101
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Abdelnabi R, Jochmans D, Donckers K, Trüeb B, Ebert N, Weynand B, Thiel V, Neyts J. Nirmatrelvir-resistant SARS-CoV-2 is efficiently transmitted in female Syrian hamsters and retains partial susceptibility to treatment. Nat Commun 2023; 14:2124. [PMID: 37059708 PMCID: PMC10101821 DOI: 10.1038/s41467-023-37773-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/24/2023] [Indexed: 04/16/2023] Open
Abstract
The SARS-CoV-2 main protease (3CLpro) is one of the promising therapeutic targets for the treatment of COVID-19. Nirmatrelvir is the first 3CLpro inhibitor authorized for treatment of COVID-19 patients at high risk of hospitalization. We recently reported on the in vitro selection of SARS-CoV-2 3CLpro resistant virus (L50F-E166A-L167F; 3CLprores) that is cross-resistant with nirmatrelvir and other 3CLpro inhibitors. Here, we demonstrate that the 3CLprores virus replicates efficiently in the lungs of intranasally infected female Syrian hamsters and causes lung pathology comparable to that caused by the WT virus. Moreover, hamsters infected with 3CLprores virus transmit the virus efficiently to co-housed non-infected contact hamsters. Importantly, at a dose of 200 mg/kg (BID) of nirmatrelvir, the compound was still able to reduce the lung infectious virus titers of 3CLprores-infected hamsters by 1.4 log10 with a modest improvement in the lung histopathology as compared to the vehicle control. Fortunately, resistance to Nirmatrelvir does not readily develop in clinical setting. Yet, as we demonstrate, in case drug-resistant viruses emerge, they may spread easily which may thus impact therapeutic options. Therefore, the use of 3CLpro inhibitors in combination with other drugs may be considered, especially in immunodeficient patients, to avoid the development of drug-resistant viruses.
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Affiliation(s)
- Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
- The VirusBank Platform, Gaston Geenslaan, B-3000, Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Kim Donckers
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium
| | - Bettina Trüeb
- Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Division of Translational Cell and Tissue Research, B-3000, Leuven, Belgium
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000, Leuven, Belgium.
- The VirusBank Platform, Gaston Geenslaan, B-3000, Leuven, Belgium.
- Global Virus Network, GVN, Baltimore, US.
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102
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Zabidi NZ, Liew HL, Farouk IA, Puniyamurti A, Yip AJW, Wijesinghe VN, Low ZY, Tang JW, Chow VTK, Lal SK. Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies. Viruses 2023; 15:v15040944. [PMID: 37112923 PMCID: PMC10145020 DOI: 10.3390/v15040944] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks.
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Affiliation(s)
- Nur Zawanah Zabidi
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Hern Liang Liew
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Isra Ahmad Farouk
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashwini Puniyamurti
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | | | - Zheng Yao Low
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Julian W Tang
- Department of Respiratory Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Vincent T K Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Sunil K Lal
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Selangor, Malaysia
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103
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Polatoğlu I, Oncu‐Oner T, Dalman I, Ozdogan S. COVID-19 in early 2023: Structure, replication mechanism, variants of SARS-CoV-2, diagnostic tests, and vaccine & drug development studies. MedComm (Beijing) 2023; 4:e228. [PMID: 37041762 PMCID: PMC10082934 DOI: 10.1002/mco2.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 04/13/2023] Open
Abstract
Coronavirus Disease-19 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome-coronaviruses-2 (SARS-CoV-2), a highly pathogenic and transmissible coronavirus. Most cases of COVID-19 have mild to moderate symptoms, including cough, fever, myalgias, and headache. On the other hand, this coronavirus can lead to severe complications and death in some cases. Therefore, vaccination is the most effective tool to prevent and eradicate COVID-19 disease. Also, rapid and effective diagnostic tests are critical in identifying cases of COVID-19. The COVID-19 pandemic has a dynamic structure on the agenda and contains up-to-date developments. This article has comprehensively discussed the most up-to-date pandemic situation since it first appeared. For the first time, not only the structure, replication mechanism, and variants of SARS-CoV-2 (Alpha, Beta, Gamma, Omicron, Delta, Epsilon, Kappa, Mu, Eta, Zeta, Theta, lota, Lambda) but also all the details of the pandemic, such as how it came out, how it spread, current cases, what precautions should be taken, prevention strategies, the vaccines produced, the tests developed, and the drugs used are reviewed in every aspect. Herein, the comparison of diagnostic tests for SARS-CoV-2 in terms of procedure, accuracy, cost, and time has been presented. The mechanism, safety, efficacy, and effectiveness of COVID-19 vaccines against SARS-CoV-2 variants have been evaluated. Drug studies, therapeutic targets, various immunomodulators, and antiviral molecules applied to patients with COVID-19 have been reviewed.
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Affiliation(s)
- Ilker Polatoğlu
- Department of BioengineeringManisa Celal Bayar UniversityYunusemreManisaTurkey
| | - Tulay Oncu‐Oner
- Department of BioengineeringManisa Celal Bayar UniversityYunusemreManisaTurkey
| | - Irem Dalman
- Department of BioengineeringEge UniversityBornovaIzmirTurkey
| | - Senanur Ozdogan
- Department of BioengineeringManisa Celal Bayar UniversityYunusemreManisaTurkey
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104
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Gu H, Quadeer AA, Krishnan P, Ng DYM, Chang LDJ, Liu GYZ, Cheng SMS, Lam TTY, Peiris M, McKay MR, Poon LLM. Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals. Nat Commun 2023; 14:1793. [PMID: 37002233 PMCID: PMC10063955 DOI: 10.1038/s41467-023-37468-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Viral and host factors can shape SARS-CoV-2 evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here, we analysed deep sequencing data from 2,820 SARS-CoV-2 respiratory samples with different viral lineages to describe the patterns of within-host diversity under different conditions, including vaccine-breakthrough infections. In unvaccinated individuals, variant of Concern (VOC) Alpha, Delta, and Omicron respiratory samples were found to have higher within-host diversity and were under neutral to purifying selection at the full genome level compared to non-VOC SARS-CoV-2. Breakthrough infections in 2-dose or 3-dose Comirnaty and CoronaVac vaccinated individuals did not increase levels of non-synonymous mutations and did not change the direction of selection pressure. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 sequence diversification. Our findings suggest that vaccination does not increase exploration of SARS-CoV-2 protein sequence space and may not facilitate emergence of viral variants.
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Affiliation(s)
- Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Daisy Y M Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lydia D J Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gigi Y Z Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tommy T Y Lam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Matthew R McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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105
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Torii S, Kim KS, Koseki J, Suzuki R, Iwanami S, Fujita Y, Jeong YD, Ito J, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Sato K, Matsuura Y, Shimamura T, Iwami S, Fukuhara T. Increased flexibility of the SARS-CoV-2 RNA-binding site causes resistance to remdesivir. PLoS Pathog 2023; 19:e1011231. [PMID: 36972312 PMCID: PMC10089321 DOI: 10.1371/journal.ppat.1011231] [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: 05/29/2022] [Revised: 04/11/2023] [Accepted: 02/22/2023] [Indexed: 03/29/2023] Open
Abstract
Mutations continue to accumulate within the SARS-CoV-2 genome, and the ongoing epidemic has shown no signs of ending. It is critical to predict problematic mutations that may arise in clinical environments and assess their properties in advance to quickly implement countermeasures against future variant infections. In this study, we identified mutations resistant to remdesivir, which is widely administered to SARS-CoV-2-infected patients, and discuss the cause of resistance. First, we simultaneously constructed eight recombinant viruses carrying the mutations detected in in vitro serial passages of SARS-CoV-2 in the presence of remdesivir. We confirmed that all the mutant viruses didn’t gain the virus production efficiency without remdesivir treatment. Time course analyses of cellular virus infections showed significantly higher infectious titers and infection rates in mutant viruses than wild type virus under treatment with remdesivir. Next, we developed a mathematical model in consideration of the changing dynamic of cells infected with mutant viruses with distinct propagation properties and defined that mutations detected in in vitro passages canceled the antiviral activities of remdesivir without raising virus production capacity. Finally, molecular dynamics simulations of the NSP12 protein of SARS-CoV-2 revealed that the molecular vibration around the RNA-binding site was increased by the introduction of mutations on NSP12. Taken together, we identified multiple mutations that affected the flexibility of the RNA binding site and decreased the antiviral activity of remdesivir. Our new insights will contribute to developing further antiviral measures against SARS-CoV-2 infection.
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Affiliation(s)
- Shiho Torii
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kwang Su Kim
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Jun Koseki
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Shoya Iwanami
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yasuhisa Fujita
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yong Dam Jeong
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | | | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
- * E-mail: (YM); (TS); (SI); (TF)
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- * E-mail: (YM); (TS); (SI); (TF)
| | - Shingo Iwami
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
- Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Saitama, Japan
- Science Groove Inc., Fukuoka, Japan
- * E-mail: (YM); (TS); (SI); (TF)
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- * E-mail: (YM); (TS); (SI); (TF)
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106
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Snell LB, Alcolea-Medina A, Charalampous T, Alder C, Williams TGS, Flaviani F, Batra R, Bakrania P, Thangarajah R, Neil SJD, van Nispen Tot Pannerden C, Botgros A, Aarons E, Douthwaite ST, Edgeworth JD, Nebbia G. Real-Time Whole Genome Sequencing to Guide Patient-Tailored Therapy of Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Clin Infect Dis 2023; 76:1125-1128. [PMID: 36327795 PMCID: PMC10029986 DOI: 10.1093/cid/ciac864] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022] Open
Abstract
The management of coronavirus disease 2019 has become more complex due to the expansion of available therapies. The presence of severe acute respiratory syndrome coronavirus 2 variants and mutations further complicates treatment due to their differing susceptibilities to therapies. Here we outline the use of real-time whole genome sequencing to detect persistent infection, evaluate for mutations confering resistance to treatments, and guide treatment decisions.
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Affiliation(s)
- Luke B Snell
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | | | - Christopher Alder
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Tom G S Williams
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Flavia Flaviani
- National Institute for Health Research Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Prijay Bakrania
- Department of Pharmacy, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rajeni Thangarajah
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Department of Pharmacy, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, United Kingdom
| | | | - Alina Botgros
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Emma Aarons
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Samuel T Douthwaite
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | - Gaia Nebbia
- Department of Infection, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King's College London, United Kingdom
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107
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Yan VC. Test of 5- Versus 10-Day Remdesivir Treatment in Immunocompromised Patients With Coronavirus Disease 2019. Clin Infect Dis 2023; 76:1154-1155. [PMID: 36346111 DOI: 10.1093/cid/ciac877] [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: 10/02/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Victoria C Yan
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston
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108
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Dobrowolska K, Zarębska-Michaluk D, Brzdęk M, Rzymski P, Rogalska M, Moniuszko-Malinowska A, Kozielewicz D, Hawro M, Rorat M, Sikorska K, Jaroszewicz J, Kowalska J, Flisiak R. Retrospective Analysis of the Effectiveness of Remdesivir in COVID-19 Treatment during Periods Dominated by Delta and Omicron SARS-CoV-2 Variants in Clinical Settings. J Clin Med 2023; 12:jcm12062371. [PMID: 36983370 PMCID: PMC10051185 DOI: 10.3390/jcm12062371] [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: 02/26/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Continuous evaluation of real-world treatment effectiveness of COVID-19 medicines is required due to the ongoing evolution of SARS-CoV-2 and the possible emergence of resistance. Therefore, this study aimed to analyze, in a retrospective manner, the outcomes in patients hospitalized with COVID-19 during the pandemic waves dominated by Delta and Omicron variants and treated with remdesivir (RDV) (n = 762) in comparison to a demographically and clinically matched group not treated with any antivirals (n = 1060). A logistic regression analysis revealed that RDV treatment was associated with a significantly lower risk of death during both Delta wave (OR = 0.42, 95%CI: 0.29-0.60; p < 0.0001) and Omicron-dominated period (OR = 0.56, 95%CI: 0.35-0.92; p = 0.02). Moreover, RDV-treated groups were characterized by a lower percentage of patients requiring mechanical ventilation, but the difference was not statistically significant. This study is the first real-world evidence that RDV remains effective during the dominance of more pathogenic SARS-CoV-2 variants and those that cause a milder course of the disease, and continues to be an essential element of COVID-19 therapy.
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Affiliation(s)
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases and Allergology, Jan Kochanowski University, 25-317 Kielce, Poland
- Department of Infectious Diseases, Provincial Hospital, 25-317 Kielce, Poland
| | - Michał Brzdęk
- Collegium Medicum, Jan Kochanowski University, 25-317 Kielce, Poland
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland
| | - Magdalena Rogalska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland
| | - Anna Moniuszko-Malinowska
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-809 Białystok, Poland
| | - Dorota Kozielewicz
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Marcin Hawro
- Department of Infectious Diseases and Hepatology, Medical Center in Łańcut, 37-100 Łańcut, Poland
| | - Marta Rorat
- Department of Forensic Medicine, Wrocław Medical University, 50-367 Wroclaw, Poland
| | - Katarzyna Sikorska
- Institute of Maritime and Tropical Medicine, Faculty of Health Sciences, Medical University of Gdansk, 81-519 Gdynia, Poland
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia, 41-902 Katowice, Poland
| | - Justyna Kowalska
- Department of Adults' Infectious Diseases, Medical University of Warsaw, 01-201 Warsaw, Poland
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland
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109
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Ford ES, Simmons W, Karmarkar EN, Yoke LH, Braimah AB, Orozco JJ, Ghiuzeli CM, Barnhill S, Sack CL, Benditt JO, Roychoudhury P, Greninger AL, Shapiro AE, Hammond JL, Rusnak JM, Dolsten M, Boeckh M, Liu C, Cheng GS, Corey L. Successful Treatment of Prolonged, Severe Coronavirus Disease 2019 Lower Respiratory Tract Disease in a B cell Acute Lymphoblastic Leukemia Patient With an Extended Course of Remdesivir and Nirmatrelvir/Ritonavir. Clin Infect Dis 2023; 76:926-929. [PMID: 36326680 PMCID: PMC10226728 DOI: 10.1093/cid/ciac868] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
A patient with B-cell acute lymphoblastic leukemia (ALL) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had persistent, progressive pneumonia with viremia after 5 months of infection despite monoclonal antibodies, intravenous (IV) remdesivir and prolonged oral steroids. Twenty days of nirmatrelvir/ritonavir and 10 days of IV remdesivir led to full recovery.
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Affiliation(s)
- Emily S Ford
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - William Simmons
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ellora N Karmarkar
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Leah H Yoke
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Ayodale B Braimah
- Division of General Internal Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Johnnie J Orozco
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Medical Oncology, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Cristina M Ghiuzeli
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Hematology, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Serena Barnhill
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Coralynn L Sack
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Joshua O Benditt
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
| | - Alexander L Greninger
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
| | - Adrienne E Shapiro
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Global Health, University of Washington,Seattle, Washington, USA
| | | | | | | | - Michael Boeckh
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Catherine Liu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Guang-Shing Cheng
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Lawrence Corey
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
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110
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Fidelity of Ribonucleotide Incorporation by the SARS-CoV-2 Replication Complex. J Mol Biol 2023; 435:167973. [PMID: 36690070 PMCID: PMC9854147 DOI: 10.1016/j.jmb.2023.167973] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
The SARS-CoV-2 coronavirus has caused a global pandemic. Despite the initial success of vaccines at preventing infection, genomic variation has led to the proliferation of variants capable of higher infectivity. Mutations in the SARS-CoV-2 genome are the consequence of replication errors, highlighting the importance of understanding the determinants of SARS-CoV-2 replication fidelity. The RNA-dependent RNA polymerase (RdRp) is the central catalytic subunit for SARS-CoV-2 RNA replication and genome transcription. Here, we report the fidelity of ribonucleotide incorporation by SARS-CoV-2 RdRp (nsp12), along with its co-factors nsp7/nsp8, using steady-state kinetic analysis. Our analysis suggests that in the absence of the proofreading subunit (nsp14), the nsp12/7/8 complex has a surprisingly low base substitution fidelity (10-1-10-3). This is orders of magnitude lower than the fidelity reported for other coronaviruses (10-6-10-7), highlighting the importance of proofreading for faithful SARS-CoV-2 replication. We performed a mutational analysis of all reported SARS-CoV-2 genomes and identified mutations in both nsp12 and nsp14 that appear likely to lower viral replication fidelity through mechanisms that include impairing the nsp14 exonuclease activity or its association with the RdRp. Our observations provide novel insight into the mechanistic basis of replication fidelity in SARS-CoV-2 and the potential effect of nsp12 and nsp14 mutations on replication fidelity, informing the development of future antiviral agents and SARS-CoV-2 vaccines.
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111
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Wei J, Patil A, Collings CK, Alfajaro MM, Liang Y, Cai WL, Strine MS, Filler RB, DeWeirdt PC, Hanna RE, Menasche BL, Ökten A, Peña-Hernández MA, Klein J, McNamara A, Rosales R, McGovern BL, Luis Rodriguez M, García-Sastre A, White KM, Qin Y, Doench JG, Yan Q, Iwasaki A, Zwaka TP, Qi J, Kadoch C, Wilen CB. Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection. Nat Genet 2023; 55:471-483. [PMID: 36894709 PMCID: PMC10011139 DOI: 10.1038/s41588-023-01307-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023]
Abstract
Identification of host determinants of coronavirus infection informs mechanisms of viral pathogenesis and can provide new drug targets. Here we demonstrate that mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) chromatin remodeling complexes, specifically canonical BRG1/BRM-associated factor (cBAF) complexes, promote severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and represent host-directed therapeutic targets. The catalytic activity of SMARCA4 is required for mSWI/SNF-driven chromatin accessibility at the ACE2 locus, ACE2 expression and virus susceptibility. The transcription factors HNF1A/B interact with and recruit mSWI/SNF complexes to ACE2 enhancers, which contain high HNF1A motif density. Notably, small-molecule mSWI/SNF ATPase inhibitors or degraders abrogate angiotensin-converting enzyme 2 (ACE2) expression and confer resistance to SARS-CoV-2 variants and a remdesivir-resistant virus in three cell lines and three primary human cell types, including airway epithelial cells, by up to 5 logs. These data highlight the role of mSWI/SNF complex activities in conferring SARS-CoV-2 susceptibility and identify a potential class of broad-acting antivirals to combat emerging coronaviruses and drug-resistant variants.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yu Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wesley L Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arya Ökten
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew McNamara
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiren Qin
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Thomas P Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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112
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023; 4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, CT, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott C Roberts
- Infectious Disease, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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113
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González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
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Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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114
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Scotto R, Buonomo AR, Iuliano A, Foggia M, Sardanelli A, Villari R, Pinchera B, Gentile I. Remdesivir Alone or in Combination with Monoclonal Antibodies as an Early Treatment to Prevent Severe COVID-19 in Patients with Mild/Moderate Disease at High Risk of Progression: A Single Centre, Real-Life Study. Vaccines (Basel) 2023; 11:vaccines11020200. [PMID: 36851078 PMCID: PMC9964994 DOI: 10.3390/vaccines11020200] [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: 12/06/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Early treatment with antivirals against SARS-CoV-2 infection can prevent the onset of severe COVID-19 in fragile and immunocompromised patients. In this real-life, prospective, observational study, we evaluated efficacy and safety of a 3-day early treatment with remdesivir in adult and fragile patients with a diagnosis of SARS-CoV-2 infection who referred to the COVID-19 early treatment service of Infectious Diseases Unit of University of Naples Federico from 10 January 2022 to 31 March 2022. The included patients could be treated with either remdesivir alone or with remdesivir plus a monoclonal antibody with activity against SARS-CoV-2. Among the 62 included patients, we showed low rates of hospitalization (8%), increase in oxygen supplementation (3.2%), ICU admission (1.6%) and death (1.6%). The rate of disease progression was 8% and it was similar in patients treated with remdesivir alone or in combination with monoclonal antibodies (6.7% and 9.4%, respectively; p = 0.531). The rate of adverse drug reaction was low and similar in the two groups (13.3% in patients treated with remdesivir, 15.6% in patients treated with the combination; p = 0.543). Most common adverse events were headache and fever. In conclusion, in our cohort of patients at a high risk of worse COVID-19 outcomes, an early course of remdesivir showed low rates of disease progression and adverse drug reactions.
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115
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Souza TML, Pinho VD, Setim CF, Sacramento CQ, Marcon R, Fintelman-Rodrigues N, Chaves OA, Heller M, Temerozo JR, Ferreira AC, Mattos M, Momo PB, Dias SSG, Gesto JSM, Pereira-Dutra F, Viola JPB, Queiroz-Junior CM, Guimarães LC, Chaves IM, Guimarães PPG, Costa VV, Teixeira MM, Bou-Habib DC, Bozza PT, Aguillón AR, Siqueira-Junior J, Macedo-Junior S, Andrade EL, Fadanni GP, Tolouei SEL, Potrich FB, Santos AA, Marques NF, Calixto JB, Rabi JA. Preclinical development of kinetin as a safe error-prone SARS-CoV-2 antiviral able to attenuate virus-induced inflammation. Nat Commun 2023; 14:199. [PMID: 36639383 PMCID: PMC9837764 DOI: 10.1038/s41467-023-35928-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Orally available antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are necessary because of the continuous circulation of new variants that challenge immunized individuals. Because severe COVID-19 is a virus-triggered immune and inflammatory dysfunction, molecules endowed with both antiviral and anti-inflammatory activity are highly desirable. We identified here that kinetin (MB-905) inhibits the in vitro replication of SARS-CoV-2 in human hepatic and pulmonary cell lines. On infected monocytes, MB-905 reduced virus replication, IL-6 and TNFα levels. MB-905 is converted into its triphosphate nucleotide to inhibit viral RNA synthesis and induce error-prone virus replication. Coinhibition of SARS-CoV-2 exonuclease, a proofreading enzyme that corrects erroneously incorporated nucleotides during viral RNA replication, potentiated the inhibitory effect of MB-905. MB-905 shows good oral absorption, its metabolites are stable, achieving long-lasting plasma and lung concentrations, and this drug is not mutagenic nor cardiotoxic in acute and chronic treatments. SARS-CoV-2-infected hACE-mice and hamsters treated with MB-905 show decreased viral replication, lung necrosis, hemorrhage and inflammation. Because kinetin is clinically investigated for a rare genetic disease at regimens beyond the predicted concentrations of antiviral/anti-inflammatory inhibition, our investigation suggests the opportunity for the rapid clinical development of a new antiviral substance for the treatment of COVID-19.
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Affiliation(s)
- Thiago Moreno L Souza
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil. .,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil.
| | - Vagner D Pinho
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Cristina F Setim
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Carolina Q Sacramento
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Marcon
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Otavio A Chaves
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Melina Heller
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Jairo R Temerozo
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil.,Laboratório de Pesquisa sobre o Timo, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - André C Ferreira
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil.,Universidade Iguaçu, Nova Iguaçu, RJ, Brazil
| | - Mayara Mattos
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia B Momo
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Suelen S G Dias
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - João S M Gesto
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Filipe Pereira-Dutra
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - João P B Viola
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rua André Cavalcanti 37, 5th floor, Centro, Rio de Janeiro, Brazil
| | - Celso Martins Queiroz-Junior
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Lays Cordeiro Guimarães
- Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ian Meira Chaves
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Pedro Pires Goulart Guimarães
- Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vivian Vasconcelos Costa
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Mauro Martins Teixeira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Dumith Chequer Bou-Habib
- National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil.,Laboratório de Pesquisa sobre o Timo, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Anderson R Aguillón
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Jarbas Siqueira-Junior
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Sergio Macedo-Junior
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Edineia L Andrade
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Guilherme P Fadanni
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Sara E L Tolouei
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Francine B Potrich
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Adara A Santos
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Naiani F Marques
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - João B Calixto
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil.
| | - Jaime A Rabi
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil.
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Hogan JI, Duerr R, Dimartino D, Marier C, Hochman SE, Mehta S, Wang G, Heguy A. Remdesivir Resistance in Transplant Recipients With Persistent Coronavirus Disease 2019. Clin Infect Dis 2023; 76:342-345. [PMID: 36156117 PMCID: PMC9619446 DOI: 10.1093/cid/ciac769] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 01/18/2023] Open
Abstract
New mutations conferring resistance to SARS-CoV-2 therapeutics have important clinical implications. We describe the first cases of an independently acquired V792I RNA-dependent RNA polymerase mutation developing in renal transplant recipients after remdesivir exposure. Our work underscores the need for augmented efforts to identify concerning mutations and address their clinical implications.
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Affiliation(s)
- John I Hogan
- Department of Medicine, NYU Long Island School of Medicine, Mineola, New York, USA
| | - Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Dacia Dimartino
- Genome Technology Center, NYU Langone Health, New York, New York, USA
| | - Christian Marier
- Genome Technology Center, NYU Langone Health, New York, New York, USA
| | - Sarah E Hochman
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Sapna Mehta
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Guiqing Wang
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Adriana Heguy
- Genome Technology Center, NYU Langone Health, New York, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
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117
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Sargsyan K, Mazmanian K, Lim C. A strategy for evaluating potential antiviral resistance to small molecule drugs and application to SARS-CoV-2. Sci Rep 2023; 13:502. [PMID: 36627366 PMCID: PMC9831016 DOI: 10.1038/s41598-023-27649-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Alterations in viral fitness cannot be inferred from only mutagenesis studies of an isolated viral protein. To-date, no systematic analysis has been performed to identify mutations that improve virus fitness and reduce drug efficacy. We present a generic strategy to evaluate which viral mutations might diminish drug efficacy and applied it to assess how SARS-CoV-2 evolution may affect the efficacy of current approved/candidate small-molecule antivirals for Mpro, PLpro, and RdRp. For each drug target, we determined the drug-interacting virus residues from available structures and the selection pressure of the virus residues from the SARS-CoV-2 genomes. This enabled the identification of promising drug target regions and small-molecule antivirals that the virus can develop resistance. Our strategy of utilizing sequence and structural information from genomic sequence and protein structure databanks can rapidly assess the fitness of any emerging virus variants and can aid antiviral drug design for future pathogens.
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Affiliation(s)
- Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
| | - Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
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118
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Pérez-Vargas J, Shapira T, Olmstead AD, Villanueva I, Thompson CAH, Ennis S, Gao G, De Guzman J, Williams DE, Wang M, Chin A, Bautista-Sánchez D, Agafitei O, Levett P, Xie X, Nuzzo G, Freire VF, Quintana-Bulla JI, Bernardi DI, Gubiani JR, Suthiphasilp V, Raksat A, Meesakul P, Polbuppha I, Cheenpracha S, Jaidee W, Kanokmedhakul K, Yenjai C, Chaiyosang B, Teles HL, Manzo E, Fontana A, Leduc R, Boudreault PL, Berlinck RGS, Laphookhieo S, Kanokmedhakul S, Tietjen I, Cherkasov A, Krajden M, Nabi IR, Niikura M, Shi PY, Andersen RJ, Jean F. Discovery of lead natural products for developing pan-SARS-CoV-2 therapeutics. Antiviral Res 2023; 209:105484. [PMID: 36503013 PMCID: PMC9729583 DOI: 10.1016/j.antiviral.2022.105484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health crisis. The reduced efficacy of therapeutic monoclonal antibodies against emerging SARS-CoV-2 variants of concern (VOCs), such as omicron BA.5 subvariants, has underlined the need to explore a novel spectrum of antivirals that are effective against existing and evolving SARS-CoV-2 VOCs. To address the need for novel therapeutic options, we applied cell-based high-content screening to a library of natural products (NPs) obtained from plants, fungi, bacteria, and marine sponges, which represent a considerable diversity of chemical scaffolds. The antiviral effect of 373 NPs was evaluated using the mNeonGreen (mNG) reporter SARS-CoV-2 virus in a lung epithelial cell line (Calu-3). The screening identified 26 NPs with half-maximal effective concentrations (EC50) below 50 μM against mNG-SARS-CoV-2; 16 of these had EC50 values below 10 μM and three NPs (holyrine A, alotaketal C, and bafilomycin D) had EC50 values in the nanomolar range. We demonstrated the pan-SARS-CoV-2 activity of these three lead antivirals against SARS-CoV-2 highly transmissible Omicron subvariants (BA.5, BA.2 and BA.1) and highly pathogenic Delta VOCs in human Calu-3 lung cells. Notably, holyrine A, alotaketal C, and bafilomycin D, are potent nanomolar inhibitors of SARS-CoV-2 Omicron subvariants BA.5 and BA.2. The pan-SARS-CoV-2 activity of alotaketal C [protein kinase C (PKC) activator] and bafilomycin D (V-ATPase inhibitor) suggest that these two NPs are acting as host-directed antivirals (HDAs). Future research should explore whether PKC regulation impacts human susceptibility to and the severity of SARS-CoV-2 infection, and it should confirm the important role of human V-ATPase in the VOC lifecycle. Interestingly, we observed a synergistic action of bafilomycin D and N-0385 (a highly potent inhibitor of human TMPRSS2 protease) against Omicron subvariant BA.2 in human Calu-3 lung cells, which suggests that these two highly potent HDAs are targeting two different mechanisms of SARS-CoV-2 entry. Overall, our study provides insight into the potential of NPs with highly diverse chemical structures as valuable inspirational starting points for developing pan-SARS-CoV-2 therapeutics and for unravelling potential host factors and pathways regulating SARS-CoV-2 VOC infection including emerging omicron BA.5 subvariants.
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Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Andrea D Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Connor A H Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Guang Gao
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - David E Williams
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Meng Wang
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Aaleigha Chin
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Diana Bautista-Sánchez
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Vitor F Freire
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Jairo I Quintana-Bulla
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Virayu Suthiphasilp
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Achara Raksat
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Pornphimol Meesakul
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Isaraporn Polbuppha
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | | | - Wuttichai Jaidee
- Medicinal Plants Innovation Center of Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Kwanjai Kanokmedhakul
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chavi Yenjai
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Boonyanoot Chaiyosang
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Helder Lopes Teles
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, CEP 78736-900, Rondonópolis, MT, Brazil
| | - Emiliano Manzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, Università di Napoli "Federico II", Via Cupa Nuova Cinthia 21, 80126, Napoli, Italy
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Surat Laphookhieo
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Somdej Kanokmedhakul
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Ian Tietjen
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, School of Biomedical Engineering, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Raymond J Andersen
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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Inhibition of p38 signaling curtails the SARS-CoV-2 induced inflammatory response but retains the IFN-dependent antiviral defense of the lung epithelial barrier. Antiviral Res 2023; 209:105475. [PMID: 36423831 PMCID: PMC9677559 DOI: 10.1016/j.antiviral.2022.105475] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
SARS-CoV-2 is the causative agent of the immune response-driven disease COVID-19 for which new antiviral and anti-inflammatory treatments are urgently needed to reduce recovery time, risk of death and long COVID development. Here, we demonstrate that the immunoregulatory kinase p38 MAPK is activated during viral entry, mediated by the viral spike protein, and drives the harmful virus-induced inflammatory responses. Using primary human lung explants and lung epithelial organoids, we demonstrate that targeting p38 signal transduction with the selective and clinically pre-evaluated inhibitors PH-797804 and VX-702 markedly reduced the expression of the pro-inflammatory cytokines IL6, CXCL8, CXCL10 and TNF-α during infection, while viral replication and the interferon-mediated antiviral response of the lung epithelial barrier were largely maintained. Furthermore, our results reveal a high level of drug synergism of both p38 inhibitors in co-treatments with the nucleoside analogs Remdesivir and Molnupiravir to suppress viral replication of the SARS-CoV-2 variants of concern, revealing an exciting and novel mode of synergistic action of p38 inhibition. These results open new avenues for the improvement of the current treatment strategies for COVID-19.
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120
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Abstract
Nirmatrelvir, an oral antiviral targeting the 3CL protease of SARS-CoV-2, has been demonstrated to be clinically useful against COVID-19 (refs. 1,2). However, because SARS-CoV-2 has evolved to become resistant to other therapeutic modalities3-9, there is a concern that the same could occur for nirmatrelvir. Here we examined this possibility by in vitro passaging of SARS-CoV-2 in nirmatrelvir using two independent approaches, including one on a large scale. Indeed, highly resistant viruses emerged from both and their sequences showed a multitude of 3CL protease mutations. In the experiment peformed with many replicates, 53 independent viral lineages were selected with mutations observed at 23 different residues of the enzyme. Nevertheless, several common mutational pathways to nirmatrelvir resistance were preferred, with a majority of the viruses descending from T21I, P252L or T304I as precursor mutations. Construction and analysis of 13 recombinant SARS-CoV-2 clones showed that these mutations mediated only low-level resistance, whereas greater resistance required accumulation of additional mutations. E166V mutation conferred the strongest resistance (around 100-fold), but this mutation resulted in a loss of viral replicative fitness that was restored by compensatory changes such as L50F and T21I. Our findings indicate that SARS-CoV-2 resistance to nirmatrelvir does readily arise via multiple pathways in vitro, and the specific mutations observed herein form a strong foundation from which to study the mechanism of resistance in detail and to inform the design of next-generation protease inhibitors.
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121
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In Silico Identification of Anti-SARS-CoV-2 Medicinal Plants Using Cheminformatics and Machine Learning. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010208. [PMID: 36615401 PMCID: PMC9821958 DOI: 10.3390/molecules28010208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/17/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of COVID-19, is spreading rapidly and has caused hundreds of millions of infections and millions of deaths worldwide. Due to the lack of specific vaccines and effective treatments for COVID-19, there is an urgent need to identify effective drugs. Traditional Chinese medicine (TCM) is a valuable resource for identifying novel anti-SARS-CoV-2 drugs based on the important contribution of TCM and its potential benefits in COVID-19 treatment. Herein, we aimed to discover novel anti-SARS-CoV-2 compounds and medicinal plants from TCM by establishing a prediction method of anti-SARS-CoV-2 activity using machine learning methods. We first constructed a benchmark dataset from anti-SARS-CoV-2 bioactivity data collected from the ChEMBL database. Then, we established random forest (RF) and support vector machine (SVM) models that both achieved satisfactory predictive performance with AUC values of 0.90. By using this method, a total of 1011 active anti-SARS-CoV-2 compounds were predicted from the TCMSP database. Among these compounds, six compounds with highly potent activity were confirmed in the anti-SARS-CoV-2 experiments. The molecular fingerprint similarity analysis revealed that only 24 of the 1011 compounds have high similarity to the FDA-approved antiviral drugs, indicating that most of the compounds were structurally novel. Based on the predicted anti-SARS-CoV-2 compounds, we identified 74 anti-SARS-CoV-2 medicinal plants through enrichment analysis. The 74 plants are widely distributed in 68 genera and 43 families, 14 of which belong to antipyretic detoxicate plants. In summary, this study provided several medicinal plants with potential anti-SARS-CoV-2 activity, which offer an attractive starting point and a broader scope to mine for potentially novel anti-SARS-CoV-2 drugs.
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122
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Genetic Study of SARS-CoV-2 Non Structural Protein 12 in COVID-19 Patients Non Responders to Remdesivir. Microbiol Spectr 2022; 10:e0244822. [PMID: 36354320 PMCID: PMC9769853 DOI: 10.1128/spectrum.02448-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Remdesivir (RDV) was the first antiviral drug approved by the FDA to treat severe coronavirus disease-2019 (COVID-19) patients. RDV inhibits SARS-CoV-2 replication by stalling the non structural protein 12 (nsp12) subunit of the RNA-dependent RNA polymerase (RdRp). No evidence of global widespread RDV-resistance mutations has been reported, however, defining genetic pathways to RDV resistance and determining emergent mutations prior and subsequent antiviral therapy in clinical settings is necessary. This study identified 57/149 (38.3%) patients who did not respond to one course (5-days) (n = 36/111, 32.4%) or prolonged (5 to 20 days) (n = 21/38, 55.3%) RDV therapy by subgenomic RNA detection. Genetic variants in the nsp12 gene were detected in 29/49 (59.2%) non responder patients by Illumina sequencing, including the de novo E83D mutation that emerged in an immunosuppressed patient after receiving 10 + 8 days of RDV, and the L838I detected at baseline and/or after prolonged RDV treatment in 9/49 (18.4%) non responder subjects. Although 3D protein modeling predicted no interference with RDV, the amino acid substitutions detected in the nsp12 involved changes on the electrostatic outer surface and in secondary structures that may alter antiviral response. It is important for health surveillance to study potential mutations associated with drug resistance as well as the benefit of RDV retreatment, especially in immunosuppressed patients and in those with persistent replication. IMPORTANCE This study provides clinical and microbiologic data of an extended population of hospitalized patients for COVID-19 pneumonia who experienced treatment failure, detected by the presence of subgenomic RNA (sgRNA). The genetic variants found in the nsp12 pharmacological target of RDV bring into focus the importance of monitoring emergent mutations, one of the objectives of the World Health Organization (WHO) for health surveillance. These mutations become even more crucial as RDV keeps being prescribed and new molecules are being repurposed for the treatment of COVID-19. The present article offers new perspectives for the clinical management of non responder patients treated and retreated with RDV and emphasizes the need of further research of the benefit of combinatorial therapies and RDV retreatment, especially in immunosuppressed patients with persistent replication after therapy.
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123
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Dioverti V, Boghdadly ZE, Shahid Z, Waghmare A, Abidi MZ, Pergam S, Boeckh M, Dadwal S, Kamboj M, Seo S, Chemaly RF, Papanicolaou GA. Revised Guidelines for Coronavirus Disease 19 Management in Hematopoietic Cell Transplantation and Cellular Therapy Recipients (August 2022). Transplant Cell Ther 2022; 28:810-821. [PMID: 36103987 PMCID: PMC9464362 DOI: 10.1016/j.jtct.2022.09.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 01/17/2023]
Abstract
This document is intended as a guide for diagnosis and management of Coronavirus Disease 2019 (COVID-19), caused by the virus SARS-CoV-2, in adult and pediatric HCT and cellular therapy patients. This document was prepared using available data and with expert opinion provided by members of the (ASTCT) Infectious Diseases Special Interest Group (ID-SIG) and is an update of pervious publication. Since our original publication in 2020, the NIH and IDSA have published extensive guidelines for management of COVID-19 which are readily accessible ( NIH Guidelines , IDSA Guidelines ). This update focuses primarily on issues pertaining specifically to HCT/cellular therapy recipients. Information provided in this manuscript may change as new information becomes available.
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Affiliation(s)
- Veronica Dioverti
- Assistant Professor of Medicine, Johns Hopkins University, Baltimore, Maryland.
| | - Zeinab El Boghdadly
- Assistant Professor of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Zainab Shahid
- Attending physician, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alpana Waghmare
- Associate Professor of Pediatrics, University of Washington, Seattle, Washington; Fred Hutchinson Cancer Center, Seattle, Washington
| | - Maheen Z Abidi
- Assistant Professor of Medicine, University of Colorado, Denver, Colorado
| | - Steven Pergam
- Professor, Fred Hutchinson Cancer Research Center, Associate Professor, University of Washington, Seattle, Washington
| | - Michael Boeckh
- Fred Hutchinson Cancer Center, Seattle, Washington; Professor of Medicine, University of Washington, Seattle, Washington
| | | | - Mini Kamboj
- Associate Professor of Medicine, Weill Cornell Medical College, New York, New York; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan Seo
- Memorial Sloan Kettering Cancer Center, New York, New York; Professor of Clinical Medicine, Weill Cornell Medical College, New York, New York
| | - Roy F Chemaly
- Professor of Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Genovefa A Papanicolaou
- Memorial Sloan Kettering Cancer Center, New York, New York; Professor of Medicine, Weill Cornell Medical College, New York, New York
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Tzou PL, Tao K, Sahoo MK, Kosakovsky Pond SL, Pinsky BA, Shafer RW. Sierra SARS-CoV-2 sequence and antiviral resistance analysis program. J Clin Virol 2022; 157:105323. [PMID: 36334368 PMCID: PMC9595491 DOI: 10.1016/j.jcv.2022.105323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/11/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Although most laboratories are capable of employing established protocols to perform full-genome SARS-CoV-2 sequencing, many are unable to assess sequence quality, select appropriate mutation-detection thresholds, or report on the potential clinical significance of mutations in the targets of antiviral therapy METHODS: We describe the technical aspects and benchmark the performance of Sierra SARS-CoV-2, a program designed to perform these functions on user-submitted FASTQ and FASTA sequence files and lists of Spike mutations. Sierra SARS-CoV-2 indicates which sequences contain an unexpectedly large number of unusual mutations and which mutations are associated with reduced susceptibility to clinical stage mAbs, the RdRP inhibitor remdesivir, or the Mpro inhibitor nirmatrelvir RESULTS: To assess the performance of Sierra SARS-CoV-2 on FASTQ files, we applied it to 600 representative FASTQ sequences and compared the results to the COVID-19 EDGE program. To assess its performance on FASTA files, we applied it to nearly one million representative FASTA sequences and compared the results to the GISAID mutation annotation. To assess its performance on mutations lists, we applied it to 13,578 distinct Spike RBD mutation patterns and showed that exactly or partially matching annotations were available for 88% of patterns CONCLUSION: Sierra SARS-CoV-2 leverages previously published data to improve the quality control of submitted viral genomic data and to provide functional annotation on the impact of mutations in the targets of antiviral SARS-CoV-2 therapy. The program can be found at https://covdb.stanford.edu/sierra/sars2/ and its source code at https://github.com/hivdb/sierra-sars2.
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Affiliation(s)
- Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Benjamin A Pinsky
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
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Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial. Nat Commun 2022; 13:7284. [PMID: 36435798 PMCID: PMC9701236 DOI: 10.1038/s41467-022-34839-9] [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: 09/26/2022] [Accepted: 11/09/2022] [Indexed: 11/28/2022] Open
Abstract
Molnupiravir is an antiviral, currently approved by the UK Medicines and Healthcare products Regulatory Agency (MHRA) for treating at-risk COVID-19 patients, that induces lethal error catastrophe in SARS-CoV-2. How this drug-induced mechanism of action might impact the emergence of resistance mutations is unclear. To investigate this, we used samples from the AGILE Candidate Specific Trial (CST)-2 (clinical trial number NCT04746183). The primary outcomes of AGILE CST-2 were to measure the drug safety and antiviral efficacy of molnupiravir in humans (180 participants randomised 1:1 with placebo). Here, we describe the pre-specified exploratory virological endpoint of CST-2, which was to determine the possible genomic changes in SARS-CoV-2 induced by molnupiravir treatment. We use high-throughput amplicon sequencing and minor variant analysis to characterise viral genomics in each participant whose longitudinal samples (days 1, 3 and 5 post-randomisation) pass the viral genomic quality criteria (n = 59 for molnupiravir and n = 65 for placebo). Over the course of treatment, no specific mutations were associated with molnupiravir treatment. We find that molnupiravir significantly increased the transition:transversion mutation ratio in SARS-CoV-2, consistent with the model of lethal error catastrophe. This study highlights the utility of examining intra-host virus populations to strengthen the prediction, and surveillance, of potential treatment-emergent adaptations.
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Nagai H, Saito M, Adachi E, Sakai-Tagawa Y, Yamayoshi S, Kiso M, Kawamata T, Koga M, Kawaoka Y, Tsutsumi T, Yotsuyanagi H. Casirivimab/Imdevimab for Active COVID-19 Pneumonia Which Persisted for Nine Months in a Patient with Follicular Lymphoma during Anti-CD20 Therapy. Jpn J Infect Dis 2022; 75:608-611. [PMID: 35768273 DOI: 10.7883/yoken.jjid.2022.092] [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: 11/17/2022]
Abstract
Immunocompromised patients are more likely to develop severe COVID-19, and exhibit high mortality. It is also hypothesized that chronic infection in these patients can be a risk factor for developing new variants. We describe a patient with prolonged active infection of COVID-19 who became infected during treatment with an anti-CD20 antibody (obinutuzumab) for follicular lymphoma. This patient had persistent RT-PCR positivity and live virus isolation for nine months despite treatment with remdesivir and other potential antiviral therapies. The computed tomography image of the chest showed that the viral pneumonia repeatedly appeared and disappeared in different lobes, as if a new infection had occurred continuously. The patient's SARS-CoV-2 antibody titer was negative throughout the illness, even after two doses of the BNT162b2 mRNA vaccine were administered in the seventh month of infection. A combination of monoclonal antibody therapy against COVID-19 (casirivimab and imdevimab) and antivirals resulted in negative RT-PCR results, and the virus was no longer isolated. The patient was clinically cured. During the 9-month active infection period, no fixed mutations in the spike (S) protein were detected, and the in vitro susceptibility to remdesivir was retained. Therapeutic administration of anti-SARS-CoV-2 monoclonal antibodies is essential in immunocompromised patients. Therefore, measures to prevent resistance against these key drugs are urgently needed.
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Affiliation(s)
- Hiroyuki Nagai
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Japan
| | - Makoto Saito
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Japan
| | - Yuko Sakai-Tagawa
- Department of Virology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Seiya Yamayoshi
- Department of Virology, The Institute of Medical Science, The University of Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Japan
| | - Maki Kiso
- Department of Virology, The Institute of Medical Science, The University of Tokyo, Japan
| | - Toyotaka Kawamata
- Department of Hematology/Oncology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Japan
| | - Michiko Koga
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Japan
- Center for Antibody and Vaccine Therapy, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Japan
| | - Yoshihiro Kawaoka
- Department of Virology, The Institute of Medical Science, The University of Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, USA
| | - Takeya Tsutsumi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Japan
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In Silico Screening of Plant-Derived Anti-virals from Shorea hemsleyana (King) King ex Foxw Against SARS CoV-2 Main Protease. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00521-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Mahilkar S, Agrawal S, Chaudhary S, Parikh S, Sonkar SC, Verma DK, Chitalia V, Mehta D, Koner BC, Vijay N, Shastri J, Sunil S. SARS-CoV-2 variants: Impact on biological and clinical outcome. Front Med (Lausanne) 2022; 9:995960. [PMID: 36438034 PMCID: PMC9685312 DOI: 10.3389/fmed.2022.995960] [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: 07/16/2022] [Accepted: 10/11/2022] [Indexed: 11/12/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that was first identified in December 2019, in Wuhan, China was found to be the etiological agent for a novel respiratory infection that led to a Coronavirus Induced Disease named COVID-19. The disease spread to pandemic magnitudes within a few weeks and since then we have been dealing with several waves across the world, due to the emergence of variants and novel mutations in this RNA virus. A direct outcome of these variants apart from the spike of cases is the diverse disease presentation and difficulty in employing effective diagnostic tools apart from confusing disease outcomes. Transmissibility rates of the variants, host response, and virus evolution are some of the features found to impact COVID-19 disease management. In this review, we will discuss the emerging variants of SARS-CoV-2, notable mutations in the viral genome, the possible impact of these mutations on detection, disease presentation, and management as well as the recent findings in the mechanisms that underlie virus-host interaction. Our aim is to invigorate a scientific debate on how pathogenic potential of the new pandemic viral strains contributes toward development in the field of virology in general and COVID-19 disease in particular.
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Affiliation(s)
- Shakuntala Mahilkar
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sachee Agrawal
- Department of Microbiology, Topiwala National Medical College (TNMC) and Bai Yamunabai Laxman Nair (BYL) Charitable Hospital, Mumbai, Maharashtra, India
| | - Sakshi Chaudhary
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Swapneil Parikh
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Subash C. Sonkar
- Multidisciplinary Research Unit, Maulana Azad Medical College and Associated Hospital, New Delhi, India
- Delhi School of Public Health, Institute of Eminence, University of Delhi, New Delhi, India
| | - Dileep Kumar Verma
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Vidushi Chitalia
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, Maharashtra, India
| | - Divya Mehta
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Bidhan Chandra Koner
- Multidisciplinary Research Unit, Maulana Azad Medical College and Associated Hospital, New Delhi, India
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospital, New Delhi, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health and Family Welfare, New Delhi, India
| | - Jayanthi Shastri
- Department of Microbiology, Topiwala National Medical College (TNMC) and Bai Yamunabai Laxman Nair (BYL) Charitable Hospital, Mumbai, Maharashtra, India
| | - Sujatha Sunil
- Vector-Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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Hettle D, Hutchings S, Muir P, Moran E. Persistent SARS-CoV-2 infection in immunocompromised patients facilitates rapid viral evolution: Retrospective cohort study and literature review. CLINICAL INFECTION IN PRACTICE 2022; 16:100210. [PMID: 36405361 PMCID: PMC9666269 DOI: 10.1016/j.clinpr.2022.100210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/03/2022] [Accepted: 11/03/2022] [Indexed: 11/17/2022] Open
Abstract
Background Most patients with SARS-CoV-2 are non-infectious within 2 weeks, though viral RNA may remain detectable for weeks. However there are reports of persistent SARS-CoV-2 infection, with viable virus and ongoing infectivity months after initial detection. Beyond individuals, viral evolution during persistent infections may be accelerated, driving emergence of mutations associated with viral variants of concern. These patients often do not meet inclusion criteria for clinical trials, meaning clinical and virologic characteristics, and optimal management strategies are poorly evidence-based. Methods We analysed cases of SARS-CoV-2 infection from a regional testing laboratory in South-West England between March 2020 and December 2021, with at least two SARS-CoV-2 positive samples separated by ≥ 56 days were identified. Excluding those with confirmed or likely re-infection, we identified patients with persistent infection, characterised by an ongoing clinical syndrome consistent with COVID-19 alongside monophyletic viral lineage of SARS-CoV-2. We examined clinical and virologic characteristics, treatment, and outcome. We further performed a literature review investigating cases of persistent SARS-CoV-2 infection, reviewing patient characteristics and treatment. Results We identified six patients with persistent SARS-CoV-2 infection. All were hypogammaglobulinaemic and had underlying haematological malignancy, with four having received B-cell depleting therapy. Evidence of viral evolution, including accrual of mutations associated with variants of concern, was demonstrated in five cases. Four patients ultimately cleared SARS-CoV-2. In two patients, clearance followed treatment with casirivimab/imdevimab. Both survived beyond thirty days following viral clearance, having experienced infections of 305- and 269-days duration respectively, after failed attempts at clearance with alternative therapies. We found 60 cases of confirmed persistent infection in the literature, with a further 31 probable cases. Of those, 80% of patients treated with monoclonal antibodies cleared SARS-CoV-2, and none died. Conclusion Haematological malignancy and patients receiving B-cell depleting therapies represent key groups at risk of persistent SARS-CoV-2 infection. Throughout persistent infection, SARS-CoV-2 can evolve rapidly, giving rise to significant mutations, including those implicated in variants of concern. Monoclonal antibodies appear to be a promising therapeutic option, potentially in combination with antivirals, crucial for individuals, and for public health.
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Affiliation(s)
- David Hettle
- Department of Infection Sciences, Southmead Hospital, Bristol BS10 5NB, United Kingdom
| | - Stephanie Hutchings
- Department of Infection Sciences, Southmead Hospital, Bristol BS10 5NB, United Kingdom
- United Kingdom Health Security Agency (UKHSA) South-West Regional Laboratory, Southmead Hospital, Bristol BS10 5NB, United Kingdom
| | - Peter Muir
- Department of Infection Sciences, Southmead Hospital, Bristol BS10 5NB, United Kingdom
- United Kingdom Health Security Agency (UKHSA) South-West Regional Laboratory, Southmead Hospital, Bristol BS10 5NB, United Kingdom
| | - Ed Moran
- Department of Infection Sciences, Southmead Hospital, Bristol BS10 5NB, United Kingdom
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Abstract
Immunocompromised hosts, which encompass a diverse population of persons with malignancies, human immunodeficiency virus disease, solid organ, and hematologic transplants, autoimmune diseases, and primary immunodeficiencies, bear a significant burden of the morbidity and mortality due to coronavirus disease-2019 (COVID-19). Immunocompromised patients who develop COVID-19 have a more severe illness, higher hospitalization rates, and higher mortality rates than immunocompetent patients. There are no well-defined treatment strategies that are specific to immunocompromised patients and vaccines, monoclonal antibodies, and convalescent plasma are variably effective. This review focuses on the specific impact of COVID-19 in immunocompromised patients and the gaps in knowledge that require further study.
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Taibe NS, Kord MA, Badawy MA, Shytaj IL, Elhefnawi MM. Progress, pitfalls, and path forward of drug repurposing for COVID-19 treatment. Ther Adv Respir Dis 2022; 16:17534666221132736. [PMID: 36282077 PMCID: PMC9597285 DOI: 10.1177/17534666221132736] [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] [Indexed: 12/15/2022] Open
Abstract
On 30 January 2020, the World Health Organization (WHO) declared the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic a public health emergency of international concern. The viral outbreak led in turn to an exponential growth of coronavirus disease 2019 (COVID-19) cases, that is, a multiorgan disease that has led to more than 6.3 million deaths worldwide, as of June 2022. There are currently few effective drugs approved for treatment of SARS-CoV-2/COVID-19 patients. Many of the compounds tested so far have been selected through a drug repurposing approach, that is, by identifying novel indications for drugs already approved for other conditions. We here present an up-to-date review of the main Food and Drug Administration (FDA)-approved drugs repurposed against SARS-CoV-2 infection, discussing their mechanism of action and their most important preclinical and clinical results. Reviewed compounds were chosen to privilege those that have been approved for use in SARS-CoV-2 patients or that have completed phase III clinical trials. Moreover, we also summarize the evidence on some novel and promising repurposed drugs in the pipeline. Finally, we discuss the current stage and possible steps toward the development of broadly effective drug combinations to suppress the onset or progression of COVID-19.
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Affiliation(s)
- Noha Samir Taibe
- Biotechnology-Biomolecular Chemistry Program, Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Maimona A. Kord
- Department of Botany, Faculty of Science, Cairo University, Giza, Egypt
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Maio N, Cherry S, Schultz DC, Hurst BL, Linehan WM, Rouault TA. TEMPOL inhibits SARS-CoV-2 replication and development of lung disease in the Syrian hamster model. iScience 2022; 25:105074. [PMID: 36093377 PMCID: PMC9444323 DOI: 10.1016/j.isci.2022.105074] [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: 06/29/2022] [Revised: 08/03/2022] [Accepted: 08/31/2022] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide outbreak, known as coronavirus disease 2019 (COVID-19). Alongside vaccines, antiviral therapeutics is an important part of the healthcare response to COVID-19. We previously reported that TEMPOL, a small molecule stable nitroxide, inactivated the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 by causing the oxidative degradation of its iron-sulfur cofactors. Here, we demonstrate that TEMPOL is effective in vivo in inhibiting viral replication in the Syrian hamster model. The inhibitory effect of TEMPOL on SARS-CoV-2 replication was observed in animals when the drug was administered 2 h before infection in a high-risk exposure model. These data support the potential application of TEMPOL as a highly efficacious antiviral against SARS-CoV-2 infection in humans. TEMPOL’s IC90 in human lung epithelial Calu-3 cells is 2.89 μM and CC50 > 10 mM TEMPOL has potent antiviral activity against highly pathogenic SARS- and MERS-Co-Vs TEMPOL inhibits SARS-CoV-2 replication and lung pathology in the Syrian hamster Fe-S cofactor insertion can be targeted to interfere with coronavirus replication
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Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, Chemogenomic Discovery Program. University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, High-throughput Screening Core, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Scaglione V, Rotundo S, Marascio N, De Marco C, Lionello R, Veneziano C, Berardelli L, Quirino A, Olivadese V, Serapide F, Tassone B, Morrone HL, Davoli C, La Gamba V, Bruni A, Cesana BM, Matera G, Russo A, Costanzo FS, Viglietto G, Trecarichi EM, Torti C. Lessons learned and implications of early therapies for coronavirus disease in a territorial service centre in the Calabria region: a retrospective study. BMC Infect Dis 2022; 22:793. [PMID: 36266619 PMCID: PMC9583059 DOI: 10.1186/s12879-022-07774-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Monoclonal antibodies (mAbs) and antivirals have been approved for early therapy of coronavirus disease (COVID-19), however, in the real-life setting, there are difficulties to prescribe these therapies within few days from symptom onset as recommended, and effectiveness of combined use of these drugs have been hypothesised in most-at-risk patients (such as those immunocompromised) but data supporting this strategy are limited. Methods We describe the real-life experience of SARS-CoV-2 antivirals and/or monoclonal antibodies (mAbs) and focus on the hospitalisation rate due to the progression of COVID-19. Clinical results obtained through our risk-stratification algorithm and benefits achieved through a strategic proximity territorial centre are provided. We also report a case series with an in-depth evaluation of SARS-CoV-2 genome in relationship with treatment strategy and clinical evolution of patients. Results Two hundred eighty-eight patients were analysed; 94/288 (32.6%) patients were treated with mAb monotherapy, 171/288 (59.4%) patients were treated with antivirals, and 23/288 (8%) patients received both mAbs and one antiviral drug. Haematological malignancies were more frequent in patients treated with combination therapy than in the other groups (p = 0.0003). There was a substantial increase in the number of treated patients since the opening of the centre dedicated to early therapies for COVID-19. The provided disease-management and treatment appeared to be effective since 98.6% patients recovered without hospital admission. Moreover, combination therapy with mAbs and antivirals seemed successful because all patients admitted to the hospital for COVID-19 did not receive such therapies, while none of the most-at-risk patients treated with combination therapy were hospitalized or reported adverse events. Conclusions A low rate of COVID-19 progression requiring hospital admission was observed in patients included in this study. The dedicated COVID-19 proximity territorial service appeared to strengthen the regional sanitary system, avoiding the overwhelming of other services. Importantly, our results also support early combination therapy: it is possible that this strategy reduces the emergence of escape mutants of SARS-CoV-2, thereby increasing efficacy of early treatment, especially in immunocompromised individuals. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07774-9.
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Affiliation(s)
- Vincenzo Scaglione
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Salvatore Rotundo
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Nadia Marascio
- Chair of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University, Catanzaro, Italy
| | - Carmela De Marco
- Department of Experimental and Clinical Medicine, "Magna Græcia" University, Catanzaro, Italy
| | - Rosaria Lionello
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Claudia Veneziano
- Department of Experimental and Clinical Medicine, "Magna Græcia" University, Catanzaro, Italy
| | - Lavinia Berardelli
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Angela Quirino
- Chair of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University, Catanzaro, Italy
| | - Vincenzo Olivadese
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Francesca Serapide
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Bruno Tassone
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Helen Linda Morrone
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Chiara Davoli
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Valentina La Gamba
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Andrea Bruni
- Chair of Intensive Care, Department of Medical and Surgical Sciences, "Magna Græcia" University, Catanzaro, Italy
| | - Bruno Mario Cesana
- Unit of Medical Statistics, Biometrics and Bioinformatics "Giulio A. Maccacaro", Department of Clinical Sciences and Community Health, Faculty of Medicine and Surgery, University of Milan, Milan, Italy
| | - Giovanni Matera
- Chair of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University, Catanzaro, Italy
| | - Alessandro Russo
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Francesco Saverio Costanzo
- Department of Experimental and Clinical Medicine, Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University, Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, "Magna Græcia" University, Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Carlo Torti
- Chair of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Græcia" University, Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy.
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Kim YS, Kwon EB, Kim B, Chung HS, Choi G, Kim YH, Choi JG. Mulberry Component Kuwanon C Exerts Potent Therapeutic Efficacy In Vitro against COVID-19 by Blocking the SARS-CoV-2 Spike S1 RBD:ACE2 Receptor Interaction. Int J Mol Sci 2022; 23:12516. [PMID: 36293371 PMCID: PMC9604257 DOI: 10.3390/ijms232012516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 11/24/2022] Open
Abstract
There has been an immense effort by global pharmaceutical companies to develop anti-COVID-19 drugs, including small molecule-based RNA replication inhibitors via drug repositioning and antibody-based spike protein blockers related to cell entry by SARS-CoV-2. However, several limitations to their clinical use have emerged in addition to a lack of progress in the development of small molecule-based cell entry inhibitors from natural products. In this study, we tested the effectiveness of kuwanon C (KC), which has mainly been researched using in silico docking simulation and can serve as an effective building block for developing anti-COVID-19 drugs, in blocking the spike S1 RBD:ACE2 receptor interaction. KC is a natural product derived from Morus alba L., commonly known as mulberry, which has known antiviral efficacy. Molecular interaction studies using competitive ELISA and the BLItz system revealed that KC targets both the spike S1 RBD and the ACE2 receptor, successfully disrupting their interaction, as supported by the in silico docking simulation. Furthermore, we established a mechanism of action by observing how KC prevents the infection of SARS-CoV-2 spike pseudotyped virus in ACE2/TPRSS2-overexpressing HEK293T cells. Finally, we demonstrated that KC inhibits clinical isolates of SARS-CoV-2 in Vero cells. Future combinations of small molecule-based cell entry inhibitors, such as KC, with the currently prescribed RNA replication inhibitors are anticipated to significantly enhance the efficacy of COVID-19 therapies.
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Affiliation(s)
- Young Soo Kim
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
| | - Eun-Bin Kwon
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
| | - Buyun Kim
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
| | - Hwan-Suck Chung
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
| | - Garam Choi
- R&D Center, Etnova Therapeutics Corp., 198 Saneop-ro, Gwonseon-gu, Suwon 13207, Korea
| | - Yeoun-Hee Kim
- R&D Center, Etnova Therapeutics Corp., 198 Saneop-ro, Gwonseon-gu, Suwon 13207, Korea
| | - Jang-Gi Choi
- Korea Institute of Oriental Medicine, Korean Medicine Application Center, 70 Cheomdan-ro, Dong-gu, Daegu 41062, Korea
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135
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Iketani S, Hong SJ, Sheng J, Bahari F, Culbertson B, Atanaki FF, Aditham AK, Kratz AF, Luck MI, Tian R, Goff SP, Montazeri H, Sabo Y, Ho DD, Chavez A. Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites. Cell Host Microbe 2022; 30:1354-1362.e6. [PMID: 36029764 PMCID: PMC9365866 DOI: 10.1016/j.chom.2022.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/20/2022] [Accepted: 08/05/2022] [Indexed: 01/03/2023]
Abstract
The SARS-CoV-2 3CL protease (3CLpro) is an attractive therapeutic target, as it is essential to the virus and highly conserved among coronaviruses. However, our current understanding of its tolerance to mutations is limited. Here, we develop a yeast-based deep mutational scanning approach to systematically profile the activity of all possible single mutants of the 3CLpro and validate a subset of our results within authentic viruses. We reveal that the 3CLpro is highly malleable and is capable of tolerating mutations throughout the protein. Yet, we also identify specific residues that appear immutable, suggesting that these may be targets for future 3CLpro inhibitors. Finally, we utilize our screening as a basis to identify E166V as a resistance-conferring mutation against the clinically used 3CLpro inhibitor, nirmatrelvir. Collectively, the functional map presented herein may serve as a guide to better understand the biological properties of the 3CLpro and for drug development against coronaviruses.
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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; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jenny Sheng
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Farideh Bahari
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Bruce Culbertson
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Fereshteh Fallah Atanaki
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Arjun K Aditham
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander F Kratz
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Maria I Luck
- 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
| | - Ruxiao Tian
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Stephen P Goff
- Aaron Diamond AIDS Research Center, 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; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hesam Montazeri
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Yosef Sabo
- 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; Department of Microbiology and Immunology, 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
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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136
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Kim YS, Kim B, Kwon EB, Chung HS, Choi JG. Mulberrofuran G, a Mulberry Component, Prevents SARS-CoV-2 Infection by Blocking the Interaction between SARS-CoV-2 Spike Protein S1 Receptor-Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor. Nutrients 2022; 14:nu14194170. [PMID: 36235822 PMCID: PMC9573737 DOI: 10.3390/nu14194170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022] Open
Abstract
Despite the recent development of RNA replication-targeted COVID-19 drugs by global pharmaceutical companies, their prescription in clinical practice is limited by certain factors, including drug interaction, reproductive toxicity, and drug resistance. COVID-19 drugs with multiple targets for the SARS-CoV-2 life cycle may lead to a successful reduction in drug resistance as well as enhanced therapeutic efficacy, and natural products are a potential source of molecules with therapeutic effects against COVID-19. In this study, we investigated the inhibitory efficacy of mulberrofuran G (MG), a component of Morus alba L., also known as mulberry, which has been used as food and traditional medicine, on the binding of the spike S1 receptor-binding domain (RBD) protein to the angiotensin-converting enzyme 2 (ACE2) receptor, which is the initial stage of the SARS-CoV-2 infection. In competitive enzyme-linked immunosorbent assays, MG effectively blocked the spike S1 RBD: ACE2 receptor molecular binding, and investigations using the BLItz system and in silico modeling revealed that MG has high affinity for both proteins. Finally, we confirmed that MG inhibits the entry of SARS-CoV-2 spike pseudotyped virus and a clinical isolate of SARS-CoV-2 into cells, suggesting that MG might be a promising therapeutic candidate for preventing SARS-CoV-2 binding to the cell surface during early infection.
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137
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Gliga S, Lübke N, Killer A, Gruell H, Walker A, Dilthey AT, Thielen A, Lohr C, Flaßhove C, Krieg S, Pereira JV, Seraphin TP, Zaufel A, Däumer M, Orth HM, Feldt T, Bode JG, Klein F, Timm J, Luedde T, Jensen BEO. Rapid Selection of Sotrovimab Escape Variants in Severe Acute Respiratory Syndrome Coronavirus 2 Omicron-Infected Immunocompromised Patients. Clin Infect Dis 2022; 76:408-415. [PMID: 36189631 PMCID: PMC9619606 DOI: 10.1093/cid/ciac802] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/30/2022] [Accepted: 09/29/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Monoclonal antibodies (mAbs) that target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are predominantly less effective against Omicron variants. Immunocompromised patients often experience prolonged viral shedding, resulting in an increased risk of viral escape. METHODS In an observational, prospective cohort, 57 patients infected with Omicron variants who received sotrovimab alone or in combination with remdesivir were followed. The study end points were a decrease in SARS-CoV-2 RNA <106 copies/mL in nasopharyngeal swabs at day 21 and the emergence of escape mutations at days 7, 14, and 21 after sotrovimab administration. All SARS-CoV-2 samples were analyzed using whole-genome sequencing. Individual variants within the quasispecies were subsequently quantified and further characterized using a pseudovirus neutralization assay. RESULTS The majority of patients (43 of 57, 75.4%) were immunodeficient, predominantly due to immunosuppression after organ transplantation or hematologic malignancies. Infections by Omicron/BA.1 comprised 82.5%, while 17.5% were infected by Omicron/BA.2. Twenty-one days after sotrovimab administration, 12 of 43 (27.9%) immunodeficient patients had prolonged viral shedding compared with 1 of 14 (7.1%) immunocompetent patients (P = .011). Viral spike protein mutations, some specific for Omicron (e.g., P337S and/or E340D/V), emerged in 14 of 43 (32.6%) immunodeficient patients, substantially reducing sensitivity to sotrovimab in a pseudovirus neutralization assay. Combination therapy with remdesivir significantly reduced emergence of escape variants. CONCLUSIONS Immunocompromised patients face a considerable risk of prolonged viral shedding and emergence of escape mutations after early therapy with sotrovimab. These findings underscore the importance of careful monitoring and the need for dedicated clinical trials in this patient population.
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Affiliation(s)
| | - Nadine Lübke
- Correspondence: N. Lübke, Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany ()
| | | | - Henning Gruell
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander T Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | | | - Carolin Lohr
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Charlotte Flaßhove
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sarah Krieg
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Joanna Ventura Pereira
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Tobias Paul Seraphin
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alex Zaufel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Martin Däumer
- Institute of Immunology and Genetics, Kaiserslautern, Germany
| | - Hans-Martin Orth
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Torsten Feldt
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Johannes G Bode
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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138
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Geneticin shows selective antiviral activity against SARS-CoV-2 by interfering with programmed −1 ribosomal frameshifting. Antiviral Res 2022; 208:105452. [PMID: 36341734 PMCID: PMC9617636 DOI: 10.1016/j.antiviral.2022.105452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 is currently causing an unprecedented pandemic. While vaccines are massively deployed, we still lack effective large-scale antiviral therapies. In the quest for antivirals targeting conserved structures, we focused on molecules able to bind viral RNA secondary structures. Aminoglycosides are a class of antibiotics known to interact with the ribosomal RNA of both prokaryotes and eukaryotes and have previously been shown to exert antiviral activities by interacting with viral RNA. Here we show that the aminoglycoside geneticin is endowed with antiviral activity against all tested variants of SARS-CoV-2, in different cell lines and in a respiratory tissue model at non-toxic concentrations. The mechanism of action is an early inhibition of RNA replication and protein expression related to a decrease in the efficiency of the −1 programmed ribosomal frameshift (PRF) signal of SARS-CoV-2. Using in silico modeling, we have identified a potential binding site of geneticin in the pseudoknot of frameshift RNA motif. Moreover, we have selected, through virtual screening, additional RNA binding compounds, interacting with the same site with increased potency.
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139
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Wang Z, Belecciu T, Eaves J, Reimers M, Bachmann MH, Woldring D. Phytochemical drug discovery for COVID-19 using high-resolution computational docking and machine learning assisted binder prediction. J Biomol Struct Dyn 2022:1-21. [PMID: 35993534 DOI: 10.1080/07391102.2022.2112976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The COVID-19 pandemic has resulted in millions of deaths around the world. Multiple vaccines are in use, but there are many underserved locations that do not have adequate access to them. Variants may emerge that are highly resistant to existing vaccines, and therefore cheap and readily obtainable therapeutics are needed. Phytochemicals, or plant chemicals, can possibly be such therapeutics. Phytochemicals can be used in a polypharmacological approach, where multiple viral proteins are inhibited and escape mutations are made less likely. Finding the right phytochemicals for viral protein inhibition is challenging, but in-silico screening methods can make this a more tractable problem. In this study, we screen a wide range of natural drug products against a comprehensive set of SARS-CoV-2 proteins using a high-resolution computational workflow. This workflow consists of a structure-based virtual screening (SBVS), where an initial phytochemical library was docked against all selected protein structures. Subsequently, ligand-based virtual screening (LBVS) was employed, where chemical features of 34 lead compounds obtained from the SBVS were used to predict 53 lead compounds from a larger phytochemical library via supervised learning. A computational docking validation of the 53 predicted leads obtained from LBVS revealed that 28 of them elicit strong binding interactions with SARS-CoV-2 proteins. Thus, the inclusion of LBVS resulted in a 4-fold increase in the lead discovery rate. Of the total 62 leads, 18 showed promising pharmacokinetic properties in a computational ADME screening. Collectively, this study demonstrates the advantage of incorporating machine learning elements into a virtual screening workflow.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zirui Wang
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Theodore Belecciu
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Joelle Eaves
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Mark Reimers
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Michael H Bachmann
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Daniel Woldring
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
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140
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Nirmatrelvir-remdesivir association for non-hospitalized adults with COVID-19, point of view. Inflammopharmacology 2022; 30:1927-1931. [PMID: 35980509 PMCID: PMC9386652 DOI: 10.1007/s10787-022-01055-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/05/2022]
Abstract
The efforts of the scientific world directed to identifying new antiviral drugs and therapies effective against SARS-CoV-2 continue. New oral antivirals against SARS-CoV-2 such as paxlovid have recently authorized. Evidence shows that these antivirals have good efficacy in reducing the risk of hospitalization in COVID-19 positive patients. Remdesivir is an authorized antiviral for the treatment of SARS-CoV-2 infection. To date, there are still few data in the literature on the safety profile and the risk of generating antiviral-resistant SARS-CoV-2 drug variants. In this manuscript we describe the evidence in the literature on the monotherapy use of paxlovid and monotherapy use of remdesivir, and the scientific hypothesis of using nirmatrelvir and remdesivir in association with the aim of increasing treatment efficacy, reducing the risk of adverse reactions and generating antiviral drug-resistant variants.
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141
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Iketani S, Mohri H, Culbertson B, Hong SJ, Duan Y, Luck MI, Annavajhala MK, Guo Y, Sheng Z, Uhlemann AC, Goff SP, Sabo Y, Yang H, Chavez A, Ho DD. Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 36032976 DOI: 10.1101/2022.08.07.499047] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nirmatrelvir, an oral antiviral targeting the 3CL protease of SARS-CoV-2, has been demonstrated to be clinically useful in reducing hospitalization or death due to COVID-19 1,2 . However, as SARS-CoV-2 has evolved to become resistant to other therapeutic modalities 3â€"9 , there is a concern that the same could occur for nirmatrelvir. Here, we have examined this possibility by in vitro passaging of SARS-CoV-2 in increasing concentrations of nirmatrelvir using two independent approaches, including one on a large scale in 480 wells. Indeed, highly resistant viruses emerged from both, and their sequences revealed a multitude of 3CL protease mutations. In the experiment done at a larger scale with many replicates, 53 independent viral lineages were selected with mutations observed at 23 different residues of the enzyme. Yet, several common mutational pathways to nirmatrelvir resistance were preferred, with a majority of the viruses descending from T21I, P252L, or T304I as precursor mutations. Construction and analysis of 13 recombinant SARS-CoV-2 clones, each containing a unique mutation or a combination of mutations showed that the above precursor mutations only mediated low-level resistance, whereas greater resistance required accumulation of additional mutations. E166V mutation conferred the strongest resistance (~100-fold), but this mutation resulted in a loss of viral replicative fitness that was restored by compensatory changes such as L50F and T21I. Structural explanations are discussed for some of the mutations that are proximal to the drug-binding site, as well as cross-resistance or lack thereof to ensitrelvir, another clinically important 3CL protease inhibitor. Our findings indicate that SARS-CoV-2 resistance to nirmatrelvir does readily arise via multiple pathways in vitro , and the specific mutations observed herein form a strong foundation from which to study the mechanism of resistance in detail and to inform the design of next generation protease inhibitors.
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142
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Gu H, Quadeer AA, Krishnan P, Ng DY, Chang LD, Liu GY, Cheng SS, Lam TT, Peiris M, McKay MR, Poon LL. Within-host diversity of SARS-CoV-2 lineages and effect of vaccination. RESEARCH SQUARE 2022:rs.3.rs-1927944. [PMID: 35982671 PMCID: PMC9387541 DOI: 10.21203/rs.3.rs-1927944/v1] [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: 11/27/2022]
Abstract
Viral and host factors can shape SARS-CoV-2 within-host viral diversity and virus evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here we analysed deep sequencing data from 2,146 SARS-CoV-2 samples with different viral lineages to describe the patterns of within-host diversity in different conditions, including vaccine-breakthrough infections. Variant of Concern (VOC) Alpha, Delta, and Omicron samples were found to have higher within-host nucleotide diversity while being under weaker purifying selection at full genome level compared to non-VOC SARS-CoV-2 viruses. Breakthrough Delta and Omicron infections in Comirnaty and CoronaVac vaccinated individuals appeared to have higher within-host purifying selection at the full-genome and/or Spike gene levels. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 evolution. Our findings suggest that vaccination does not increase SARS-CoV-2 protein sequence space and may not facilitate emergence of more viral variants.
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Affiliation(s)
- Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Daisy Y.M. Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lydia D.J Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gigi Y.Z. Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Samuel S.M. Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tommy T.Y. Lam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Matthew R. McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Leo L.M. Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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143
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Martinez MA, Chen TY, Choi H, Hwang M, Navarathna D, Hao L, Gale M, Camus G, Ramirez HE, Jinadatha C. Extended Remdesivir Infusion for Persistent Coronavirus Disease 2019 Infection. Open Forum Infect Dis 2022; 9:ofac382. [PMID: 36039098 PMCID: PMC9384609 DOI: 10.1093/ofid/ofac382] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/28/2022] [Indexed: 01/26/2023] Open
Abstract
Persistent severe acute respiratory syndrome coronavirus 2 infection is difficult to treat. Here, we report a case of 5-month persistent coronavirus disease 2019 in an immunocompromised patient who was successfully treated with 30 consecutive days of remdesivir. Prolonged remdesivir infusion with concurrent cycle threshold monitoring might provide a potential solution to cure these patients with difficult-to-treat infections.
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Affiliation(s)
- Mario A Martinez
- Division of Infectious Diseases, Baylor Scott and White Health, Temple, Texas, USA
| | - Ting-Yi Chen
- Department of Medicine, Central Texas Veterans Health Care System, Temple, Texas, USA
| | - Hosoon Choi
- Department of Research, Central Texas Veterans Health Care System, Temple, Texas, USA
| | - Munok Hwang
- Department of Research, Central Texas Veterans Health Care System, Temple, Texas, USA
| | - Dhammika Navarathna
- Department of Microbiology and Pathology, Central Texas Veterans Health Care System, Temple, Texas, USA
| | - Linhue Hao
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | | | - Hector E Ramirez
- Division of Infectious Diseases, Baylor Scott and White Health, Temple, Texas, USA
| | - Chetan Jinadatha
- Correspondence: Chetan Jinadatha, MD, MPH, Department of Medicine, Central Texas Veterans Health Care System, 1901 South Veterans Drive, Temple, TX 76504, USA ()
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144
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Iketani S, Hong SJ, Sheng J, Bahari F, Culbertson B, Atanaki FF, Aditham AK, Kratz AF, Luck MI, Tian R, Goff SP, Montazeri H, Sabo Y, Ho DD, Chavez A. The Functional Landscape of SARS-CoV-2 3CL Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.23.497404. [PMID: 35860222 PMCID: PMC9298129 DOI: 10.1101/2022.06.23.497404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) as the etiologic agent of COVID-19 (coronavirus disease 2019) has drastically altered life globally. Numerous efforts have been placed on the development of therapeutics to treat SARS-CoV-2 infection. One particular target is the 3CL protease (3CL pro ), which holds promise as it is essential to the virus and highly conserved among coronaviruses, suggesting that it may be possible to find broad inhibitors that treat not just SARS-CoV-2 but other coronavirus infections as well. While the 3CL protease has been studied by many groups for SARS-CoV-2 and other coronaviruses, our understanding of its tolerance to mutations is limited, knowledge which is particularly important as 3CL protease inhibitors become utilized clinically. Here, we develop a yeast-based deep mutational scanning approach to systematically profile the activity of all possible single mutants of the SARS-CoV-2 3CL pro , and validate our results both in yeast and in authentic viruses. We reveal that the 3CL pro is highly malleable and is capable of tolerating mutations throughout the protein, including within the substrate binding pocket. Yet, we also identify specific residues that appear immutable for function of the protease, suggesting that these interactions may be novel targets for the design of future 3CL pro inhibitors. Finally, we utilize our screening results as a basis to identify E166V as a resistance-conferring mutation against the therapeutic 3CL pro inhibitor, nirmatrelvir, in clinical use. Collectively, the functional map presented herein may serve as a guide for further understanding of the biological properties of the 3CL protease and for drug development for current and future coronavirus pandemics.
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145
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.06.29.22276868. [PMID: 35794895 PMCID: PMC9258298 DOI: 10.1101/2022.06.29.22276868] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A. Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I. Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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146
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Markarian NM, Galli G, Patel D, Hemmings M, Nagpal P, Berghuis AM, Abrahamyan L, Vidal SM. Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency. Front Microbiol 2022; 13:933983. [PMID: 35847101 PMCID: PMC9283111 DOI: 10.3389/fmicb.2022.933983] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Since the end of 2019, the world has been challenged by the coronavirus disease 2019 (COVID-19) pandemic. With COVID-19 cases rising globally, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, resulting in the emergence of variants of interest (VOI) and of concern (VOC). Of the hundreds of millions infected, immunodeficient patients are one of the vulnerable cohorts that are most susceptible to this virus. These individuals include those with preexisting health conditions and/or those undergoing immunosuppressive treatment (secondary immunodeficiency). In these cases, several researchers have reported chronic infections in the presence of anti-COVID-19 treatments that may potentially lead to the evolution of the virus within the host. Such variations occurred in a variety of viral proteins, including key structural ones involved in pathogenesis such as spike proteins. Tracking and comparing such mutations with those arisen in the general population may provide information about functional sites within the SARS-CoV-2 genome. In this study, we reviewed the current literature regarding the specific features of SARS-CoV-2 evolution in immunocompromised patients and identified recurrent de novo amino acid changes in virus isolates of these patients that can potentially play an important role in SARS-CoV-2 pathogenesis and evolution.
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Affiliation(s)
- Nathan M. Markarian
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Gaël Galli
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- CNRS, ImmunoConcEpT, UMR 5164, Université de Bordeaux, Bordeaux, France
- CHU de Bordeaux, FHU ACRONIM, Centre National de Référence des Maladies Auto-Immunes et Systémiques Rares Est/Sud-Ouest, Bordeaux, France
| | - Dhanesh Patel
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
| | - Mark Hemmings
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Priya Nagpal
- Department of Pharmacology, McGill University, Montréal, QC, Canada
| | | | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
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147
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Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. J Infect Chemother 2022; 28:1001-1004. [PMID: 35430092 PMCID: PMC8986523 DOI: 10.1016/j.jiac.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/20/2022] [Accepted: 04/03/2022] [Indexed: 12/14/2022]
Abstract
A concern has been raised that the persistent COVID-19 infection in an immunocompromised host can be the source of the SARS-CoV-2 variants. This is the case of a 61-year-old man in complete remission of a follicular lymphoma after six cycles of rituximab and bendamustine with additional two cycles of rituximab completed eight months prior to the episode of COVID-19 pneumonia. The patient's respiratory failure was long-lasting, and required mechanical ventilation until day 75. Acquired immunity tested negative throughout the observational period. The viral RNA was detectable until day 100 while the infectious virus was isolated until day 79. Seven haplotypes were identified and the non-synonymous mutations accumulated in the spike gene which included E484Q and S494P. In the management of COVID-19 cases with suppressed immune statuses, initial evaluation of existing immunity and monitoring for infectiousness throughout the clinical course including the convalescent stage may be necessary.
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148
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Hogan JI, Duerr R, Dimartino D, Marier C, Hochman S, Mehta S, Wang G, Heguy A. Remdesivir resistance in transplant recipients with persistent COVID-19. RESEARCH SQUARE 2022:rs.3.rs-1800050. [PMID: 35794888 PMCID: PMC9258299 DOI: 10.21203/rs.3.rs-1800050/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The medical community currently lacks robust data regarding the incidence, prevalence, and clinical significance of mutations associated with resistance to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) therapeutics. This report describes two renal transplant recipients who, after remdesivir exposure, developed a de novo V792I RNA-dependent RNA polymerase (RdRp) mutation that has recently been found to confer resistance to remdesivir in vitro . To the best of our knowledge, this publication is the first to document the emergence of V792I in patients treated with remdesivir. Our work underscores the critical need for augmented efforts to identify concerning mutations and address their clinical implications.
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149
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In Vitro Selection of Remdesivir-Resistant SARS-CoV-2 Demonstrates High Barrier to Resistance. Antimicrob Agents Chemother 2022; 66:e0019822. [PMID: 35708323 PMCID: PMC9295571 DOI: 10.1128/aac.00198-22] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In vitro selection of remdesivir-resistant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed the emergence of a V166L substitution, located outside of the polymerase active site of the Nsp12 protein, after 9 passages of a single lineage. V166L remained the only Nsp12 substitution after 17 passages (10 μM remdesivir), conferring a 2.3-fold increase in 50% effective concentration (EC50). When V166L was introduced into a recombinant SARS-CoV-2 virus, a 1.5-fold increase in EC50 was observed, indicating a high in vitro barrier to remdesivir resistance.
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150
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Sharifan A. COVID-19 and the Functionality of Antivirals: The Day After Tomorrow. Health Secur 2022; 20:270-271. [DOI: 10.1089/hs.2022.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Amin Sharifan
- Amin Sharifan, PharmD, is a Pharmacist and Researcher, Department of Pharmaceutical Care, Sina Hospital, and Research Center for Rational Use of Drugs; both at the Tehran University of Medical Sciences, Tehran, Iran
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