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Götz V, Mathé P, Agarwal P, Hornuss D, Pfau S, Panning M, Prager E, Voll RE, Engelhardt M, Frye BC, Bamberg F, Fuchs J, Müller M, Wagner D, Rieg S. Clinical phenotype and outcome of persistent SARS-CoV-2 replication in immunocompromised hosts: a retrospective observational study in the Omicron era. Infection 2024; 52:923-933. [PMID: 38095753 PMCID: PMC11142974 DOI: 10.1007/s15010-023-02138-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/10/2023] [Indexed: 06/02/2024]
Abstract
PURPOSE This study aims to describe clinical, virological and radiological characteristics as well as treatment strategies and outcomes of immunocompromised patients with persistent SARS-CoV-2 replication. METHODS We performed a retrospective cohort study of immunocompromised patients at the University Medical Center Freiburg between 01/2022 and 05/2023. Patients with substantial immunosuppression and persistent SARS-CoV-2 detection (Ct-value < 30 after 14 days) were included. RESULTS 36 patients in our cohort reported mainly fever, dyspnoea or continuous cough. Viral load was significantly higher in concurrent samples taken from the lower respiratory tract (Ct-value = 26) than from the upper respiratory tract (Ct-value = 34). Time of detectable viral RNA after start of antiviral treatment was shorter in patients receiving two antivirals (median 15 days vs. 31 days with one antiviral agent). Short-course antiviral therapy (≤ 5 days) was less efficient in reduction of symptoms and viral load than prolonged therapy > 10 days. In 30% (8/27) of patients with repeated CT scans, we found the emergence of chronic pulmonary changes, which were more frequently in patients with B cell depletion (37%, 7/19) compared to patients with organ transplantation (12%, 2/17). CONCLUSION Ongoing SARS-CoV-2 replication in the lower respiratory tract is a relevant differential diagnosis in patients with severe immunosuppression and continuous cough, fever or dyspnoea even if nasopharyngeal swabs test negative for SARS-CoV-2. Especially in B cell-depleted patients, this may lead to inflammatory or fibrotic-like pulmonary changes, which are partially reversible after inhibition of viral replication. Antiviral therapy seems to be most effective in combination and over a prolonged period of time of > 10 days. TRIAL REGISTRATION NUMBER DRKS 00027299.
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Affiliation(s)
- Veronika Götz
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany.
| | - Philipp Mathé
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany.
| | - Prerana Agarwal
- Faculty of Medicine, Department of Radiology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Daniel Hornuss
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Stefanie Pfau
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Marcus Panning
- Faculty of Medicine, Institute of Virology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Eric Prager
- Faculty of Medicine, Department of Nephrology, University Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Reinhard E Voll
- Faculty of Medicine, Department of Rheumatology and Clinical Immunology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Monika Engelhardt
- Faculty of Medicine, Department of Internal Medicine I, Hematology, Oncology and Stem Cell Transplantation, University Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Björn C Frye
- Faculty of Medicine, Department of Pneumology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Fabian Bamberg
- Faculty of Medicine, Department of Radiology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Jonas Fuchs
- Faculty of Medicine, Institute of Virology, Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Matthias Müller
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
- Department of Infection Medicine, Medical Service Centre Clotten, 79106, Freiburg, Germany
| | - Dirk Wagner
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Siegbert Rieg
- Faculty of Medicine, Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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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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Mózner O, Moldvay J, Szabó KS, Vaskó D, Domján J, Ács D, Ligeti Z, Fehér C, Hirsch E, Puskás L, Stahl C, Frey M, Sarkadi B. Application of a Receptor-Binding-Domain-Based Simple Immunoassay for Assessing Humoral Immunity against Emerging SARS-CoV-2 Virus Variants. Biomedicines 2023; 11:3193. [PMID: 38137414 PMCID: PMC10740953 DOI: 10.3390/biomedicines11123193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
We have developed a simple, rapid, high-throughput RBD-based ELISA to assess the humoral immunity against emerging SARS-CoV-2 virus variants. The cDNAs of the His-tagged RBD proteins of the virus variants were stably engineered into HEK cells secreting the protein into the supernatant, and RBD purification was performed by Ni-chromatography and buffer exchange by membrane filtration. The simplified assay uses single dilutions of sera from finger-pricked native blood samples, purified RBD in 96-well plates, and a chromogenic dye for development. The results of this RBD-ELISA were confirmed to correlate with those of a commercial immunoassay measuring antibodies against the Wuhan strain, as well as direct virus neutralization assays assessing the cellular effects of the Wuhan and the Omicron (BA.5) variants. Here, we document the applicability of this ELISA to assess the variant-specific humoral immunity in vaccinated and convalescent patients, as well as to follow the time course of selective vaccination response. This simple and rapid assay, easily modified to detect humoral immunity against emerging SARS-CoV-2 virus variants, may help to assess the level of antiviral protection after vaccination or infection.
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Affiliation(s)
- Orsolya Mózner
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
| | - Judit Moldvay
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
- I. Department of Pulmonology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Kata Sára Szabó
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
| | - Dorottya Vaskó
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Júlia Domján
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Dorottya Ács
- I. Department of Pulmonology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Zoltán Ligeti
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
| | - Csaba Fehér
- Biorefinery Research Group, Department of Applied Biotechnology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Edit Hirsch
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | | | - Cordula Stahl
- Steinbeis-Innovationszentrum Zellkulturtechnik, c/o University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10, D-68163 Mannheim, Germany
| | - Manfred Frey
- Steinbeis-Innovationszentrum Zellkulturtechnik, c/o University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10, D-68163 Mannheim, Germany
| | - Balázs Sarkadi
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
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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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Meade E, Rowan N, Garvey M. Bioprocessing and the Production of Antiviral Biologics in the Prevention and Treatment of Viral Infectious Disease. Vaccines (Basel) 2023; 11:vaccines11050992. [PMID: 37243096 DOI: 10.3390/vaccines11050992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Emerging, re-emerging and zoonotic viral pathogens represent a serious threat to human health, resulting in morbidity, mortality and potentially economic instability at a global scale. Certainly, the recent emergence of the novel SARS-CoV-2 virus (and its variants) highlighted the impact of such pathogens, with the pandemic creating unprecedented and continued demands for the accelerated production of antiviral therapeutics. With limited effective small molecule therapies available for metaphylaxis, vaccination programs have been the mainstay against virulent viral species. Traditional vaccines remain highly effective at providing high antibody titres, but are, however, slow to manufacture in times of emergency. The limitations of traditional vaccine modalities may be overcome by novel strategies, as outlined herein. To prevent future disease outbreaks, paradigm shift changes in manufacturing and distribution are necessary to advance the production of vaccines, monoclonal antibodies, cytokines and other antiviral therapies. Accelerated paths for antivirals have been made possible due to advances in bioprocessing, leading to the production of novel antiviral agents. This review outlines the role of bioprocessing in the production of biologics and advances in mitigating viral infectious disease. In an era of emerging viral diseases and the proliferation of antimicrobial resistance, this review provides insight into a significant method of antiviral agent production which is key to protecting public health.
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Affiliation(s)
- Elaine Meade
- Department of Life Science, Atlantic Technological University, F91 YW50 Sligo, Ireland
- Centre for Precision Engineering, Materials and Manufacturing Research (PEM), Atlantic Technological University, F91 YW50 Sligo, Ireland
| | - Neil Rowan
- Bioscience Research Institute, Technical University Shannon Midlands Midwest, N37 HD68 Athlone, Ireland
| | - Mary Garvey
- Department of Life Science, Atlantic Technological University, F91 YW50 Sligo, Ireland
- Centre for Precision Engineering, Materials and Manufacturing Research (PEM), Atlantic Technological University, F91 YW50 Sligo, Ireland
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