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Lieber CM, Kang HJ, Aggarwal M, Lieberman NA, Sobolik EB, Yoon JJ, Natchus MG, Cox RM, Greninger AL, Plemper RK. Influenza A virus resistance to 4'-fluorouridine coincides with viral attenuation in vitro and in vivo. PLoS Pathog 2024; 20:e1011993. [PMID: 38300953 PMCID: PMC10863857 DOI: 10.1371/journal.ppat.1011993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/13/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Pre-existing or rapidly emerging resistance of influenza viruses to approved antivirals makes the development of novel therapeutics to mitigate seasonal influenza and improve preparedness against future influenza pandemics an urgent priority. We have recently identified the chain-terminating broad-spectrum nucleoside analog clinical candidate 4'-fluorouridine (4'-FlU) and demonstrated oral efficacy against seasonal, pandemic, and highly pathogenic avian influenza viruses in the mouse and ferret model. Here, we have resistance-profiled 4'-FlU against a pandemic A/CA/07/2009 (H1N1) (CA09). In vitro viral adaptation yielded six independently generated escape lineages with distinct mutations that mediated moderate resistance to 4'-FlU in the genetically controlled background of recombinant CA09 (recCA09). Mutations adhered to three distinct structural clusters that are all predicted to affect the geometry of the active site of the viral RNA-dependent RNA polymerase (RdRP) complex for phosphodiester bond formation. Escape could be achieved through an individual causal mutation, a combination of mutations acting additively, or mutations functioning synergistically. Fitness of all resistant variants was impaired in cell culture, and all were attenuated in the mouse model. Oral 4'-FlU administered at lowest-efficacious (2 mg/kg) or elevated (10 mg/kg) dose overcame moderate resistance when mice were inoculated with 10 LD50 units of parental or resistant recCA09, demonstrated by significantly reduced virus load and complete survival. In the ferret model, invasion of the lower respiratory tract by variants representing four adaptation lineages was impaired. Resistant variants were either transmission-incompetent, or spread to untreated sentinels was fully blocked by therapeutic treatment of source animals with 4'-FlU.
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Affiliation(s)
- Carolin M. Lieber
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Hae-Ji Kang
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Megha Aggarwal
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Nicole A. Lieberman
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Elizabeth B. Sobolik
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Jeong-Joong Yoon
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Michael G. Natchus
- Emory Institute for Drug Development, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Robert M. Cox
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Richard K. Plemper
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
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Lieber CM, Kang HJ, Aggarwal M, Lieberman NA, Sobolik EB, Yoon JJ, Natchus MG, Cox RM, Greninger AL, Plemper RK. Influenza A virus resistance to 4'-fluorouridine coincides with viral attenuation in vitro and in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563370. [PMID: 37905070 PMCID: PMC10614940 DOI: 10.1101/2023.10.20.563370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Pre-existing or rapidly emerging resistance of influenza viruses to approved antivirals makes the development of novel therapeutics to mitigate seasonal influenza and improve preparedness against future influenza pandemics an urgent priority. We have recently identified the chain-terminating broad-spectrum nucleoside analog clinical candidate 4'-fluorouridine (4'-FlU) and demonstrated oral efficacy against seasonal, pandemic, and highly pathogenic avian influenza viruses in the mouse and ferret model. Here, we have resistance-profiled 4'-FlU against a pandemic A/CA/07/2009 (H1N1) (CA09). In vitro viral adaptation yielded six independently generated escape lineages with distinct mutations that mediated moderate resistance to 4'-FlU in the genetically controlled background of recombinant CA09 (recCA09). Mutations adhered to three distinct structural clusters that are all predicted to affect the geometry of the active site of the viral RNA-dependent RNA polymerase (RdRP) complex for phosphodiester bond formation. Escape could be achieved through an individual causal mutation, a combination of mutations acting additively, or mutations functioning synergistically. Fitness of all resistant variants was impaired in cell culture, and all were attenuated in the mouse model. Oral 4'-FlU administered at lowest-efficacious (2 mg/kg) or elevated (10 mg/kg) dose overcame moderate resistance when mice were inoculated with 10 LD 50 units of parental or resistant recCA09, demonstrated by significantly reduced virus load and complete survival. In the ferret model, invasion of the lower respiratory tract by variants representing four adaptation lineages was impaired. Resistant variants were either transmission-incompetent, or spread to untreated sentinels was fully blocked by therapeutic treatment of source animals with 4'-FlU. Author Summary Reduced sensitivity to FDA-approved influenza drugs is a major obstacle to effective antiviral therapy. We have previously demonstrated oral efficacy of a novel clinical candidate drug, 4'-FlU, against seasonal, pandemic, and highly pathogenic avian influenza viruses. In this study, we have determined possible routes of influenza virus escape from 4'-FlU and addressed whether resistance imposes a viral fitness penalty, affecting pathogenicity or ability to transmit. We identified three distinct clusters of mutations that lead to moderately reduced viral sensitivity to the drug. Testing of resistant variants against two chemically unrelated nucleoside analog inhibitors of influenza virus, conditionally approved favipiravir and the broad-spectrum SARS-CoV-2 drug molnupiravir, revealed cross-resistance of one cluster with favipiravir, whereas no viral escape from molnupiravir was noted. We found that the resistant variants are severely attenuated in mice, impaired in their ability to invade the lower respiratory tract and cause viral pneumonia in ferrets, and transmission-defective or compromised. We could fully mitigate lethal infection of mice with the resistant variants with standard or 5-fold elevated oral dose of 4'-FlU. These results demonstrate that partial viral escape from 4'-FlU is feasible in principle, but escape mutation clusters are unlikely to reach clinical significance or persist in circulating influenza virus strains.
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Tomris I, Unione L, Nguyen L, Zaree P, Bouwman KM, Liu L, Li Z, Fok JA, Ríos Carrasco M, van der Woude R, Kimpel ALM, Linthorst MW, Kilavuzoglu SE, Verpalen ECJM, Caniels TG, Sanders RW, Heesters BA, Pieters RJ, Jiménez-Barbero J, Klassen JS, Boons GJ, de Vries RP. SARS-CoV-2 Spike N-Terminal Domain Engages 9- O-Acetylated α2-8-Linked Sialic Acids. ACS Chem Biol 2023; 18:1180-1191. [PMID: 37104622 PMCID: PMC10178783 DOI: 10.1021/acschembio.3c00066] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 viruses engage ACE2 as a functional receptor with their spike protein. The S1 domain of the spike protein contains a C-terminal receptor binding domain (RBD) and an N-terminal domain (NTD). The NTD of other coronaviruses includes a glycan binding cleft. However, for the SARS-CoV-2 NTD, protein-glycan binding was only observed weakly for sialic acids with highly sensitive methods. Amino acid changes in the NTD of variants of concern (VoC) show antigenic pressure, which can be an indication of NTD-mediated receptor binding. Trimeric NTD proteins of SARS-CoV-2, alpha, beta, delta, and omicron did not reveal a receptor binding capability. Unexpectedly, the SARS-CoV-2 beta subvariant strain (501Y.V2-1) NTD binding to Vero E6 cells was sensitive to sialidase pretreatment. Glycan microarray analyses identified a putative 9-O-acetylated sialic acid as a ligand, which was confirmed by catch-and-release ESI-MS, STD-NMR analyses, and a graphene-based electrochemical sensor. The beta (501Y.V2-1) variant attained an enhanced glycan binding modality in the NTD with specificity toward 9-O-acetylated structures, suggesting a dual-receptor functionality of the SARS-CoV-2 S1 domain, which was quickly selected against. These results indicate that SARS-CoV-2 can probe additional evolutionary space, allowing binding to glycan receptors on the surface of target cells.
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Affiliation(s)
- Ilhan Tomris
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Luca Unione
- CICbioGUNE,
Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Bizkaia, Spain
| | - Linh Nguyen
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton T6G 2G2, Canada
| | - Pouya Zaree
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Kim M. Bouwman
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Lin Liu
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Zeshi Li
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Jelle A. Fok
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - María Ríos Carrasco
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Roosmarijn van der Woude
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Anne L. M. Kimpel
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Mirte W. Linthorst
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sinan E. Kilavuzoglu
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Enrico C. J. M. Verpalen
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Tom G. Caniels
- Department
of Medical Microbiology, Amsterdam UMC,
University of Amsterdam, 1081 HZ Amsterdam, The Netherlands
- Amsterdam
Institute for Infection and Immunity, Infectious Diseases, 1081 HZ Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Department
of Medical Microbiology, Amsterdam UMC,
University of Amsterdam, 1081 HZ Amsterdam, The Netherlands
- Amsterdam
Institute for Infection and Immunity, Infectious Diseases, 1081 HZ Amsterdam, The Netherlands
- Department
of Microbiology and Immunology, Weill Medical
Center of Cornell University, 1300 York Avenue, New York, New York 10065, United States
| | - Balthasar A. Heesters
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Roland J. Pieters
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Jesús Jiménez-Barbero
- CICbioGUNE,
Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
- Department
of Microbiology and Immunology, Weill Medical
Center of Cornell University, 1300 York Avenue, New York, New York 10065, United States
- Department
of Organic Chemistry, II Faculty of Science
and Technology University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
- Centro
de Investigación Biomédica En Red de Enfermedades Respiratorias, Av. Monforte de Lemos, 3-5. Pabellón
11. Planta 0, 28029 Madrid, Spain
| | - John S. Klassen
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton T6G 2G2, Canada
| | - Geert-Jan Boons
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Robert P. de Vries
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
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Shin WJ, Choi S, Seong BL. What are the considerations when selecting a model for influenza drug discovery? Expert Opin Drug Discov 2023; 18:1-3. [PMID: 36529907 DOI: 10.1080/17460441.2023.2157812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Woo-Jin Shin
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, Florida, USA
| | - Seongil Choi
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 03721, Seoul, South Korea
| | - Baik-Lin Seong
- Department of Microbiology, Yonsei University College of Medicine, 03721, Seoul, South Korea.,Vaccine Innovation Technology ALliance (Vital)-Korea, Yonsei University, 03721, Seoul South Korea
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Tomris I, Unione L, Nguyen L, Zaree P, Bouwman KM, Liu L, Li Z, Fok JA, Ríos Carrasco M, van der Woude R, Kimpel ALM, Linthorst MW, Verpalen ECJM, Caniels TG, Sanders RW, Heesters BA, Pieters RJ, Jiménez-Barbero J, Klassen JS, Boons GJ, de Vries RP. The SARS-CoV-2 spike N-terminal domain engages 9- O -acetylated α2-8-linked sialic acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.14.507904. [PMID: 36263070 PMCID: PMC9580382 DOI: 10.1101/2022.09.14.507904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
SARS-CoV-2 viruses engage ACE2 as a functional receptor with their spike protein. The S1 domain of the spike protein contains a C-terminal receptor-binding domain (RBD) and an N-terminal domain (NTD). The NTD of other coronaviruses includes a glycan-binding cleft. However, for the SARS-CoV-2 NTD protein-glycan binding was only observed weakly for sialic acids with highly sensitive methods. Amino acid changes in the NTD of Variants of Concern (VoC) shows antigenic pressure, which can be an indication of NTD-mediated receptor binding. Trimeric NTD proteins of SARS-CoV-2, Alpha, Beta, Delta, and Omicron did not reveal a receptor binding capability. Unexpectedly, the SARS-CoV-2 Beta subvariant strain (501Y.V2-1) NTD binding to Vero E6 cells was sensitive to sialidase pretreatment. Glycan microarray analyses identified a putative 9- O -acetylated sialic acid as a ligand, which was confirmed by catch-and-release ESI-MS, STD-NMR analyses, and a graphene-based electrochemical sensor. The Beta (501Y.V2-1) variant attained an enhanced glycan binding modality in the NTD with specificity towards 9- O -acetylated structures, suggesting a dual-receptor functionality of the SARS-CoV-2 S1 domain, which was quickly selected against. These results indicate that SARS-CoV-2 can probe additional evolutionary space, allowing binding to glycan receptors on the surface of target cells. Graphical abstract Synopsis Coronaviruses utilize their N-terminal domain (NTD) for initial reversible low-affinity interaction to (sialylated) glycans. This initial low-affinity/high-avidity engagement enables viral surfing on the target membrane, potentially followed by a stronger secondary receptor interaction. Several coronaviruses, such as HKU1 and OC43, possess a hemagglutinin-esterase for viral release after sialic acid interaction, thus allowing viral dissemination. Other coronaviruses, such as MERS-CoV, do not possess a hemagglutinin-esterase, but interact reversibly to sialic acids allowing for viral surfing and dissemination. The early 501Y.V2-1 subvariant of the Beta SARS-CoV-2 Variant of Concern has attained a receptor-binding functionality towards 9- O -acetylated sialic acid using its NTD. This binding functionality was selected against rapidly, most likely due to poor dissemination. Ablation of sialic acid binding in more recent SARS-CoV-2 Variants of Concern suggests a fine balance of sialic acid interaction of SARS-CoV-2 is required for infection and/or transmission.
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Recent Advances in Influenza, HIV and SARS-CoV-2 Infection Prevention and Drug Treatment—The Need for Precision Medicine. CHEMISTRY 2022. [DOI: 10.3390/chemistry4020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Viruses, and in particular, RNA viruses, dominate the WHO’s current list of ten global health threats. Of these, we review the widespread and most common HIV, influenza virus, and SARS-CoV-2 infections, as well as their possible prevention by vaccination and treatments by pharmacotherapeutic approaches. Beyond the vaccination, we discuss the virus-targeting and host-targeting drugs approved in the last five years, in the case of SARS-CoV-2 in the last one year, as well as new drug candidates and lead molecules that have been published in the same periods. We share our views on vaccination and pharmacotherapy, their mutually reinforcing strategic significance in combating pandemics, and the pros and cons of host and virus-targeted drug therapy. The COVID-19 pandemic has provided evidence of our limited armamentarium to fight emerging viral diseases. Novel broad-spectrum vaccines as well as drugs that could even be applied as prophylactic treatments or in early phases of the viremia, possibly through oral administration, are needed in all three areas. To meet these needs, the use of multi-data-based precision medicine in the practice and innovation of vaccination and drug therapy is inevitable.
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Aljehany BM. Antiviral and Anti-SARS-CoV-2 Activity of Natural Chlorogenic Acid and Its Synthetic Derivatives. ARCHIVES OF PHARMACY PRACTICE 2022. [DOI: 10.51847/pg8lad1tqf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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8
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[Identification of a metabolic immune regulator in the host that protects against influenzal pneumonia]. Rev Mal Respir 2021; 38:567-571. [PMID: 34024644 DOI: 10.1016/j.rmr.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/21/2022]
Abstract
The 'flu, caused mostly by influenza A and B viruses, represents a major public health issue. Despite vaccines and antiviral drugs, the therapeutic arsenal is still suboptimal. Recently, several studies have reported the antiviral and anti-inflammatory properties of several host metabolites. Now, we show that a metabolite (called here "C2") has a potent anti-influenza activity by blocking the viral replication and by limiting the downstream pro-inflammatory signalling. These results pave the way for the development of innovative metabolic therapy against influenzal pneumonia.
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Bolge SC, Kariburyo F, Yuce H, Fleischhackl R. Predictors and Outcomes of Hospitalization for Influenza: Real-World Evidence from the United States Medicare Population. Infect Dis Ther 2021; 10:213-228. [PMID: 33108613 PMCID: PMC7954998 DOI: 10.1007/s40121-020-00354-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/06/2020] [Indexed: 10/26/2022] Open
Abstract
INTRODUCTION The purpose of this study was to identify predictors of initial hospitalization and describe the outcomes of high-risk patients hospitalized with influenza. METHODS Data were taken from the 5% national US Medicare database from 2012 to 2015. Patients (aged at least 13 years) were required to have at least one diagnosis for influenza and have continuous health plan enrollment for 6 months before (baseline) and 3 months (follow-up) after the date of influenza diagnosis. Patients who died during follow-up were included. Patients were categorized as initially hospitalized if hospitalized within 0-1 day of diagnosis. High-risk initially hospitalized patients were defined as patients aged at least 65 years or those that had a diagnostic code for chronic lung disease, cardiovascular or cerebrovascular disease, or weakened immune system during baseline period. Logistic regression models were developed to determine predictors of initial hospitalization. RESULTS The study population included 8127 high-risk patients who were initially hospitalized and 16,784 who were not hospitalized. Among high-risk patients, 89.3% were diagnosed in the emergency room, whereas 7.5% and 3.2% were diagnosed in a physician's office or other Medicare settings, respectively. Chronic obstructive pulmonary disorder, congestive heart failure, chronic kidney disease, older age, being male, other comorbidities, number of comorbidities, and baseline healthcare resource use were the predictors of hospitalization. Median length of stay for the hospitalization was 5.0 days, and the 30-day readmission rate was 14%. All-cause mortality rate was 5.1% during the inpatient stay and 9.2% within 30 days of diagnosis. Hospitalized patients with influenza incurred an increase of $16,568 per patient in total all-cause healthcare costs from pre-influenza to post-influenza diagnosis. CONCLUSION The study characterized the burden of hospitalization for influenza and found that hospitalized high-risk patients experience greater comorbidity burden, higher likelihood of multiple inpatient admissions, and costly medical interventions compared to patients who were not hospitalized.
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Affiliation(s)
| | - Furaha Kariburyo
- SIMR, LLC, Ann Arbor, MI, USA.
- New York City College of Technology, City University of New York, New York, NY, USA.
| | - Huseyin Yuce
- New York City College of Technology, City University of New York, New York, NY, USA
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Hernandez-Vargas EA, Velasco-Hernandez JX. In-host Mathematical Modelling of COVID-19 in Humans. ANNUAL REVIEWS IN CONTROL 2020; 50:448-456. [PMID: 33020692 PMCID: PMC7526677 DOI: 10.1016/j.arcontrol.2020.09.006] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 05/14/2023]
Abstract
COVID-19 pandemic has underlined the impact of emergent pathogens as a major threat to human health. The development of quantitative approaches to advance comprehension of the current outbreak is urgently needed to tackle this severe disease. Considering different starting times of infection, mathematical models are proposed to represent SARS-CoV-2 dynamics in infected patients. Based on the target cell limited model, the within-host reproductive number for SARS-CoV-2 is consistent with the broad values of human influenza infection. The best model to fit the data was including immune cell response, which suggests a slow immune response peaking between 5 to 10 days post-onset of symptoms. The model with the eclipse phase, time in a latent phase before becoming productively infected cells, was not supported. Interestingly, model simulations predict that SARS-CoV-2 may replicate very slowly in the first days after infection, and viral load could be below detection levels during the first 4 days post infection. A quantitative comprehension of SARS-CoV-2 dynamics and the estimation of standard parameters of viral infections is the key contribution of this pioneering work. These models can serve for future evaluation of control theoretical approaches to tailor new drugs against COVID-19.
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Affiliation(s)
- Esteban A Hernandez-Vargas
- Instituto de Matemáticas, Universidad Nacional Autonoma de Mexico, Boulevard Juriquilla 3001, Querétaro, Qro., 76230, México
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
| | - Jorge X Velasco-Hernandez
- Instituto de Matemáticas, Universidad Nacional Autonoma de Mexico, Boulevard Juriquilla 3001, Querétaro, Qro., 76230, México
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Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. J Comput Aided Mol Des 2019; 34:27-37. [PMID: 31773463 DOI: 10.1007/s10822-019-00251-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 11/09/2019] [Indexed: 12/24/2022]
Abstract
Influenza epidemics are responsible for an average of 3-5 millions of severe cases and up to 500,000 deaths around the world. One of flu pandemic types is influenza A(H1N1)pdm09 virus (pdm09H1N1). Oseltamivir is the antiviral drug used to treat influenza targeting at neuraminidase (NA) located on the viral surface. Influenza virus undergoes high mutation rates and leads to drug resistance, and thus the development of more efficient drugs is required. In the present study, all-atom molecular dynamics simulations were applied to understand the oseltamivir resistance caused by the single E119D and double E119D/H274Y mutations on NA. The obtained results in terms of binding free energy and intermolecular interactions in the ligand-protein interface showed that the oseltamivir could not be well accommodated in the binding pocket of both NA mutants and the 150-loop moves out from oseltamivir as an "open" state. A greater number of water molecules accessible to the binding pocket could disrupt the oseltamivir binding with NA target as seen be high mobility of oseltamivir at the active site. Additionally, our finding could guide to the design and development of novel NA inhibitor drugs.
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Vecoso LVZ, Silva MT, Resende MR, da Silva EN, Galvao TF. Cost-Effectiveness Analysis of Influenza A (H1N1) Chemoprophylaxis in Brazil. Front Pharmacol 2019; 10:945. [PMID: 31572172 PMCID: PMC6749104 DOI: 10.3389/fphar.2019.00945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 07/24/2019] [Indexed: 01/08/2023] Open
Abstract
Background: Oseltamivir and zanamivir are recommended for treating and preventing influenza A (H1N1) worldwide. In Brazil, this official recommendation lacks an economic evaluation. Our objective was to assess the efficiency of influenza A chemoprophylaxis in the Brazilian context. Methods: We assessed the cost-effectiveness of oseltamivir and zanamivir for prophylaxis of influenza for high risk population, compared to no prophylaxis, in the perspective of Brazilian public health system. Quality-adjusted life years (QALY) and effectiveness data were based on literature review and costs in Brazilian real (BRL) were estimated from official sources and micro-costing of 2016's H1N1 admissions at a university hospital. We used a decision-tree model considering prophylaxis and no prophylaxis and the probabilities of H1N1, ambulatory care, admission to hospital, intensive care, patient discharge, and death. Adherence and adverse events from prophylaxis were included. Incremental cost-effectiveness ratio was converted to 2016 United States dollar (USD). Uncertainty was assessed with univariated and probabilistic sensitivity analysis. Results: Adherence to prophylaxis was 0.70 [95% confidence interval (CI) 0.54; 0.83]; adverse events, 0.09 (95% CI 0.02; 0.18); relative risk of H1N1 infection in chemoprophylaxis, 0.43 (95% CI 0.33; 0.57); incidence of H1N1, 0.14 (95% CI 0.11; 0.16); ambulatory care, 0.67 (95% CI 0.58; 0.75); hospital admission, 0.43 (CI 95% 0.39; 0.42); hospital mortality, 0.14 (CI 95% 0.12; 0.15); intensive care unit admission, 0.23 (95% CI 0.20; 0.27); and intensive care mortality, 0.40 (95% CI 0.29; 0.52). QALY in H1N1 state was 0.50 (95% CI 0.46; 0.53); in H1N1 inpatients, 0.23 (95% CI 0.18; 0.28); healthy, 0.885 (95% CI 0.879; 0.891); death, 0. Adverse events estimated to affect QALY in -0.185 (95% CI -0.290; -0.050). Cost for chemoprophylaxis was BRL 39.42 [standard deviation (SD) 17.94]; ambulatory care, BRL 12.47 (SD 5.21); hospital admission, BRL 5,727.59 (SD 7,758.28); intensive care admission, BRL 19,217.25 (SD 7,917.33); and adverse events, BRL 292.05 (SD 724.95). Incremental cost-effectiveness ratio was BRL -4,080.63 (USD -1,263.74)/QALY and -982.39 (USD -304.24)/H1N1 prevented. Results were robust to sensitivity analysis. Conclusion: Chemoprophylaxis of influenza A (H1N1) is cost-saving in Brazilian health system context.
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Sharma-Chawla N, Stegemann-Koniszewski S, Christen H, Boehme JD, Kershaw O, Schreiber J, Guzmán CA, Bruder D, Hernandez-Vargas EA. In vivo Neutralization of Pro-inflammatory Cytokines During Secondary Streptococcus pneumoniae Infection Post Influenza A Virus Infection. Front Immunol 2019; 10:1864. [PMID: 31474978 PMCID: PMC6702285 DOI: 10.3389/fimmu.2019.01864] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
An overt pro-inflammatory immune response is a key factor contributing to lethal pneumococcal infection in an influenza pre-infected host and represents a potential target for therapeutic intervention. However, there is a paucity of knowledge about the level of contribution of individual cytokines. Based on the predictions of our previous mathematical modeling approach, the potential benefit of IFN-γ- and/or IL-6-specific antibody-mediated cytokine neutralization was explored in C57BL/6 mice infected with the influenza A/PR/8/34 strain, which were subsequently infected with the Streptococcus pneumoniae strain TIGR4 on day 7 post influenza. While single IL-6 neutralization had no effect on respiratory bacterial clearance, single IFN-γ neutralization enhanced local bacterial clearance in the lungs. Concomitant neutralization of IFN-γ and IL-6 significantly reduced the degree of pneumonia as well as bacteremia compared to the control group, indicating a positive effect for the host during secondary bacterial infection. The results of our model-driven experimental study reveal that the predicted therapeutic value of IFN-γ and IL-6 neutralization in secondary pneumococcal infection following influenza infection is tightly dependent on the experimental protocol while at the same time paving the way toward the development of effective immune therapies.
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Affiliation(s)
- Niharika Sharma-Chawla
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany.,Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Infection Immunology Group, Institute of Medical Microbiology, Infection Prevention and Control, Health Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Sabine Stegemann-Koniszewski
- Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Infection Immunology Group, Institute of Medical Microbiology, Infection Prevention and Control, Health Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Experimental Pneumology, University Hospital of Pneumology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Henrike Christen
- Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Julia D Boehme
- Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Infection Immunology Group, Institute of Medical Microbiology, Infection Prevention and Control, Health Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Olivia Kershaw
- Department of Veterinary Medicine, Institute of Veterinary Pathology, Free University Berlin, Berlin, Germany
| | - Jens Schreiber
- Experimental Pneumology, University Hospital of Pneumology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Carlos A Guzmán
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Centre for Individualized Infection Medicine (CiiM), Hanover, Germany
| | - Dunja Bruder
- Immune Regulation Group, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Infection Immunology Group, Institute of Medical Microbiology, Infection Prevention and Control, Health Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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Principi N, Camilloni B, Alunno A, Polinori I, Argentiero A, Esposito S. Drugs for Influenza Treatment: Is There Significant News? Front Med (Lausanne) 2019; 6:109. [PMID: 31192211 PMCID: PMC6546914 DOI: 10.3389/fmed.2019.00109] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/02/2019] [Indexed: 12/16/2022] Open
Abstract
Vaccines remain the best measure to reduce total influenza burden. However, presently available influenza vaccines have some limitations that cause a reduced efficacy compared to immunization practices with other respiratory pathogens. This paper shows the clinical roles of antiviral drugs against influenza that have been licensed in at least one country and the potential roles of compounds that are in development. Several attempts have been made to develop new agents against influenza viruses to overcome the supposed or demonstrated limitations of neuraminidase inhibitors (NAIs). Antibodies against the highly conserved stem region of the haemagglutinin molecule of influenza A viruses and drugs that target different stages of the influenza virus life cycle than NAIs in human cells have been developed and tested. Among these preparations, baloxavir marboxil (BAM), and favipiravir (FP) (i.e., polymerase inhibitors) are the only drugs that have reached the market (the first in Japan and the USA, and the second only in Japan). Other antiviral compounds and monoclonal antibodies are in advanced stage of development, but none of these new drugs and monoclonal antibodies in development have adequate characteristics to substitute for NAIs at present. However, although NAIs remain the drug of choice for influenza treatment, their overuse has to be avoided. Accurate selection of patients for whom treatment is truly needed is required.
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Affiliation(s)
| | - Barbara Camilloni
- Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Anna Alunno
- Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Ilaria Polinori
- Department of Surgical and Biomedical Sciences, Pediatric Clinic, Università degli Studi di Perugia, Perugia, Italy
| | - Alberto Argentiero
- Department of Surgical and Biomedical Sciences, Pediatric Clinic, Università degli Studi di Perugia, Perugia, Italy
| | - Susanna Esposito
- Department of Surgical and Biomedical Sciences, Pediatric Clinic, Università degli Studi di Perugia, Perugia, Italy
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15
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Lakdawala SS, Brooke CB. What's New with Flu? An Overview. Viruses 2019; 11:v11050433. [PMID: 31083357 PMCID: PMC6563513 DOI: 10.3390/v11050433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Seema S Lakdawala
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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