1
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Kiso M, Uraki R, Yamayoshi S, Imai M, Kawaoka Y. Drug susceptibility and the potential for drug-resistant SARS-CoV-2 emergence in immunocompromised animals. iScience 2024; 27:110729. [PMID: 39280602 PMCID: PMC11402253 DOI: 10.1016/j.isci.2024.110729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/24/2024] [Accepted: 08/09/2024] [Indexed: 09/18/2024] Open
Abstract
The reduced susceptibility of mRNA vaccines and diminished neutralizing activity of therapeutic monoclonal antibodies against Omicron variants, including BQ.1.1, XBB, and their descendants, highlight the importance of antiviral therapies. Here, we assessed the efficacy of two antivirals, molnupiravir, targeting a viral RNA-dependent RNA polymerase, and nirmatrelvir, targeting a main protease, against BQ.1.1 in hamsters. We found that prophylactic or therapeutic treatment with either drug significantly reduced the viral load in the lungs of infected hamsters. We also evaluated the risk of emergence of drug-resistant viruses in immunocompromised hamsters. Although 13 days of drug treatment reduced viral titers, the immunocompromised hosts could not completely clear the virus. Viruses isolated from drug-treated immunocompromised hamsters did not show reduced susceptibility to the drugs. Molnupiravir and nirmatrelvir remain effective in vivo against variants with reduced susceptibility to monoclonal antibodies and mRNA vaccine-induced antibodies, with limited emergence of drug-resistant variants under the conditions tested.
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Affiliation(s)
- Maki Kiso
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), The University of Tokyo, Tokyo 108-8639, Japan
| | - Ryuta Uraki
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), The University of Tokyo, Tokyo 108-8639, Japan
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Seiya Yamayoshi
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), The University of Tokyo, Tokyo 108-8639, Japan
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Masaki Imai
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), The University of Tokyo, Tokyo 108-8639, Japan
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
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2
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Nooruzzaman M, Johnson KEE, Rani R, Finkelsztein EJ, Caserta LC, Kodiyanplakkal RP, Wang W, Hsu J, Salpietro MT, Banakis S, Albert J, Westblade LF, Zanettini C, Marchionni L, Soave R, Ghedin E, Diel DG, Salvatore M. Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections. Nat Commun 2024; 15:7999. [PMID: 39294134 DOI: 10.1038/s41467-024-51924-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024] Open
Abstract
We investigated the impact of antiviral treatment on the emergence of SARS-CoV-2 resistance during persistent infections in immunocompromised patients (n = 15). All patients received remdesivir and some also received nirmatrelvir-ritonavir (n = 3) or therapeutic monoclonal antibodies (n = 4). Sequence analysis showed that nine patients carried viruses with mutations in the nsp12 (RNA dependent RNA polymerase), while four had viruses with nsp5 (3C protease) mutations. Infectious SARS-CoV-2 with a double mutation in nsp5 (T169I) and nsp12 (V792I) was recovered from respiratory secretions 77 days after initial COVID-19 diagnosis from a patient sequentially treated with nirmatrelvir-ritonavir and remdesivir. In vitro characterization confirmed its decreased sensitivity to remdesivir and nirmatrelvir, which was overcome by combined antiviral treatment. Studies in golden Syrian hamsters demonstrated efficient transmission to contact animals. This study documents the isolation of SARS-CoV-2 carrying resistance mutations to both nirmatrelvir and remdesivir from a patient and demonstrates its transmissibility in vivo.
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Affiliation(s)
- Mohammed Nooruzzaman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Ruchi Rani
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Leonardo C Caserta
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Wei Wang
- Systems Genomics Section, NIH/NIAID/DIR/LPD, Bethesda, MD, USA
| | - Jingmei Hsu
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Transplantation and Cellular Therapy Program, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Maria T Salpietro
- Institutional Biorepository Core, Weill Cornell Medicine, New York, NY, USA
| | | | - Joshua Albert
- Systems Genomics Section, NIH/NIAID/DIR/LPD, Bethesda, MD, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Claudio Zanettini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rosemary Soave
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Elodie Ghedin
- Systems Genomics Section, NIH/NIAID/DIR/LPD, Bethesda, MD, USA.
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Department of Population Health Science, Weill Cornell Medicine, New York, NY, USA.
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3
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Ip JD, Chu WM, Chan WM, Chu AWH, Leung RCY, Peng Q, Tam AR, Chan BPC, Cai JP, Yuen KY, Kok KH, Shi Y, Hung IFN, To KKW. The significance of recurrent de novo amino acid substitutions that emerged during chronic SARS-CoV-2 infection: an observational study. EBioMedicine 2024; 107:105273. [PMID: 39146693 PMCID: PMC11379563 DOI: 10.1016/j.ebiom.2024.105273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 07/24/2024] [Accepted: 07/27/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND De novo amino acid substitutions (DNS) frequently emerge among immunocompromised patients with chronic SARS-CoV-2 infection. While previous studies have reported these DNS, their significance has not been systematically studied. METHODS We performed a review of DNS that emerged during chronic SARS-CoV-2 infection. We searched PubMed until June 2023 using the keywords "(SARS-CoV-2 or COVID-19) and (mutation or sequencing) and ((prolonged infection) or (chronic infection) or (long term))". We included patients with chronic SARS-CoV-2 infection who had SARS-CoV-2 sequencing performed for at least 3 time points over at least 60 days. We also included 4 additional SARS-CoV-2 patients with chronic infection of our hospital not reported previously. We determined recurrent DNS that has appeared in multiple patients and determined the significance of these mutations among epidemiologically-significant variants. FINDINGS A total of 34 cases were analyzed, including 30 that were published previously and 4 from our hospital. Twenty two DNS appeared in ≥3 patients, with 14 (64%) belonging to lineage-defining mutations (LDMs) of epidemiologically-significant variants and 10 (45%) emerging among chronically-infected patients before the appearance of the corresponding variant. Notably, nsp9-T35I substitution (Orf1a T4175I) emerged in all three patients with BA.2.2 infection in 2022 before the appearance of Variants of Interest that carry nsp9-T35I as LDM (EG.5 and BA.2.86/JN.1). Structural analysis suggests that nsp9-T35I substitution may affect nsp9-nsp12 interaction, which could be critical for the function of the replication and transcription complex. INTERPRETATION DNS that emerges recurrently in different chronically-infected patients may be used as a marker for potential epidemiologically-significant variants. FUNDING Theme-Based Research Scheme [T11/709/21-N] of the Research Grants Council (See acknowledgements for full list).
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Affiliation(s)
- Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wing-Ming Chu
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Rhoda Cheuk-Ying Leung
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anthony Raymond Tam
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Brian Pui-Chun Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Kin-Hang Kok
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ivan Fan-Ngai Hung
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Infectious Diseases Division, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
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4
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Ille AM, Markosian C, Burley SK, Mathews MB, Pasqualini R, Arap W. Generative artificial intelligence performs rudimentary structural biology modeling. Sci Rep 2024; 14:19372. [PMID: 39169047 PMCID: PMC11339285 DOI: 10.1038/s41598-024-69021-2] [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: 03/26/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Natural language-based generative artificial intelligence (AI) has become increasingly prevalent in scientific research. Intriguingly, capabilities of generative pre-trained transformer (GPT) language models beyond the scope of natural language tasks have recently been identified. Here we explored how GPT-4 might be able to perform rudimentary structural biology modeling. We prompted GPT-4 to model 3D structures for the 20 standard amino acids and an α-helical polypeptide chain, with the latter incorporating Wolfram mathematical computation. We also used GPT-4 to perform structural interaction analysis between the anti-viral nirmatrelvir and its target, the SARS-CoV-2 main protease. Geometric parameters of the generated structures typically approximated close to experimental references. However, modeling was sporadically error-prone and molecular complexity was not well tolerated. Interaction analysis further revealed the ability of GPT-4 to identify specific amino acid residues involved in ligand binding along with corresponding bond distances. Despite current limitations, we show the current capacity of natural language generative AI to perform basic structural biology modeling and interaction analysis with atomic-scale accuracy.
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Affiliation(s)
- Alexander M Ille
- School of Graduate Studies, Rutgers, The State University of New Jersey, Newark, NJ, USA
- Rutgers Cancer Institute, Newark, NJ, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Christopher Markosian
- School of Graduate Studies, Rutgers, The State University of New Jersey, Newark, NJ, USA
- Rutgers Cancer Institute, Newark, NJ, USA
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Rutgers Cancer Institute, New Brunswick, NJ, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California-San Diego, La Jolla, San Diego, CA, USA
| | - Michael B Mathews
- School of Graduate Studies, Rutgers, The State University of New Jersey, Newark, NJ, USA
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Renata Pasqualini
- Rutgers Cancer Institute, Newark, NJ, USA.
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA.
| | - Wadih Arap
- Rutgers Cancer Institute, Newark, NJ, USA.
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA.
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5
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Rhodin MHJ, Reyes AC, Balakrishnan A, Bisht N, Kelly NM, Gibbons JS, Lloyd J, Vaine M, Cressey T, Crepeau M, Shen R, Manalo N, Castillo J, Levene RE, Leonard D, Zang T, Jiang L, Daniels K, Cox RM, Lieber CM, Wolf JD, Plemper RK, Leist SR, Scobey T, Baric RS, Wang G, Goodwin B, Or YS. The small molecule inhibitor of SARS-CoV-2 3CLpro EDP-235 prevents viral replication and transmission in vivo. Nat Commun 2024; 15:6503. [PMID: 39090095 PMCID: PMC11294338 DOI: 10.1038/s41467-024-50931-8] [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: 12/21/2023] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
The COVID-19 pandemic has led to the deaths of millions of people and severe global economic impacts. Small molecule therapeutics have played an important role in the fight against SARS-CoV-2, the virus responsible for COVID-19, but their efficacy has been limited in scope and availability, with many people unable to access their benefits, and better options are needed. EDP-235 is specifically designed to inhibit the SARS-CoV-2 3CLpro, with potent nanomolar activity against all SARS-CoV-2 variants to date, as well as clinically relevant human and zoonotic coronaviruses. EDP-235 maintains potency against variants bearing mutations associated with nirmatrelvir resistance. Additionally, EDP-235 demonstrates a ≥ 500-fold selectivity index against multiple host proteases. In a male Syrian hamster model of COVID-19, EDP-235 suppresses SARS-CoV-2 replication and viral-induced hamster lung pathology. In a female ferret model, EDP-235 inhibits production of SARS-CoV-2 infectious virus and RNA at multiple anatomical sites. Furthermore, SARS-CoV-2 contact transmission does not occur when naïve ferrets are co-housed with infected, EDP-235-treated ferrets. Collectively, these results demonstrate that EDP-235 is a broad-spectrum coronavirus inhibitor with efficacy in animal models of primary infection and transmission.
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Affiliation(s)
| | | | | | - Nalini Bisht
- Enanta Pharmaceuticals, Inc., Watertown, MA, USA
| | | | | | | | | | | | | | - Ruichao Shen
- Enanta Pharmaceuticals, Inc., Watertown, MA, USA
| | | | | | | | | | - Tianzhu Zang
- Enanta Pharmaceuticals, Inc., Watertown, MA, USA
| | - Lijuan Jiang
- Enanta Pharmaceuticals, Inc., Watertown, MA, USA
| | | | - Robert M Cox
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Carolin M Lieber
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Josef D Wolf
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sarah R Leist
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trevor Scobey
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Yat Sun Or
- Enanta Pharmaceuticals, Inc., Watertown, MA, USA
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6
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Zhu Y, Yurgelonis I, Noell S, Yang Q, Guan S, Li Z, Hao L, Rothan H, Rai DK, McMonagle P, Baniecki ML, Greasley SE, Plotnikova O, Lee J, Nicki JA, Ferre R, Byrnes LJ, Liu W, Craig TK, Steppan CM, Liberator P, Soares HD, Allerton CMN, Anderson AS, Cardin RD. In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance. SCIENCE ADVANCES 2024; 10:eadl4013. [PMID: 39047088 PMCID: PMC11268423 DOI: 10.1126/sciadv.adl4013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
To facilitate the detection and management of potential clinical antiviral resistance, in vitro selection of drug-resistant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) against the virus Mpro inhibitor nirmatrelvir (Paxlovid active component) was conducted. Six Mpro mutation patterns containing T304I alone or in combination with T21I, L50F, T135I, S144A, or A173V emerged, with A173V+T304I and T21I+S144A+T304I mutations showing >20-fold resistance each. Biochemical analyses indicated inhibition constant shifts aligned to antiviral results, with S144A and A173V each markedly reducing nirmatrelvir inhibition and Mpro activity. SARS-CoV-2 surveillance revealed that in vitro resistance-associated mutations from our studies and those reported in the literature were rarely detected in the Global Initiative on Sharing All Influenza Data database. In the Paxlovid Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients trial, E166V was the only emergent resistance mutation, observed in three Paxlovid-treated patients, none of whom experienced COVID-19-related hospitalization or death.
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Affiliation(s)
- Yuao Zhu
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Irina Yurgelonis
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Stephen Noell
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Qingyi Yang
- Pfizer Worldwide Research, Development & Medical, Cambridge MA 02139, USA
| | - Shunjie Guan
- Pfizer Worldwide Research, Development & Medical, Cambridge MA 02139, USA
| | - Zhenghui Li
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Li Hao
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Hussin Rothan
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Devendra K. Rai
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Patricia McMonagle
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Mary Lynn Baniecki
- Pfizer Worldwide Research, Development & Medical, Cambridge MA 02139, USA
| | | | - Olga Plotnikova
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Jonathan Lee
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Jennifer A. Nicki
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - RoseAnn Ferre
- Pfizer Worldwide Research, Development & Medical, La Jolla, CA 92121, USA
| | - Laura J. Byrnes
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Wei Liu
- Pfizer Worldwide Research, Development & Medical, La Jolla, CA 92121, USA
| | - Timothy K. Craig
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Paul Liberator
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Holly D. Soares
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | | | | | - Rhonda D. Cardin
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
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7
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Nooruzzaman M, Johnson KEE, Rani R, Finkelsztein EJ, Caserta LC, Kodiyanplakkal RP, Wang W, Hsu J, Salpietro MT, Banakis S, Albert J, Westblade L, Zanettini C, Marchionni L, Soave R, Ghedin E, Diel DG, Salvatore M. Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.14.24308523. [PMID: 38946967 PMCID: PMC11213110 DOI: 10.1101/2024.06.14.24308523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
We investigated the impact of antiviral treatment on the emergence of SARS-CoV-2 resistance during persistent infections in immunocompromised patients (n=15). All patients received remdesivir and some also received nirmatrelvir-ritonavir or monoclonal antibodies. Sequence analysis showed that nine patients carried viruses with mutations in the nsp12 (RNA dependent RNA polymerase), while four had viruses with nsp5 (3C protease) mutations. Infectious SARS-CoV-2 with a double mutation in nsp5 (T169I) and nsp12 (V792I) was recovered from respiratory secretions 77 days after initial COVID-19 diagnosis from a patient treated with remdesivir and nirmatrelvir-ritonavir. In vitro characterization confirmed its decreased sensitivity to remdesivir and nirmatrelvir, which was overcome by combined antiviral treatment. Studies in golden Syrian hamsters demonstrated efficient transmission to contact animals. This study documents the isolation of SARS-CoV-2 carrying resistance mutations to both nirmatrelvir and remdesivir from a patient and demonstrates its transmissibility in vivo.
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Affiliation(s)
- Mohammed Nooruzzaman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Ruchi Rani
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Leonardo C Caserta
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Wei Wang
- Systems Genomics Section, NIH/NIAID/DIR/LPD
| | - Jingmei Hsu
- Department of Medicine, Weill Cornell Medicine
| | | | | | | | - Lars Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Claudio Zanettini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | | | | | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine
- Department of Population Health Science, Weill Cornell Medicine
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8
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Focosi D, Franchini M, Maggi F, Shoham S. COVID-19 therapeutics. Clin Microbiol Rev 2024; 37:e0011923. [PMID: 38771027 PMCID: PMC11237566 DOI: 10.1128/cmr.00119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
SUMMARYSince the emergence of COVID-19 in 2020, an unprecedented range of therapeutic options has been studied and deployed. Healthcare providers have multiple treatment approaches to choose from, but efficacy of those approaches often remains controversial or compromised by viral evolution. Uncertainties still persist regarding the best therapies for high-risk patients, and the drug pipeline is suffering fatigue and shortage of funding. In this article, we review the antiviral activity, mechanism of action, pharmacokinetics, and safety of COVID-19 antiviral therapies. Additionally, we summarize the evidence from randomized controlled trials on efficacy and safety of the various COVID-19 antivirals and discuss unmet needs which should be addressed.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Massimo Franchini
- Division of Hematology and Transfusion Medicine, Carlo Poma Hospital, Mantua, Italy
| | - Fabrizio Maggi
- National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Shmuel Shoham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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9
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Futatsusako H, Hashimoto R, Yamamoto M, Ito J, Matsumura Y, Yoshifuji H, Shirakawa K, Takaori-Kondo A, Sato K, Nagao M, Takayama K. Longitudinal analysis of genomic mutations in SARS-CoV-2 isolates from persistent COVID-19 patient. iScience 2024; 27:109597. [PMID: 38638575 PMCID: PMC11024907 DOI: 10.1016/j.isci.2024.109597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
A primary reason for the ongoing spread of coronavirus disease 2019 (COVID-19) is the continuous acquisition of mutations by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the mechanism of acquiring mutations is not fully understood. In this study, we isolated SARS-CoV-2 from an immunocompromized patient persistently infected with Omicron strain BF.5 for approximately 4 months to analyze its genome and evaluate drug resistance. Although the patient was administered the antiviral drug remdesivir (RDV), there were no acquired mutations in RDV binding site, and all isolates exhibited susceptibility to RDV. Notably, upon analyzing the S protein sequence of the day 119 isolate, we identified mutations acquired by mutant strains emerging from the BF.5 variant, suggesting that viral genome analysis in persistent COVID-19 patients may be useful in predicting viral evolution. These results suggest mutations in SARS-CoV-2 are acquired during long-term viral replication rather than in response to antiviral drugs.
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Affiliation(s)
- Hiroki Futatsusako
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 6068507, Japan
| | - Rina Hashimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 6068507, Japan
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 1138654, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Kotaro Shirakawa
- Department of Hematology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - The Genotype to Phenotype Japan (G2P-Japan) Consortium
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 6068507, Japan
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 1138654, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
- Department of Hematology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2770882, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo 1000004, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 1138654, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2770882, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 6068507, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo 1000004, Japan
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10
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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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11
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Tan B, Zhang X, Ansari A, Jadhav P, Tan H, Li K, Chopra A, Ford A, Chi X, Ruiz FX, Arnold E, Deng X, Wang J. Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. Science 2024; 383:1434-1440. [PMID: 38547259 DOI: 10.1126/science.adm9724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. We designed and synthesized 85 noncovalent PLpro inhibitors that bind to a recently discovered ubiquitin binding site and the known BL2 groove pocket near the S4 subsite. Leads inhibited PLpro with the inhibitory constant Ki values from 13.2 to 88.2 nanomolar. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 micromolar. Oral treatment with Jun12682 improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting that PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.
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Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ahmadullah Ansari
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alexandra Ford
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Xiang Chi
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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12
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Westberg M, Su Y, Zou X, Huang P, Rustagi A, Garhyan J, Patel PB, Fernandez D, Wu Y, Hao C, Lo CW, Karim M, Ning L, Beck A, Saenkham-Huntsinger P, Tat V, Drelich A, Peng BH, Einav S, Tseng CTK, Blish C, Lin MZ. An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med 2024; 16:eadi0979. [PMID: 38478629 PMCID: PMC11193659 DOI: 10.1126/scitranslmed.adi0979] [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: 04/03/2023] [Accepted: 02/21/2024] [Indexed: 05/09/2024]
Abstract
Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.
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Affiliation(s)
- Michael Westberg
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Department of Chemistry, Aarhus University; 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University; 8000 Aarhus C, Denmark
| | - Yichi Su
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
| | - Pinghan Huang
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Jaishree Garhyan
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University; Stanford, CA 94305, USA
| | - Puja Bhavesh Patel
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University; Stanford, CA 94305, USA
| | - Daniel Fernandez
- Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University; Stanford, CA 94305, USA
- Sarafan ChEM-H, Macromolecular Structure Knowledge Center, Stanford University; Stanford, CA 94305, USA
| | - Yan Wu
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
| | - Chenzhou Hao
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
| | - Chieh-Wen Lo
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Marwah Karim
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
| | - Aimee Beck
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | | | - Vivian Tat
- Department of Pathology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Bi-Hung Peng
- Department of Neuroscience, Cell Biology, and Anatomy, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Shirit Einav
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University; Stanford, CA 94305, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
- Department of Pathology, The University of Texas Medical Branch; Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology, and Anatomy, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Catherine Blish
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Michael Z. Lin
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University; Stanford, CA 94305, USA
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13
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Hirotsu Y, Takatori M, Mochizuki H, Omata M. Effectiveness of the severe acute respiratory syndrome coronavirus 2 Omicron BA.5 bivalent vaccine on symptoms in healthcare workers with BA.5 infection. Vaccine X 2024; 17:100433. [PMID: 38299200 PMCID: PMC10826328 DOI: 10.1016/j.jvacx.2024.100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/14/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024] Open
Abstract
Background The infection status of healthcare workers (HCWs) with coronavirus disease 2019 has become a major concern worldwide. In this study, we investigated the efficacy of the number of vaccine doses on symptoms after BA.5-adapted bivalent vaccination in HCWs. Methods We analyzed the occupation, route of infection, symptoms, and vaccination history of all HCWs who tested positive for severe acute respiratory syndrome coronavirus 2 and worked in our hospital from November 2020 to March 2023. A logistic regression analysis was performed to examine the association between the presence of BA.5-adapted bivalent vaccination and symptoms. Results During the observation period, 531 HCWs became infected. Of these, 72 % were women, with a median age of 30 years. Nurses accounted for 57 % of the infected cases, and many of the infection routes were from family members. We examined the relationship between symptoms in 352 HCWs infected with the Omicron BA.5* variant and the number of vaccine doses. As the number of vaccine doses increased, the rate of fever decreased, while symptoms such as a runny nose and sore throat tended to increase. The logistic regression analysis showed that the rate of fever tended to decrease (odds ratio = 0.52, 95 % confidence interval: 0.26-1.01, p = 0.056) and that of a runny nose increased (odds ratio = 3.68, 95 % confidence interval: 1.17-10.6, p = 0.018) after BA.5-adapted bivalent vaccination. Conclusion This study shows that fever is reduced and mild symptoms are increased after BA.5-adapted bivalent vaccination in BA.5-infected HCWs. This result highlights the potential effectiveness of tailored vaccination strategies in the management of emerging COVID-19 variants.
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Mika Takatori
- Division of Infection Control and Prevention, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
- Central Clinical Laboratory, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
- The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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14
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Tey SF, Tsai YW, Wu JY, Liu TH, Chuang MH, Hsu WH, Huang PY, Lai CC, Hsu CK. Comparative outcomes of SARS-CoV-2 primary and reinfection in older adult patients. Front Public Health 2024; 12:1337646. [PMID: 38435287 PMCID: PMC10904610 DOI: 10.3389/fpubh.2024.1337646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Background The outcomes of older adult people acquiring SARS-CoV-2 reinfection was unclear. This study aimed to compare the outcomes of older adult patients with COVID-19 reinfection and those with primary infection. Methods This retrospective cohort study used electronic medical records from the TriNetX Research Network. Older adult patients (aged ≥65 years) with COVID-19 between January 1, 2022, and December 31, 2022, were included in the study. The patients were subsequently categorized into reinfection or primary infection groups, according to whether they manifested two distinct COVID-19 episodes with an intervening period of more than 90 days. Propensity score matching was performed for covariate adjustment between the reinfection and primary infection groups. The primary outcome was a composite outcome, including emergency department visits, hospitalization, intensive care unit admission, mechanical ventilation use, and mortality, following primary infection and reinfection. Results After matching, 31,899 patients were identified in both the reinfection and primary infection groups. The risk of primary composite outcomes was 7.15% (n = 2,281) in the reinfection group and 7.53% (n = 2,403) in the primary infection group. No significant difference in the primary outcome was observed between groups (HR, 0.96; 95% CI, 0.91 to 1.02, p = 0.17). In addition, there was no significant differences between the reinfection and primary infection groups in terms of emergency department visit (HR, 1.03; 95% CI, 0.95 to 1.11, p = 0.49), all-cause hospitalization (HR, 0.94; 95% CI, 0.86 to 1.02, p = 0.14), intensive care unit admission (HR, 0.92; 95% CI, 0.67 to 1.28, p = 0.62), mechanical ventilation use (HR,1.35 95% CI, 0.69 to 2.64 p = 0.38), and all-cause mortality (HR, 0.94; 95% CI, 0.74 to 1.20, p = 0.62). Conclusion There were no significant differences in clinical outcomes between older adult patients with COVID-19 reinfection and those with primary infection.
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Affiliation(s)
- Shu-Farn Tey
- Department of Medical Laboratory Science and Biotechnology, Chung Hwa University of Medical Technology, Tainan, Taiwan
- Division of Pulmonary Medicine, Chi-Mei Medical Center, Tainan, Taiwan
| | - Ya-Wen Tsai
- Center for Integrative Medicine, Chi Mei Medical Center, Tainan City, Taiwan
- Department of Medical Laboratory Sciences and Biotechnology, Fooyin University, Kaohsiung, Taiwan
| | - Jheng-Yan Wu
- Department of Nutrition, Chi Mei Medical Center, Tainan, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ting-Hui Liu
- Department of Psychiatry, Chi Mei Medical Center, Tainan, Taiwan
| | - Min-Hsiang Chuang
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Wan-Hsuan Hsu
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Po-Yu Huang
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Chih-Cheng Lai
- Division of Hospital Medicine, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chi-Kuei Hsu
- Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine for International Students, College of Medicine, I-Shou University, Kaohsiung, Taiwan
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15
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Melenotte C, Chavarot N, L'Honneur AS, Bodard S, Cheminant M, Flahault A, Nguyen Y, Burgard M, Dannaoui E, Bougnoux ME, Parize P, Rouzaud C, Scemla A, Canouï E, Lafont E, Vimpere D, Zuber J, Charlier C, Suarez F, Anglicheau D, Hermine O, Lanternier F, Mouthon L, Lortholary O. Increased Risk of Invasive Aspergillosis in Immunocompromised Patients With Persistent SARS-CoV-2 Viral Shedding >8 Weeks, Retrospective Case-control Study. Open Forum Infect Dis 2024; 11:ofae012. [PMID: 38390457 PMCID: PMC10883287 DOI: 10.1093/ofid/ofae012] [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: 12/04/2023] [Accepted: 01/07/2024] [Indexed: 02/24/2024] Open
Abstract
Background Immunocompromised patients now represent the population most at risk for severe coronavirus disease 2019. Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral shedding was reported in these patients ranging from several weeks up to 9 months. We conducted a bicentric retrospective case-control study to identify risk and prognostic factors associated with persistent viral shedding in immunocompromised patients. Material and Methods Symptomatic immunocompromised adults with persistent SARS-CoV-2 viral shedding >8 weeks were retrospectively included between 1 March 2020 and 24 April 2022 at 2 university hospitals in Paris, France, and matched with a control group consisting of symptomatic immunocompromised patients without persistent viral shedding. Results Twenty-nine immunocompromised patients with persistent viral shedding were compared with 40 controls. In multivariate analysis, fever and lymphocytopenia (<0.5 G/L) were associated with an increased risk of persistent viral shedding (odds ratio [OR]: 3.3; 95% confidence interval [CI], 1.01-11.09) P = .048 and OR: 4.3; 95% CI, 1.2-14.7; P = .019, respectively). Unvaccinated patients had a 6-fold increased risk of persistent viral shedding (OR, 6.6; 95% CI, 1.7-25.1; P = .006). Patients with persistent viral shedding were at risk of hospitalization (OR: 4.8; 95 CI, 1.5-15.6; P = .008), invasive aspergillosis (OR: 10.17; 95 CI, 1.15-89.8; P = .037) and death (log-rank test <0.01). Conclusions Vaccine coverage was protective against SARS-CoV-2 persistent viral shedding in immunocompromised patients. This new group of immunocompromised patients with SARS-CoV-2 persistent viral shedding is at risk of developing invasive aspergillosis and death and should therefore be systematically screened for this fungal infection for as long as the viral shedding persists.
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Affiliation(s)
- Cléa Melenotte
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Nathalie Chavarot
- Department of Nephrology and Kidney Transplantation, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
- Department of Nephrology and Kidney Transplantation, European Hospital Georges Pompidou, Public Assistance of the Hospital of Paris, Paris, France
| | - Anne-Sophie L'Honneur
- Paris-Cité University, Paris, France
- Department of Virology, Cochin University Hospital, Public Assistance of the Hospital of Paris, Paris, France
| | - Sylvain Bodard
- Paris-Cité University, Paris, France
- Department of Imaging, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Morgane Cheminant
- Paris-Cité University, Paris, France
- Department of Hematology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Adrien Flahault
- Department of Nephrology and Kidney Transplantation, European Hospital Georges Pompidou, Public Assistance of the Hospital of Paris, Paris, France
| | - Yann Nguyen
- Department of Internal Medicine, University Hospital Cochin, Public Assistance of the Hospital of Paris, Paris, France
| | - Marianne Burgard
- Department of Virology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Eric Dannaoui
- Paris-Cité University, Paris, France
- Department of Mycology and Parasitology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Marie-Elisabeth Bougnoux
- Paris-Cité University, Paris, France
- Department of Mycology and Parasitology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Perrine Parize
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Claire Rouzaud
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Anne Scemla
- Department of Nephrology and Kidney Transplantation, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Etienne Canouï
- Mobile Team of Infectious Diseases and Tropical Medicine, Cochin University Hospital, Public Assistance of the Hospital of Paris, France
| | - Emmanuel Lafont
- Department of Internal Medicine, European Hospital Georges Pompidou, Public Assistance of the Hospital of Paris, Paris, France
| | - Damien Vimpere
- Department of Intensive Care Unit, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Julien Zuber
- Department of Nephrology and Kidney Transplantation, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
| | - Caroline Charlier
- Paris-Cité University, Paris, France
- Mobile Team of Infectious Diseases and Tropical Medicine, Cochin University Hospital, Public Assistance of the Hospital of Paris, France
| | - Felipe Suarez
- Paris-Cité University, Paris, France
- Department of Hematology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Dany Anglicheau
- Department of Nephrology and Kidney Transplantation, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
| | - Olivier Hermine
- Paris-Cité University, Paris, France
- Department of Hematology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Fanny Lanternier
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
| | - Luc Mouthon
- Paris-Cité University, Paris, France
- Department of Internal Medicine, University Hospital Cochin, Public Assistance of the Hospital of Paris, Paris, France
| | - Olivier Lortholary
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
- Mycology Department, Institut Pasteur, Université Paris Cité, National Reference Center for Invasives Mycoses and Antifungals, Mycology Translational Research Group, Paris, France
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16
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Colson P, Delerce J, Pontarotti P, Devaux C, La Scola B, Fantini J, Raoult D. Resistance-associated mutations to the anti-SARS-CoV-2 agent nirmatrelvir: Selection not induction. J Med Virol 2024; 96:e29462. [PMID: 38363015 DOI: 10.1002/jmv.29462] [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: 11/20/2023] [Revised: 01/21/2024] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Mutations associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resistance to antiprotease nirmatrelvir were reported. We aimed to detect them in SARS-CoV-2 genomes and quasispecies retrieved in our institute before drug availability in January 2022 and to analyze the impact of mutations on protease (3CLpro) structure. We sought for 38 3CLpro nirmatrelvir resistance mutations in a set of 62 673 SARS-CoV-2 genomes obtained in our institute from respiratory samples collected between 2020 and 2023 and for these mutations in SARS-CoV-2 quasispecies for 90 samples collected in 2020, using Python. SARS-CoV-2 protease with major mutation E166V was generated with Swiss Pdb Viewer and Molegro Molecular Viewer. We detected 22 (58%) of the resistance-associated mutations in 417 (0.67%) of the genomes analyzed; 325 (78%) of these genomes had been obtained from samples collected in 2020-2021. APOBEC signatures were found for 12/22 mutations. We also detected among viral quasispecies from 90 samples some minority reads harboring any of 15 nirmatrelvir resistance mutations, including E166V. Also, we predicted that E166V has a very limited effect on 3CLpro structure but may prevent drug attachment. Thus, we evidenced that mutations associated with nirmatrelvir resistance pre-existed in SARS-CoV-2 before drug availability. These findings further warrant SARS-CoV-2 genomic surveillance and SARS-CoV-2 quasispecies characterization.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | | | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
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17
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Focosi D, Casadevall A, Franchini M, Maggi F. Sotrovimab: A Review of Its Efficacy against SARS-CoV-2 Variants. Viruses 2024; 16:217. [PMID: 38399991 PMCID: PMC10891757 DOI: 10.3390/v16020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024] Open
Abstract
Among the anti-Spike monoclonal antibodies (mAbs), the S-309 derivative sotrovimab was the most successful in having the longest temporal window of clinical use, showing a high degree of resiliency to SARS-CoV-2 evolution interrupted only by the appearance of the BA.2.86* variant of interest (VOI). This success undoubtedly reflects rational selection to target a highly conserved epitope in coronavirus Spike proteins. We review here the efficacy of sotrovimab against different SARS-CoV-2 variants in outpatients and inpatients, discussing both randomized controlled trials and real-world evidence. Although it could not be anticipated at the time of its development and introduction, sotrovimab's use in immunocompromised individuals who harbor large populations of variant viruses created the conditions for its eventual demise, as antibody selection and viral evolution led to its eventual withdrawal due to inefficacy against later variant lineages. Despite this, based on observational and real-world data, some authorities have continued to promote the use of sotrovimab, but the lack of binding to newer variants strongly argues for the futility of continued use. The story of sotrovimab highlights the power of modern biomedical science to generate novel therapeutics while also providing a cautionary tale for the need to devise strategies to minimize the emergence of resistance to antibody-based therapeutics.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, via Paradisa 2, 56124 Pisa, Italy
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
| | - Massimo Franchini
- Department of Transfusion Medicine and Hematology, Carlo Poma Hospital, 46100 Mantua, Italy;
| | - Fabrizio Maggi
- National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
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18
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Furuya C, Yasuda H, Hiki M, Shirane S, Yamana T, Uchimura A, Inano T, Takaku T, Hamano Y, Ando M. Case report: Ensitrelvir for treatment of persistent COVID-19 in lymphoma patients: a report of two cases. Front Immunol 2024; 15:1287300. [PMID: 38333218 PMCID: PMC10850233 DOI: 10.3389/fimmu.2024.1287300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024] Open
Abstract
Persistent COVID-19 is a well recognized issue of concern in patients with hematological malignancies. Such patients are not only at risk of mortality due to the infection itself, but are also at risk of suboptimal malignancy-related outcomes because of delays and terminations of chemotherapy. We report two lymphoma patients with heavily pretreated persistent COVID-19 in which ensitrelvir brought about radical changes in the clinical course leading to rapid remissions. Patient 1 was on ibrutinib treatment for mantle cell lymphoma when he developed COVID-19 pneumonia which was severe and ongoing for 2 months despite therapy with molnupiravir, multiple courses of remdesivir, one course of sotrovimab, tocilizumab, and steroids. Patient 2 was administered R-CHOP therapy for diffuse large B-cell lymphoma when he developed COVID-19 which was ongoing for a month despite treatment with multiple courses of remdesivir and one course of sotrovimab. A 5-day administration of ensitrelvir promptly resolved the persistent COVID-19 accommodated by negative conversions of RT-qPCR tests in both patients within days. Ensitrelvir is a novel COVID-19 therapeutic that accelerates viral clearance through inhibition of the main protease of SARS-CoV-2, 3-chymotrypsin-like protease, which is vital for viral replication. Ensitrelvir is a promising treatment approach for immunocompromised lymphoma patients suffering from persisting and severe COVID-19.
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Affiliation(s)
- Chiho Furuya
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hajime Yasuda
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Makoto Hiki
- Department of Cardiovascular Biology and Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shuichi Shirane
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomohito Yamana
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ayana Uchimura
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tadaaki Inano
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomoiku Takaku
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yasuharu Hamano
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miki Ando
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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19
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Palomino-Cabrera R, Tejerina F, Molero-Salinas A, Veintimilla C, Catalán P, Ferris M, Osorio S, Alonso R, Muñoz P, de García de Viedma D, Pérez-Lago L. No emergence of resistance mutations in COVID-19 patients receiving nirmatrelvir/ritonavir. J Med Virol 2024; 96:e29337. [PMID: 38149407 DOI: 10.1002/jmv.29337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/28/2023]
Affiliation(s)
- Rosalía Palomino-Cabrera
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Francisco Tejerina
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas-CIBERINFEC, Madrid, Spain
| | - Andrea Molero-Salinas
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Cristina Veintimilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - María Ferris
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Farmacia, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Santiago Osorio
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Hematología, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Roberto Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES, Madrid, Spain
| | - Darío de García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
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20
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Tan B, Zhang X, Ansari A, Jadhav P, Tan H, Li K, Chopra A, Ford A, Chi X, Ruiz FX, Arnold E, Deng X, Wang J. Design of SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569653. [PMID: 38076941 PMCID: PMC10705561 DOI: 10.1101/2023.12.01.569653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. In this study, we designed and synthesized 85 noncovalent PLpro inhibitors that bind to the newly discovered Val70Ub site and the known BL2 groove pocket. Potent compounds inhibited PLpro with inhibitory constant Ki values from 13.2 to 88.2 nM. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 μM. Oral treatment with Jun12682 significantly improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.
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Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Ahmadullah Ansari
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Alexandra Ford
- Deprtment of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiang Chi
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
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