tract serves an appropriate surrogate for a person's infectiousness. Using data on how viral load changes during infection, we further evaluated the effectiveness of PCR and antigen-based testing strategies for averting transmission and identifying infected individuals.
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Affiliation(s)
- Ruian Ke
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, 4200 West Jemez Road, Los Alamos, NM 87544
| | - Carolin Zitzmann
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, 4200 West Jemez Road, Los Alamos, NM 87544
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43
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Garrido MM, Ribeiro RM, Krüger K, Pinheiro LC, Guimarães JT, Holdenrieder S. Are Proinflammatory Cytokines Relevant for the Diagnosis of Prostate Cancer? Anticancer Res 2021; 41:3067-3073. [PMID: 34083299 DOI: 10.21873/anticanres.15090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/02/2021] [Accepted: 05/18/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Inflammation plays an important role in prostate cancer (PCa). We evaluated proinflammatory cytokines regarding differential diagnosis of PCa in men with PSA levels between 2-10 ng/ml. PATIENTS AND METHODS Serum samples of 79 men (PSA 2-10 ng/ml) were analyzed for 10 proinflammatory cytokines (IL-6, IL-8, TNF-α, IFN-γ, IL-10, IL-1β, IL-2, IL-4, IL-12p70, IL-13) and results were evaluated regarding presence of PCa and disease severity. RESULTS Significant differences between PCa patients and controls were found for IL-6 (p=0.002), IL-8 (p=0.030), and TNF-α (p=0.009), although they were not predictors of PCa in a logistic regression analysis. In addition, IL-6 and TNF-α levels were significantly higher in patients with high-risk PCa (p<0.05). No significant differences were observed regarding the other cytokines. CONCLUSION In patients with PSA levels between 2-10 ng/ml, IL-6, IL-8, and TNF-α are associated with PCa, and IL-6 and TNF-α are associated with high-risk PCa.
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Affiliation(s)
- Manuel M Garrido
- Department of Clinical Pathology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal; .,Department of Laboratory Medicine, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Ruy M Ribeiro
- Biomathematics Laboratory, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Kimberly Krüger
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Luís C Pinheiro
- Department of Urology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal.,Department of Urology, Faculdade de Ciências Médicas da Universidade Nova de Lisboa, Lisbon, Portugal
| | - João T Guimarães
- Department of Clinical Pathology, Centro Hospitalar Universitário de São João, Porto, Portugal.,Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Porto, Portugal.,EPIUnit, Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
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44
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Garrido MM, Ribeiro RM, Pinheiro LC, Holdenrieder S, Guimarães JT. The prostate health index (PHI) density: Are there advantages over PHI or over the prostate-specific antigen density? Clin Chim Acta 2021; 520:133-138. [PMID: 34097882 DOI: 10.1016/j.cca.2021.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND AND AIMS Overdiagnosis of prostate cancer (PCa) should be minimized. We wanted to evaluate the diagnostic performance of the prostate health index density (PHID) and compare it with that of the prostate health index (PHI) alone and of the prostate-specific antigen density (PSAD). MATERIALS AND METHODS 232 men scheduled for a prostate biopsy (prostate-specific antigen level: 2-10 µg/L), were enrolled. PHI, PHID and PSAD were evaluated considering PCa and clinically significant PCa (csPCa) as the outcomes. RESULTS For PCa, the area under the curve (AUC) was higher for PHID (0.823) than for PHI (0.779) and PSAD (0.776). For csPCa, the AUC was also higher for PHID (0.851) but closer to that of PSAD (0.819) and PHI (0.813). For equal sensitivities (90%) for PCa, PHID and PSAD offered the highest specificities (37%), missing the same number of cancers (n = 11). Considering csPCa, PHI and PHID had similar specificities. PSAD reached the highest specificity (50.0%), sparing 32.8% of biopsies, while missing 9 cases of csPCa. CONCLUSIONS PHID has a better diagnostic performance than PHI for overall PCa detection, but very close to the PSAD performance. Considering csPCa, PHI and PHID perform almost equally, but PSAD has a better diagnostic performance.
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Affiliation(s)
- Manuel M Garrido
- Department of Clinical Pathology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal; Department of Laboratory Medicine, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal.
| | - Ruy M Ribeiro
- Biomathematics Laboratory, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Luís C Pinheiro
- Department of Urology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal; Department of Urology, Faculdade de Ciências Médicas da Universidade Nova de Lisboa, Lisbon, Portugal
| | - Stefan Holdenrieder
- Institute of Laboratory Medicine, Munich Biomarker Research Center, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - João T Guimarães
- Department of Clinical Pathology, Centro Hospitalar Universitário de São João, Porto, Portugal; Department of Biomedicine, Faculdade de Medicina da Universidade do Porto, Porto, Portugal; EPIUnit, Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
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45
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Calderon V S, Ribeiro RM, Ferreira PJ. Manganese Migration in Li 1-xMn 2O 4 Cathode Materials. Ultramicroscopy 2021; 225:113285. [PMID: 33932733 DOI: 10.1016/j.ultramic.2021.113285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/30/2021] [Accepted: 04/10/2021] [Indexed: 11/28/2022]
Abstract
LiMn2O4 has been considered one of the most promising cathode materials for Li-ion batteries due to its thermal stability, abundance, environmental affinity, and the possibility to exchange Li-ions in three-dimensions. However, it still suffers from major problems, such as capacity fading and voltage decay, which has been associated to phase transformations and dissolution of transition metals. In this report, we use scanning transmission electron microscopy, coupled with differential phase contrast (DPC), to better understand the mechanisms behind the structural transformations occurring in LiMn2O4. We use the fact that DPC has the ability to observe simultaneously light and heavy elements, as well as measure projected electric fields and charge distribution at the atomic level. This approach allows us to monitor the migration of very low amounts of Mn to the Li atomic positions, at the surface and subsurface regions, which otherwise is very challenging to observe using other techniques such as HAADF and ABF. These observations not only provide a fundamental understanding of the structure of LiMn2O4 but also reveal DPC as a novel technique to determine local structural changes in materials consisting of heavy and light elements, as well as identify the location of light elements, monitor low concentrations of substitutional species and identify phase transformations.
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Affiliation(s)
- S Calderon V
- INL-International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - R M Ribeiro
- INL-International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; Departamento de Física and Centro de Física das Universidades do Minho e do Porto and QuantaLab, University of Minho, P-4710-057, Braga, Portugal
| | - P J Ferreira
- INL-International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; Materials Science and Engineering Program, the University of Texas at Austin, Austin, Texas 78712, USA; Mechanical Engineering Department and IDMEC, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
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46
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Garrido MM, Marta JC, Ribeiro RM, Pinheiro LC, Guimarães JT. Serum lipids and prostate cancer. J Clin Lab Anal 2021; 35:e23705. [PMID: 33724557 PMCID: PMC8059719 DOI: 10.1002/jcla.23705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Conflicting results are found in the literature relating serum lipids levels and prostate cancer. Some results imply a relationship between them; others contradict this association. The purpose of this study was to investigate a possible association between serum lipids levels and prostate cancer, at time of diagnosis. METHODS We measured serum levels of total cholesterol, HDL cholesterol, LDL cholesterol, and triglycerides in 237 patients submitted to a prostate biopsy, with PSA between 2 and 10 ng/ml. Patients without cancer at biopsy were used as controls, and the others were considered as cases. No information about lipid-lowering therapy, including statins, was available neither in cases nor in controls. Cases were divided into risk groups, according to the disease severity, based on staging. Lipids levels were compared between groups, using parametric and nonparametric tests. Logistic regression analysis and odds ratios were calculated. RESULTS LDL and total cholesterol levels were lower in patients with cancer, with the difference being statistically significant for LDL cholesterol (p = 0.010) and borderline for total cholesterol (p = 0.050). No significant differences were found between the several risk groups. Odds ratios for low LDL cholesterol (<130 mg/dl) and low total cholesterol (<200 mg/dl), with prostate cancer as the outcome, were 1.983 and 1.703, respectively. There were no significant differences between cases and controls for the other lipids. CONCLUSION Lower LDL cholesterol (<130 mg/dl) and lower total cholesterol (<200 mg/dl) serum levels seem to associate with prostate cancer, at time of diagnosis.
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Affiliation(s)
- Manuel M. Garrido
- Department of Clinical PathologyCentral Lisbon University Hospital Center & Department of Laboratory Medicine, School of Medicine, University of LisbonLisbonPortugal
| | - José C. Marta
- Department of Clinical PathologyCentral Lisbon University Hospital CenterLisbonPortugal
| | - Ruy M. Ribeiro
- Biomathematics LaboratorySchool of Medicine, University of LisbonLisbonPortugal
| | - Luís C. Pinheiro
- Department of UrologyCentral Lisbon University Hospital Center & Department of Urology, Nova Medical SchoolLisbonPortugal
| | - João T. Guimarães
- Department of Clinical PathologySao Joao University Hospital Center & Department of Biomedicine, School of Medicine & Institute of Public Health, University of PortoPortoPortugal
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47
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de Sousa C, Ribeiro RM, Pinto FJ. The burden of infective endocarditis in Portugal in the last 30 years - a systematic review of observational studies. Rev Port Cardiol 2021; 40:205-217. [PMID: 33648807 DOI: 10.1016/j.repc.2020.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/16/2020] [Accepted: 07/15/2020] [Indexed: 01/29/2023] Open
Abstract
INTRODUCTION Infective endocarditis affects cardiac valves or devices and has a potentially uncertain prognosis. Little information is available on the epidemiology of this disease in Portugal. OBJECTIVE A systematic review of all evidence published in the last 30 years to assess epidemiological data in patients hospitalized with infective endocarditis in Portuguese hospital centers. METHODS Extensive search of all published evidence using Medline, Scopus, general search databases and in addition Portuguese medical journals was performed. All relevant studies in Portuguese or English that reported short- or long-term mortality were included. RESULTS Eighteen retrospective cohort studies (15 medical and three surgical series) were included with a total of 1872 patients assessed. The medical series included 1279 patients. Older males with predominant native left heart valve involvement were identified. Staphylococcus and streptococcus were the most frequent reported pathogens. Surgical intervention was performed on average in 29.8% of cases. The short-term mortality rate ranged from three to 37.2% (average 21.9%). Surgical cases involved older males with affected native left heart valves, emergent/urgent indication was dominant and short-term mortality ranged from 13.6 to 16%. CONCLUSIONS The current study provides a descriptive analysis of the published series of infective endocarditis in Portugal over the last 30 years. Therefore, it may serve as a starting point for the development and implementation of a multicentric prospective registry on infective endocarditis patients in Portugal that will allow a better and more accurate characterization of this special patient population.
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Affiliation(s)
- Catarina de Sousa
- Centro Cardiovascular da Universidade de Lisboa (CCUL), Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal; Serviço de Cardiologia, Centro Hospitalar Barreiro Montijo (CHBM), EPE, Barreiro, Portugal.
| | - Ruy M Ribeiro
- Laboratório de Biomatemática, Instituto de Medicina Preventiva, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Fausto J Pinto
- Centro Cardiovascular da Universidade de Lisboa (CCUL), Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal; Departamento Coração e Vasos, Centro Hospitalar e Universitário Lisboa Norte (CHULN), EPE, Lisboa, Portugal
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Goyal A, Perelson AS, Kandathil AJ, Quinn J, Balagopal A, Ribeiro RM. HIV influences clustering and intracellular replication of hepatitis C virus. J Viral Hepat 2021; 28:334-344. [PMID: 33128322 PMCID: PMC7855861 DOI: 10.1111/jvh.13429] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/21/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022]
Abstract
HCV and HIV coinfection is common and HIV leads to increased HCV viraemia and accelerated disease progression. However, the biological basis of this interaction remains poorly understood and little is known about the impact of HIV on HCV replication at the cellular level. We analysed HCV RNA, based on single-cell laser-capture microdissection, in liver biopsies from monoinfected (n = 4) and HCV/HIV-coinfected (n = 5) participants. HCV RNA was assayed in 3200 hepatocytes with information of spatial position. We compared HCV RNA levels and clustering properties of infection between mono- and coinfected participants, and developed a mathematical model of infection. Although the median plasma HCV RNA level and the fraction of infected cells were comparable in monoinfected (7.0 log10 IU/mL and ~ 30%) and coinfected (7.3 log10 IU/mL and ~ 40%) participants, the median HCV RNA per infected hepatocyte in monoinfected (2.8IU) was significantly lower than in coinfected (8.2IU) participants (p = .03). Clustering of infected cells was more prominent in monoinfected participants (91% of samples) than in coinfected participants (~48%), p = .0045, suggesting that spatial spread may be influenced by HIV coinfection. Interestingly, when clustering does occur, the size of clusters is similar in both types of infection. A mathematical model of infection suggested that HIV allows higher intracellular accumulation of HCV RNA by impeding the export of HCV RNA. Our observations show that HIV coinfection impacts intracellular accumulation of HCV RNA and the clustering of HCV-infected cells, but to a less extent the fraction of HCV-infected cells.
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Affiliation(s)
- Ashish Goyal
- 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
| | | | - Jeffrey Quinn
- Department of Medicine, Johns Hopkins University, Baltimore, MD USA
| | - Ashwin Balagopal
- Department of Medicine, Johns Hopkins University, Baltimore, MD USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM USA,Laboratório de Biomatemática and Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Portugal
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Best K, Barouch DH, Guedj J, Ribeiro RM, Perelson AS. Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference. PLoS Comput Biol 2021; 17:e1008564. [PMID: 33471814 PMCID: PMC7817008 DOI: 10.1371/journal.pcbi.1008564] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/27/2020] [Indexed: 12/11/2022] Open
Abstract
Experimental Zika virus infection in non-human primates results in acute viral load dynamics that can be well-described by mathematical models. The inoculum dose that would be received in a natural infection setting is likely lower than the experimental infections and how this difference affects the viral dynamics and immune response is unclear. Here we study a dataset of experimental infection of non-human primates with a range of doses of Zika virus. We develop new models of infection incorporating both an innate immune response and viral interference with that response. We find that such a model explains the data better than models with no interaction between virus and the immune response. We also find that larger inoculum doses lead to faster dynamics of infection, but approximately the same total amount of viral production. The relationship between the infecting dose of a pathogen and the subsequent viral dynamics is unclear in many disease settings, and this relationship has implications for both the timing and the required efficacy of antiviral therapy. Since experimental challenge studies often employ higher doses of virus than would generally be present in natural infection assessment of this relationship is particularly important for translation of findings. In this study we used mathematical modelling of viral load data from a multi-dose study of Zika virus infection in a macaque model to describe the impact of varying the dose of Zika virus on model parameters, and developed a novel mathematical model incorporating viral interference with the innate immune response.
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Affiliation(s)
- Katharine Best
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, 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
| | | | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Laboratório de Biomatemática, Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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Balagopal A, Grudda T, Ribeiro RM, Saad YS, Hwang HS, Quinn J, Murphy M, Ward K, Sterling RK, Zhang Y, Perelson AS, Sulkowski MS, Osburn WO, Thio CL. Single hepatocytes show persistence and transcriptional inactivity of hepatitis B. JCI Insight 2020; 5:140584. [PMID: 33004689 PMCID: PMC7566712 DOI: 10.1172/jci.insight.140584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
There is no cure for the more than 270 million people chronically infected with HBV. Nucleos(t)ide analogs (NUCs), the mainstay of anti-HBV treatment, block HBV reverse transcription. NUCs do not eliminate the intranuclear covalently closed circular DNA (cccDNA), from which viral RNAs, including pregenomic RNA (pgRNA), are transcribed. A key gap in designing a cure is understanding how NUCs affect HBV replication and transcription because serum markers yield an incomplete view of intrahepatic HBV. We applied single-cell laser capture microdissection and droplet digital PCR to paired liver biopsies collected from 5 HBV/HIV-coinfected persons who took NUCs over 2–4 years. From biopsy 1 to 2, proportions of HBV-infected hepatocytes declined with adherence to NUC treatment (P < 0.05); we extrapolated that eradication of HBV will take over 10 decades with NUCs in these participants. In individual hepatocytes, pgRNA levels diminished 28- to 73-fold during NUC treatment, corresponding with decreased tissue HBV core antigen staining (P < 0.01). In 4 out of 5 participants, hepatocytes with cccDNA but undetectable pgRNA (transcriptionally inactive) were present, and these were enriched in 3 participants during NUC treatment. Further work to unravel mechanisms of cccDNA transcriptional inactivation may lead to therapies that can achieve this in all hepatocytes, resulting in a functional cure. Single-cell laser capture microdissection integrated with droplet digital PCR was used to study hepatocytes from individuals with chronic hepatitis B.
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Affiliation(s)
- Ashwin Balagopal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tanner Grudda
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.,Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Yasmeen S Saad
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hyon S Hwang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey Quinn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Murphy
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kathleen Ward
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard K Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yang Zhang
- Department of Pathology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Mark S Sulkowski
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William O Osburn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chloe L Thio
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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