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Fonager J, Nytofte NJS, Schouw CH, Poulsen CB, Wiese L, Fomsgaard A, Bennedbæk M, Rasmussen M, Nielsen XC. Emergence and fixation of SARS-CoV-2 minority variants in a chronically infected patient receiving therapy in Denmark. APMIS 2024. [PMID: 38961316 DOI: 10.1111/apm.13454] [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: 02/07/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
SARS-CoV-2 variants of concern (VOC), such as Delta and Omicron have harbored mutations, which increased viral infectivity or ability to evade neutralizing antibodies. Immunocompromised patients might be a source of some of these emerging variants. In this study, we sequenced 17 consecutive samples from an immunocompromised patient with a long-term SARS-CoV-2 infection with the pre-VOC era lineage B.1.177.35. We here describe the emergence of 73 nonsynonymous minority variants in this patient and show that 10 of these mutations became dominant in the viral population during the treatment period. Four of these were seen throughout the infection period and had a very low global prevalence, although three of them were also observed later in the Alpha, Delta, and Omicron lineages. We also found that two adjacent nsp12 variants (M785I and S786P) belonged to different quasi-species and competed during the early stages of infection and remdesivir administration. This emphasizes the importance of ongoing genome surveillance of SARS-CoV-2 among immunocpromised patients.
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Affiliation(s)
- Jannik Fonager
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Nikolaj Julian Skrøder Nytofte
- Department of Medicine, Zealand University Hospital, Køge, Denmark
- Centre for Thrombosis and Anticoagulation, NSR Hospitals, Næstved, Denmark
| | | | | | - Lothar Wiese
- Department of Infectious Diseases, Zealand University Hospital, Roskilde, Denmark
| | - Anders Fomsgaard
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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2
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Pandey K, Acharya A, Pal D, Jain P, Singh K, Durden DL, Kutateladze TG, Deshpande AJ, Byrareddy SN. SRX3177, a CDK4/6-PI3K-BET inhibitor, in combination with an RdRp inhibitor, Molnupiravir, or an entry inhibitor MU-UNMC-2, has potent antiviral activity against the Omicron variant of SARS-CoV-2. Antiviral Res 2024; 227:105904. [PMID: 38729306 DOI: 10.1016/j.antiviral.2024.105904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Despite considerable progress in developing vaccines and antivirals to combat COVID-19, the rapid mutations of the SARS-CoV-2 genome have limited the durability and efficacy of the current vaccines and therapeutic interventions. Hence, it necessitates the development of novel therapeutic approaches or repurposing existing drugs that target either viral life cycle, host factors, or both. Here, we report that SRX3177, a potent triple-activity CDK4/6-PI3K-BET inhibitor, blocks replication of the SARS-CoV-2 Omicron variant with IC50 values at sub-micromolar concentrations without any impact on the cell proliferation of Calu-3 cells at and below its IC50 concentration. When SRX3177 is combined with EIDD-1931 (active moiety of a small-molecule prodrug Molnupiravir) or MU-UNMC-2 (a SARS-CoV-2 entry inhibitor) at a fixed doses matrix, a synergistic effect was observed, leading to the significant reduction in the dose of the individual compounds to achieve similar inhibition of SARS-CoV-2 replication. Herein, we report that the combination of SRX3177/MPV or SRX3177/UM-UNMC-2 has the potential for further development as a combinational therapy against SARS-CoV-2 and in any future outbreak of beta coronavirus.
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Affiliation(s)
- Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68131, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68131, USA
| | - Dhananjaya Pal
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute, Charlotte, NC, 28204, USA; Division of Hematology and Oncology, Department of Pediatrics, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Prashant Jain
- Cancer Genome and Epigenetics Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92127, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Donald L Durden
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute, Charlotte, NC, 28204, USA; Division of Hematology and Oncology, Department of Pediatrics, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Aniruddha J Deshpande
- Cancer Genome and Epigenetics Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92127, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68131, USA.
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Kang BM, Kim D, Kim J, Baek K, Park S, Shin HE, Lee MH, Kim M, Kim S, Lee Y, Kwon HJ. Analysis of SARS-CoV-2 Mutations after Nirmatrelvir Treatment in a Lung Cancer Xenograft Mouse Model. Biomol Ther (Seoul) 2024; 32:481-491. [PMID: 38835145 PMCID: PMC11214963 DOI: 10.4062/biomolther.2023.195] [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: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 06/06/2024] Open
Abstract
Paxlovid is the first approved oral treatment for coronavirus disease 2019 and includes nirmatrelvir, a protease inhibitor targeting the main protease (Mpro) of SARS-CoV-2, as one of the key components. While some specific mutations emerged in Mpro were revealed to significantly reduce viral susceptibility to nirmatrelvir in vitro, there is no report regarding resistance to nirmatrelvir in patients and animal models for SARS-CoV-2 infection yet. We recently developed xenograft tumors derived from Calu-3 cells in immunodeficient mice and demonstrated extended replication of SARS-CoV-2 in the tumors. In this study, we investigated the effect of nirmatrelvir administration on SARS-CoV-2 replication. Treatment with nirmatrelvir after virus infection significantly reduced the replication of the parental SARS-CoV-2 and SARS-CoV-2 Omicron at 5 days post-infection (dpi). However, the virus titers were completely recovered at the time points of 15 and 30 dpi. The virus genomes in the tumors at 30 dpi were analyzed to investigate whether nirmatrelvir-resistant mutant viruses had emerged during the extended replication of SARS-CoV-2. Various mutations in several genes including ORF1ab, ORF3a, ORF7a, ORF7b, ORF8, and N occurred in the SARS-CoV-2 genome; however, no mutations were induced in the Mpro sequence by a single round of nirmatrelvir treatment, and none were observed even after two rounds of treatment. The parental SARS-CoV-2 and its sublineage isolates showed similar IC50 values of nirmatrelvir in Vero E6 cells. Therefore, it is probable that inducing viral resistance to nirmatrelvir in vivo is challenging differently from in vitro passage.
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Affiliation(s)
- Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ha-Eun Shin
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Myeong-Heon Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Hyung-Joo Kwon
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
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4
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Penrice-Randal R, Bentley EG, Sharma P, Kirby A, Donovan-Banfield I, Kipar A, Mega DF, Bramwell C, Sharp J, Owen A, Hiscox JA, Stewart JP. The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582110. [PMID: 38464327 PMCID: PMC10925244 DOI: 10.1101/2024.02.27.582110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Objectives Immunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context during the first 7 days of infection. Methods Mice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed. Results Treatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of A>G and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs). Conclusions Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development, especially by taking persistence into consideration, and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.
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Affiliation(s)
| | - Eleanor G. Bentley
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - I’ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Daniele F. Mega
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Chloe Bramwell
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
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5
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Kinsella PM, Moso MA, Morrissey CO, Dendle C, Guy S, Bond K, Sasadeusz J, Slavin MA. Antiviral therapies for the management of persistent coronavirus disease 2019 in immunocompromised hosts: A narrative review. Transpl Infect Dis 2024; 26:e14301. [PMID: 38809102 DOI: 10.1111/tid.14301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024]
Abstract
Antiviral agents with activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have played a critical role in disease management; however, little is known regarding the efficacy of these medications in the treatment of SARS-CoV-2 infection in immunocompromised patients, particularly in the management of persistent SARS-CoV-2 positivity. This narrative review discusses the management of persistent coronavirus disease 2019 in immunocompromised hosts, with a focus on antiviral therapies. We identified 84 cases from the literature describing a variety of approaches, including prolonged antiviral therapy (n = 11), combination antivirals (n = 13), and mixed therapy with antiviral and antibody treatments (n = 60). A high proportion had an underlying haematologic malignancy (n = 67, 80%), and were in receipt of anti-CD20 agents (n = 51, 60%). Success was reported in 70 cases (83%) which varied according to the therapy type. Combination therapies with antivirals may be an effective approach for individuals with persistent SARS-CoV-2 positivity, particularly those that incorporate treatments aimed at increasing neutralizing antibody levels. Any novel approaches taken to this difficult management dilemma should be mindful of the emergence of antiviral resistance.
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Affiliation(s)
- Paul M Kinsella
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne at the Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Michael A Moso
- Department of Infectious Diseases, University of Melbourne at the Doherty Institute of Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Doherty Institute of Infection and Immunity, Melbourne, Australia
| | | | - Claire Dendle
- Monash Infectious Diseases, Monash Health, Melbourne, Australia
- School of Clinical Sciences, Monash University, Melbourne, Australia
| | - Stephen Guy
- Department of Infectious Diseases, Eastern Health, Melbourne, Australia
- Eastern Health Clinical School, Monash University, Melbourne, Australia
| | - Katherine Bond
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia
- Victorian Infectious Diseases Reference Laboratory (VIDRL) at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Joseph Sasadeusz
- Department of Infectious Diseases, University of Melbourne at the Doherty Institute of Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Doherty Institute of Infection and Immunity, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
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6
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Martinez DR, Moreira FR, Catanzaro NJ, Diefenbacher MV, Zweigart MR, Gully KL, De la Cruz G, Brown AJ, Adams LE, Yount B, Baric TJ, Mallory ML, Conrad H, May SR, Dong S, Scobey DT, Nguyen C, Montgomery SA, Perry J, Babusis D, Barrett KT, Nguyen AH, Nguyen AQ, Kalla R, Bannister R, Feng JY, Cihlar T, Baric RS, Mackman RL, Bilello JP, Schäfer A, Sheahan TP. The oral nucleoside prodrug GS-5245 is efficacious against SARS-CoV-2 and other endemic, epidemic, and enzootic coronaviruses. Sci Transl Med 2024; 16:eadj4504. [PMID: 38776389 PMCID: PMC11333937 DOI: 10.1126/scitranslmed.adj4504] [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: 06/27/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Despite the wide availability of several safe and effective vaccines that prevent severe COVID-19, the persistent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that can evade vaccine-elicited immunity remains a global health concern. In addition, the emergence of SARS-CoV-2 VOCs that can evade therapeutic monoclonal antibodies underscores the need for additional, variant-resistant treatment strategies. Here, we characterize the antiviral activity of GS-5245, obeldesivir (ODV), an oral prodrug of the parent nucleoside GS-441524, which targets the highly conserved viral RNA-dependent RNA polymerase (RdRp). We show that GS-5245 is broadly potent in vitro against alphacoronavirus HCoV-NL63, SARS-CoV, SARS-CoV-related bat-CoV RsSHC014, Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 WA/1, and the highly transmissible SARS-CoV-2 BA.1 Omicron variant. Moreover, in mouse models of SARS-CoV, SARS-CoV-2 (WA/1 and Omicron B1.1.529), MERS-CoV, and bat-CoV RsSHC014 pathogenesis, we observed a dose-dependent reduction in viral replication, body weight loss, acute lung injury, and pulmonary function with GS-5245 therapy. Last, we demonstrate that a combination of GS-5245 and main protease (Mpro) inhibitor nirmatrelvir improved outcomes in vivo against SARS-CoV-2 compared with the single agents. Together, our data support the clinical evaluation of GS-5245 against coronaviruses that cause or have the potential to cause human disease.
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Affiliation(s)
- David R. Martinez
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Fernando R. Moreira
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nicholas J. Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Meghan V. Diefenbacher
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mark R. Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kendra L. Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ariane J. Brown
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Lily E. Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Thomas J. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael L. Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Helen Conrad
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Samantha R. May
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephanie Dong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - D. Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Cameron Nguyen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephanie A. Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jason Perry
- Gilead Sciences, Inc, Foster City, CA, 94404, USA
| | | | | | | | | | - Rao Kalla
- Gilead Sciences, Inc, Foster City, CA, 94404, USA
| | | | - Joy Y. Feng
- Gilead Sciences, Inc, Foster City, CA, 94404, USA
| | - Tomas Cihlar
- Gilead Sciences, Inc, Foster City, CA, 94404, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Timothy P. Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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7
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Asadipooya K, Asadipooya A, Adatorwovor R. Combination of spironolactone and DPP-4 inhibitors for treatment of SARS-CoV-2 infection: a literature review. Arch Virol 2024; 169:122. [PMID: 38753071 DOI: 10.1007/s00705-024-06043-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 03/23/2024] [Indexed: 05/21/2024]
Abstract
Coronavirus disease 2019 (COVID-19) is still causing hospitalization and death, and vaccination appears to become less effective with each emerging variant. Spike, non-spike, and other possible unrecognized mutations have reduced the efficacy of recommended therapeutic approaches, including monoclonal antibodies, plasma transfusion, and antivirals. SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) and probably dipeptidyl peptidase 4 (DPP-4) to initiate the process of endocytosis by employing host proteases such as transmembrane serine protease-2 (TMPRSS-2) and ADAM metallopeptidase domain 17 (ADAM17). Spironolactone reduces the amount of soluble ACE2 and antagonizes TMPRSS-2 and ADAM17. DPP-4 inhibitors play immunomodulatory roles and may block viral entry. The efficacy of treatment with a combination of spironolactone and DPP-4 inhibitors does not appear to be affected by viral mutations. Therefore, the combination of spironolactone and DPP-4 inhibitors might improve the clinical outcome for COVID-19 patients by decreasing the efficiency of SARS-CoV-2 entry into cells and providing better anti-inflammatory, antiproliferative, and antifibrotic effects than those achieved using current therapeutic approaches such as antivirals and monoclonal antibodies.
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Affiliation(s)
- Kamyar Asadipooya
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Barnstable Brown Diabetes and Obesity Center, University of Kentucky, 2195 Harrodsburg Rd, Suite 125, Lexington, KY, 40504, USA.
| | - Artin Asadipooya
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
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8
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Diaz J, Sears J, Chang CK, Burdick J, Law I, Sanders W, Linnertz C, Sylvester P, Moorman N, Ferris MT, Heise MT. U-CAN-seq: A Universal Competition Assay by Nanopore Sequencing. Viruses 2024; 16:636. [PMID: 38675976 PMCID: PMC11054411 DOI: 10.3390/v16040636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
RNA viruses quickly evolve subtle genotypic changes that can have major impacts on viral fitness and host range, with potential consequences for human health. It is therefore important to understand the evolutionary fitness of novel viral variants relative to well-studied genotypes of epidemic viruses. Competition assays are an effective and rigorous system with which to assess the relative fitness of viral genotypes. However, it is challenging to quickly and cheaply distinguish and quantify fitness differences between very similar viral genotypes. Here, we describe a protocol for using reverse transcription PCR in combination with commercial nanopore sequencing services to perform competition assays on untagged RNA viruses. Our assay, called the Universal Competition Assay by Nanopore Sequencing (U-CAN-seq), is relatively cheap and highly sensitive. We used a well-studied N24A mutation in the chikungunya virus (CHIKV) nsp3 gene to confirm that we could detect a competitive disadvantage using U-CAN-seq. We also used this approach to show that mutations to the CHIKV 5' conserved sequence element that disrupt sequence but not structure did not affect the fitness of CHIKV. However, similar mutations to an adjacent CHIKV stem loop (SL3) did cause a fitness disadvantage compared to wild-type CHIKV, suggesting that structure-independent, primary sequence determinants in this loop play an important role in CHIKV biology. Our novel findings illustrate the utility of the U-CAN-seq competition assay.
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Affiliation(s)
- Jennifer Diaz
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
| | - John Sears
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
| | - Che-Kang Chang
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
| | - Jane Burdick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Isabella Law
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Wes Sanders
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
| | - Colton Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Paul Sylvester
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Nathaniel Moorman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
- The Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 275114, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Mark T. Heise
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; (J.D.)
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
- The Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 275114, USA
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9
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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10
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Hedskog C, Spinner CD, Protzer U, Hoffmann D, Ko C, Gottlieb RL, Askar M, Roestenberg M, de Vries JJC, Carbo EC, Martin R, Li J, Han D, Rodriguez L, Parvangada A, Perry JK, Ferrer R, Antón A, Andrés C, Casares V, Günthard HF, Huber M, McComsey GA, Sadri N, Aberg JA, van Bakel H, Porter DP. No Remdesivir Resistance Observed in the Phase 3 Severe and Moderate COVID-19 SIMPLE Trials. Viruses 2024; 16:546. [PMID: 38675889 PMCID: PMC11053423 DOI: 10.3390/v16040546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Remdesivir (RDV) is a broad-spectrum nucleotide analog prodrug approved for the treatment of COVID-19 in hospitalized and non-hospitalized patients with clinical benefit demonstrated in multiple Phase 3 trials. Here we present SARS-CoV-2 resistance analyses from the Phase 3 SIMPLE clinical studies evaluating RDV in hospitalized participants with severe or moderate COVID-19 disease. The severe and moderate studies enrolled participants with radiologic evidence of pneumonia and a room-air oxygen saturation of ≤94% or >94%, respectively. Virology sample collection was optional in the study protocols. Sequencing and related viral load data were obtained retrospectively from participants at a subset of study sites with local sequencing capabilities (10 of 183 sites) at timepoints with detectable viral load. Among participants with both baseline and post-baseline sequencing data treated with RDV, emergent Nsp12 substitutions were observed in 4 of 19 (21%) participants in the severe study and none of the 2 participants in the moderate study. The following 5 substitutions emerged: T76I, A526V, A554V, E665K, and C697F. The substitutions T76I, A526V, A554V, and C697F had an EC50 fold change of ≤1.5 relative to the wildtype reference using a SARS-CoV-2 subgenomic replicon system, indicating no significant change in the susceptibility to RDV. The phenotyping of E665K could not be determined due to a lack of replication. These data reveal no evidence of relevant resistance emergence and further confirm the established efficacy profile of RDV with a high resistance barrier in COVID-19 patients.
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Affiliation(s)
- Charlotte Hedskog
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Christoph D. Spinner
- TUM School of Medicine and Health, Department of Clinical Medicine—Clinical Department for Internal Medicine II, University Medical Center, Technical University of Munich, 81675 Munich, Germany;
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany; (U.P.); (D.H.)
- Institute of Virology, Technical University of Munich School of Medicine, 81675 Munich, Germany;
- Institute of Virology, Helmholtz Munich, 85764 Munich, Germany
| | - Dieter Hoffmann
- German Center for Infection Research (DZIF), Munich Partner Site, 81675 Munich, Germany; (U.P.); (D.H.)
- Institute of Virology, Technical University of Munich School of Medicine, 81675 Munich, Germany;
| | - Chunkyu Ko
- Institute of Virology, Technical University of Munich School of Medicine, 81675 Munich, Germany;
- Institute of Virology, Helmholtz Munich, 85764 Munich, Germany
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Robert L. Gottlieb
- Center for Advanced Heart and Lung Disease, Department of Internal Medicine, Baylor University Medical Center, Dallas, TX 75246, USA; (R.L.G.); (M.A.)
- Baylor Scott & White Research Institute, Dallas, TX 75246, USA
- Department of Internal Medicine, Texas A&M Health Science Center, Dallas, TX 75246, USA
- Department of Internal Medicine, Burnett School of Medicine at TCU, Fort Worth, TX 76109, USA
| | - Medhat Askar
- Center for Advanced Heart and Lung Disease, Department of Internal Medicine, Baylor University Medical Center, Dallas, TX 75246, USA; (R.L.G.); (M.A.)
- QU Health and Department of Immunology, College of Medicine, Qatar University, Doha P.O. Box 2713, Qatar
| | - Meta Roestenberg
- Leiden University Medical Center for Infectious Diseases (LUCID), 2333 ZA Leiden, The Netherlands; (M.R.); (J.J.C.d.V.); (E.C.C.)
| | - Jutte J. C. de Vries
- Leiden University Medical Center for Infectious Diseases (LUCID), 2333 ZA Leiden, The Netherlands; (M.R.); (J.J.C.d.V.); (E.C.C.)
| | - Ellen C. Carbo
- Leiden University Medical Center for Infectious Diseases (LUCID), 2333 ZA Leiden, The Netherlands; (M.R.); (J.J.C.d.V.); (E.C.C.)
| | - Ross Martin
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Jiani Li
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Dong Han
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Lauren Rodriguez
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Aiyappa Parvangada
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Jason K. Perry
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
| | - Ricard Ferrer
- Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Medicine Department, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (R.F.); (A.A.); (C.A.); (V.C.)
| | - Andrés Antón
- Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Medicine Department, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (R.F.); (A.A.); (C.A.); (V.C.)
| | - Cristina Andrés
- Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Medicine Department, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (R.F.); (A.A.); (C.A.); (V.C.)
| | - Vanessa Casares
- Vall d’Hebron Hospital Universitari, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Medicine Department, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (R.F.); (A.A.); (C.A.); (V.C.)
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8057 Zurich, Switzerland;
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Grace A. McComsey
- Department of Medicine, University Hospitals of Cleveland and Case Western Reserve University, Cleveland, OH 44106, USA; (G.A.M.); (N.S.)
| | - Navid Sadri
- Department of Medicine, University Hospitals of Cleveland and Case Western Reserve University, Cleveland, OH 44106, USA; (G.A.M.); (N.S.)
| | - Judith A. Aberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Danielle P. Porter
- Gilead Sciences, Inc., Foster City, CA 94404, USA; (R.M.); (J.L.); (D.H.); (L.R.); (A.P.); (J.K.P.); (D.P.P.)
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11
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Manuto L, Bado M, Cola M, Vanzo E, Antonello M, Mazzotti G, Pacenti M, Cordioli G, Sasset L, Cattelan AM, Toppo S, Lavezzo E. Immune System Deficiencies Do Not Alter SARS-CoV-2 Evolutionary Rate but Favour the Emergence of Mutations by Extending Viral Persistence. Viruses 2024; 16:447. [PMID: 38543811 PMCID: PMC10974344 DOI: 10.3390/v16030447] [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: 02/19/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 05/23/2024] Open
Abstract
During the COVID-19 pandemic, immunosuppressed patients showed prolonged SARS-CoV-2 infections, with several studies reporting the accumulation of mutations in the viral genome. The weakened immune system present in these individuals, along with the effect of antiviral therapies, are thought to create a favourable environment for intra-host viral evolution and have been linked to the emergence of new viral variants which strongly challenged containment measures and some therapeutic treatments. To assess whether impaired immunity could lead to the increased instability of viral genomes, longitudinal nasopharyngeal swabs were collected from eight immunocompromised patients and fourteen non-immunocompromised subjects, all undergoing SARS-CoV-2 infection. Intra-host viral evolution was compared between the two groups through deep sequencing, exploiting a probe-based enrichment method to minimise the possibility of artefactual mutations commonly generated in amplicon-based methods, which heavily rely on PCR amplification. Although, as expected, immunocompromised patients experienced significantly longer infections, the acquisition of novel intra-host viral mutations was similar between the two groups. Moreover, a thorough analysis of viral quasispecies showed that the variability of viral populations in the two groups is comparable not only at the consensus level, but also when considering low-frequency mutations. This study suggests that a compromised immune system alone does not affect SARS-CoV-2 within-host genomic variability.
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Affiliation(s)
- Laura Manuto
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Martina Bado
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Marco Cola
- Department of Medicine, DIMED, University of Padova, 35128 Padova, Italy;
| | - Elena Vanzo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Maria Antonello
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Giorgia Mazzotti
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Monia Pacenti
- Unit of Microbiology and Virology, University Hospital of Padova, 35128 Padova, Italy;
| | - Giampaolo Cordioli
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Lolita Sasset
- Unit of Infectious Diseases, University Hospital of Padova, 35128 Padova, Italy;
| | - Anna Maria Cattelan
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
- Unit of Infectious Diseases, University Hospital of Padova, 35128 Padova, Italy;
| | - Stefano Toppo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Enrico Lavezzo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
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12
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Marques AD, Graham-Wooten J, Fitzgerald AS, Sobel Leonard A, Cook EJ, Everett JK, Rodino KG, Moncla LH, Kelly BJ, Collman RG, Bushman FD. SARS-CoV-2 evolution during prolonged infection in immunocompromised patients. mBio 2024; 15:e0011024. [PMID: 38364100 PMCID: PMC10936176 DOI: 10.1128/mbio.00110-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Prolonged infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients provides an opportunity for viral evolution, potentially leading to the generation of new pathogenic variants. To investigate the pathways of viral evolution, we carried out a study on five patients experiencing prolonged SARS-CoV-2 infection (quantitative polymerase chain reaction-positive for 79-203 days) who were immunocompromised due to treatment for lymphoma or solid organ transplantation. For each timepoint analyzed, we generated at least two independent viral genome sequences to assess the heterogeneity and control for sequencing error. Four of the five patients likely had prolonged infection; the fifth apparently experienced a reinfection. The rates of accumulation of substitutions in the viral genome per day were higher in hospitalized patients with prolonged infection than those estimated for the community background. The spike coding region accumulated a significantly greater number of unique mutations than other viral coding regions, and the mutation density was higher. Two patients were treated with monoclonal antibodies (bebtelovimab and sotrovimab); by the next sampled timepoint, each virus population showed substitutions associated with monoclonal antibody resistance as the dominant forms (spike K444N and spike E340D). All patients received remdesivir, but remdesivir-resistant substitutions were not detected. These data thus help elucidate the trends of emergence, evolution, and selection of mutational variants within long-term infected immunocompromised individuals. IMPORTANCE SARS-CoV-2 is responsible for a global pandemic, driven in part by the emergence of new viral variants. Where do these new variants come from? One model is that long-term viral persistence in infected individuals allows for viral evolution in response to host pressures, resulting in viruses more likely to replicate efficiently in humans. In this study, we characterize replication in several hospitalized and long-term infected individuals, documenting efficient pathways of viral evolution.
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Affiliation(s)
- Andrew D. Marques
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | | | - Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emma J. Cook
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise H. Moncla
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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13
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Tanino Y, Nishioka K, Yamamoto C, Watanabe Y, Daidoji T, Kawamoto M, Uda S, Kirito S, Nakagawa Y, Kasamatsu Y, Kawahara Y, Sakai Y, Nobori S, Inaba T, Ota B, Fujita N, Hoshino A, Nukui Y, Nakaya T. Emergence of SARS-CoV-2 with Dual-Drug Resistant Mutations During a Long-Term Infection in a Kidney Transplant Recipient. Infect Drug Resist 2024; 17:531-541. [PMID: 38348230 PMCID: PMC10860503 DOI: 10.2147/idr.s438915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Introduction Various therapeutic agents are being developed for the treatment of coronavirus disease 2019 (COVID-19). Therefore, it is crucial to accumulate information regarding the features of drug-resistant viruses to these antiviral drugs. Methods We investigated the emergence of dual-drug resistance in a kidney transplant recipient who received sotrovimab (from day 0) and remdesivir (RDV) (from day 8 to day 17). We sequenced the whole viral genomes from nasopharyngeal swabs taken on day 0 and seven points after starting treatment (on days 12, 19, 23, 37, 43, 48, and 58). The genetic traits of the wild-type (day 0) and descendant viruses (after day 12) were determined by comparing the genomes with those of a Wuhan strain and the day 0 wild-type strain, respectively. Three viral isolates (from samples collected on days 0, 23, and 37) were investigated for their escape ability and growth kinetics in vitro. Results The sotrovimab resistant mutation (S:E340K) and the RDV resistant mutation RdRp:V792I (nt: G15814A) emerged within 12 days (day 12) and 11 days (day 19) after the treatment, respectively. The day 23 isolate harboring S:E340K/RdRp:V791I was resistant to both sotrovimab and RDV, showing 364- and 2.73-fold higher resistance respectively, compared with the wild-type. Moreover, compared with the day 23 isolate, the day 37 isolate accumulated multiple additional mutations and had a higher level of resistance to both drugs. Conclusion Drug-resistant variants with double mutations (S:E340K/RdRp:V791I) became dominant within 23 days after starting treatment, suggesting that even a combination therapy involving sotrovimab and RDV, dual-drug resistant viruses may emerge rapidly in immunocompromised patients. The dual-resistant variants had lower virus yields than those of the wild-type virus in vitro, suggesting that they paid a fitness cost.
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Affiliation(s)
- Yoko Tanino
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Keisuke Nishioka
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chie Yamamoto
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yohei Watanabe
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- JST, MIRAI, Tokyo, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Masataka Kawamoto
- Department of Forensics Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Sayaka Uda
- Department of Pulmonary Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shoko Kirito
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuta Nakagawa
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yu Kasamatsu
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiyuki Kawahara
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Yuri Sakai
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Shuji Nobori
- Department of Organ Transplantation and General Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tohru Inaba
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Bon Ota
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naohisa Fujita
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoko Nukui
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
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14
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Cianfarini C, Hassler L, Wysocki J, Hassan A, Nicolaescu V, Elli D, Gula H, Ibrahim AM, Randall G, Henkin J, Batlle D. Soluble Angiotensin-Converting Enzyme 2 Protein Improves Survival and Lowers Viral Titers in Lethal Mouse Model of Severe Acute Respiratory Syndrome Coronavirus Type 2 Infection with the Delta Variant. Cells 2024; 13:203. [PMID: 38334597 PMCID: PMC10854654 DOI: 10.3390/cells13030203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/10/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) utilizes angiotensin-converting enzyme 2 (ACE2) as its main receptor for cell entry. We bioengineered a soluble ACE2 protein termed ACE2 618-DDC-ABD that has increased binding to SARS-CoV-2 and prolonged duration of action. Here, we investigated the protective effect of this protein when administered intranasally to k18-hACE2 mice infected with the aggressive SARS-CoV-2 Delta variant. k18-hACE2 mice were infected with the SARS-CoV-2 Delta variant by inoculation of a lethal dose (2 × 104 PFU). ACE2 618-DDC-ABD (10 mg/kg) or PBS was administered intranasally six hours prior and 24 and 48 h post-viral inoculation. All animals in the PBS control group succumbed to the disease on day seven post-infection (0% survival), whereas, in contrast, there was only one casualty in the group that received ACE2 618-DDC-ABD (90% survival). Mice in the ACE2 618-DDC-ABD group had minimal disease as assessed using a clinical score and stable weight, and both brain and lung viral titers were markedly reduced. These findings demonstrate the efficacy of a bioengineered soluble ACE2 decoy with an extended duration of action in protecting against the aggressive Delta SARS-CoV-2 variant. Together with previous work, these findings underline the universal protective potential against current and future emerging SARS-CoV-2 variants.
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Affiliation(s)
- Cosimo Cianfarini
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
- Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Luise Hassler
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Jan Wysocki
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Abdelsabour Hassan
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Vlad Nicolaescu
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Derek Elli
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Haley Gula
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Amany M. Ibrahim
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Glenn Randall
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Jack Henkin
- Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
| | - Daniel Batlle
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
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15
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Illingworth CJR, Guerra-Assuncao JA, Gregg S, Charles O, Pang J, Roy S, Abdelnabi R, Neyts J, Breuer J. Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus Evol 2024; 10:veae001. [PMID: 38486802 PMCID: PMC10939363 DOI: 10.1093/ve/veae001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/23/2023] [Accepted: 01/03/2024] [Indexed: 03/17/2024] Open
Abstract
Mutagenic antiviral drugs have shown promise against multiple viruses, but concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Recently, genetic signatures associated with molnupiravir use have been identified in the global SARS-COV-2 population. Here, we examine the consequences of using favipiravir and molnupiravir to treat SARS-CoV-2 infection in a hamster model, comparing viral genome sequence data collected from (1) untreated hamsters, and (2) from hamsters receiving effective and suboptimal doses of treatment. We identify a broadly linear relationship between drug dose and the extent of variation in treated viral populations, with a high proportion of this variation being composed of variants at frequencies of less than 1 per cent, below typical thresholds for variant calling. Treatment with an effective dose of antiviral drug was associated with a gain of between 7 and 10 variants per viral genome relative to drug-free controls: even after a short period of treatment a population founded by a transmitted virus could contain multiple sequence differences to that of the original host. Treatment with a suboptimal dose of drug showed intermediate gains of variants. No dose-dependent signal was identified in the numbers of single-nucleotide variants reaching frequencies in excess of 5 per cent. We did not find evidence to support the emergence of drug resistance or of novel immune phenotypes. Our study suggests that where onward transmission occurs, a short period of treatment with mutagenic drugs may be sufficient to generate a significant increase in the number of viral variants transmitted.
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Affiliation(s)
| | - Jose A Guerra-Assuncao
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Samuel Gregg
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Oscar Charles
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Juanita Pang
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Sunando Roy
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Leuven B-3000, Belgium
- The VirusBank Platform, Gaston Geenslaan, Leuven B-3000, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Leuven B-3000, Belgium
- The VirusBank Platform, Gaston Geenslaan, Leuven B-3000, Belgium
| | - Judith Breuer
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH, UK
- Infection, Immunity and Inflammation Research and Teaching Department, University College London, Gower Street, London WC1E 6BT, UK
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16
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Arman BY, Brun J, Hill ML, Zitzmann N, von Delft A. An Update on SARS-CoV-2 Clinical Trial Results-What We Can Learn for the Next Pandemic. Int J Mol Sci 2023; 25:354. [PMID: 38203525 PMCID: PMC10779148 DOI: 10.3390/ijms25010354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has claimed over 7 million lives worldwide, providing a stark reminder of the importance of pandemic preparedness. Due to the lack of approved antiviral drugs effective against coronaviruses at the start of the pandemic, the world largely relied on repurposed efforts. Here, we summarise results from randomised controlled trials to date, as well as selected in vitro data of directly acting antivirals, host-targeting antivirals, and immunomodulatory drugs. Overall, repurposing efforts evaluating directly acting antivirals targeting other viral families were largely unsuccessful, whereas several immunomodulatory drugs led to clinical improvement in hospitalised patients with severe disease. In addition, accelerated drug discovery efforts during the pandemic progressed to multiple novel directly acting antivirals with clinical efficacy, including small molecule inhibitors and monoclonal antibodies. We argue that large-scale investment is required to prepare for future pandemics; both to develop an arsenal of broad-spectrum antivirals beyond coronaviruses and build worldwide clinical trial networks that can be rapidly utilised.
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Affiliation(s)
- Benediktus Yohan Arman
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Juliane Brun
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Michelle L. Hill
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK;
| | - Nicole Zitzmann
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Annette von Delft
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
- Centre for Medicine Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
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17
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Zhdanov KV, Maltsev OV, Kasyanenko KV, Kozlov KV, Sukachev VS, Lvov NI, Sharabkhanov VV, Litvinov AA. [Clinical efficiency and safety of riamilovir under various dosage regimens for treatment of acute respiratory viral infections in adults]. TERAPEVT ARKH 2023; 95:930-936. [PMID: 38158948 DOI: 10.26442/00403660.2023.11.202471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024]
Abstract
AIM To evaluate the clinical efficacy and safety of antiviral drug riamilovir in patients with acute respiratory viral infections (ARVI) of non-coronavirus (SARS-CoV-2) etiology with different dosing regimens. MATERIALS AND METHODS The study included 150 patients with ARVI aged 18-27 years (50 patients received riamilovir in the regimen of 250 mg 3 times a day for 5 days, 50 patients received riamilovir in the off label regimen of 250 mg 5 times a day for 5 days, 50 patients received only pathogenetic treatment). RESULTS The use of riamilovir in both treatment regimens led to a reduction in the duration of inpatient treatment. The shortest periods of hospitalization were noted in patients who received the study drug at higher daily dosages. The use of riamilovir reduced the duration and severity of general infectious manifestations of the disease, while the shortest total duration of fever and a number of respiratory tract syndromes was registered among people who received riamilovir in the regimen of 1250 mg per day for 5 days, no adverse events were registered, additionally, 100% elimination of ARVI pathogens was noted in 1250 mg per day group. CONCLUSION Riamilovir has shown clinical efficacy and a good safety profile in in both treatment regimens. The dosage regimen of 1250 mg per day led to more significant clinical effects and to 100% elimination of ARVI pathogens in the study group by the 6th day of hospitalization.
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18
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Lombardo D, Musolino C, Chines V, Caminiti G, Palermo C, Cacciola I, Raffa G, Pollicino T. Assessing Genomic Mutations in SARS-CoV-2: Potential Resistance to Antiviral Drugs in Viral Populations from Untreated COVID-19 Patients. Microorganisms 2023; 12:2. [PMID: 38276171 PMCID: PMC10821222 DOI: 10.3390/microorganisms12010002] [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: 10/30/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Naturally occurring SARS-CoV-2 variants mutated in genomic regions targeted by antiviral drugs have not been extensively studied. This study investigated the potential of the RNA-dependent RNA polymerase (RdRp) complex subunits and non-structural protein (Nsp)5 of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to accumulate natural mutations that could affect the efficacy of antiviral drugs. To this aim, SARS-CoV-2 genomic sequences isolated from 4155 drug-naive individuals from southern Italy were analyzed using the Illumina MiSeq platform. Sequencing of the 4155 samples showed the following viral variant distribution: 71.2% Delta, 22.2% Omicron, and 6.4% Alpha. In the Nsp12 sequences, we found 84 amino acid substitutions. The most common one was P323L, detected in 3777/4155 (91%) samples, with 2906/3777 (69.9%) also showing the G671S substitution in combination. Additionally, we identified 28, 14, and 24 different amino acid substitutions in the Nsp5, Nsp7, and Nsp8 genomic regions, respectively. Of note, the V186F and A191V substitutions, affecting residues adjacent to the active site of Nsp5 (the target of the antiviral drug Paxlovid), were found in 157/4155 (3.8%) and 3/4155 (0.07%) samples, respectively. In conclusion, the RdRp complex subunits and the Nsp5 genomic region exhibit susceptibility to accumulating natural mutations. This susceptibility poses a potential risk to the efficacy of antiviral drugs, as these mutations may compromise the drug ability to inhibit viral replication.
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Affiliation(s)
- Daniele Lombardo
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Cristina Musolino
- Department of Human Pathology, University Hospital of Messina, 98124 Messina, Italy;
| | - Valeria Chines
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Giuseppe Caminiti
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Claudia Palermo
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Irene Cacciola
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Giuseppina Raffa
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
| | - Teresa Pollicino
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (V.C.); (G.C.); (C.P.); (I.C.); (G.R.)
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19
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Hirotsu Y, Kobayashi H, Kakizaki Y, Saito A, Tsutsui T, Kawaguchi M, Shimamura S, Hata K, Hanawa S, Toyama J, Miyashita Y, Omata M. Multidrug-resistant mutations to antiviral and antibody therapy in an immunocompromised patient infected with SARS-CoV-2. MED 2023; 4:813-824.e4. [PMID: 37683636 DOI: 10.1016/j.medj.2023.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/19/2023] [Accepted: 08/15/2023] [Indexed: 09/10/2023]
Abstract
BACKGROUND Antiviral and antibody therapies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being recommended for high-risk patients, but the potential for the development of multidrug-resistant mutations in immunocompromised patients is unclear. METHODS To investigate the treatment course in cases of prolonged viral shedding in an immunocompromised patient with SARS-CoV-2 infection, we conducted longitudinal measurements of laboratory tests, chest computed tomography (CT) image evaluations, antibody titers, and antigen levels in nasopharyngeal swabs. Furthermore, we performed whole-genome sequencing and digital PCR analysis to examine the mechanisms of drug resistance. FINDINGS We present a case of a 65-year-old man with a history of malignant lymphoma who was treated with multiple antiviral and antibody therapies, including sotrovimab, remdesivir, paxlovid (nirmatrelvir/ritonavir), and molnupiravir. Initially, viral antigen levels decreased after treatments. However, after the virus rebounded, the patient showed no virologic response. The viral genome analysis revealed a single Omicron subvariant (BA.1.1), which evolved within the host during the disease progression. The viruses had acquired multiple resistance mutations to nirmatrelvir (3 chymotrypsin-like protease [3CLpro] E166 A/V), sotrovimab (spike P337L and E340K), and remdesivir (RNA-dependent RNA polymerase [RdRp] V166L). CONCLUSIONS Our results indicate that viruses with multidrug-resistant mutations and survival fitness persist in the infected subpopulation after drug selection pressure. FUNDING This study was supported by the JSPS KAKENHI Early-Career Scientists 18K16292 (Y.H.), Grant-in-Aid for Scientific Research (B) 20H03668 and 23H02955 (Y.H.), the YASUDA Medical Foundation (Y.H.), the Uehara Memorial Foundation (Y.H.), the Takeda Science Foundation (Y.H.), and Kato Memorial Bioscience Foundation (Y.H.).
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan.
| | - Hiroaki Kobayashi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Akitoshi Saito
- Department of Radiology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Makoto Kawaguchi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Sou Shimamura
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Kouki Hata
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Syunya Hanawa
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Jun Toyama
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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20
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Shimazu H, Wada D, Maruyama S, Inoue A, Kashihara M, Yoshihara T, Saito F, Yoshiya K, Nakamori Y, Kuwagata Y. Clinical experience of treatment of immunocompromised individuals with persistent SARS-CoV-2 infection based on drug resistance mutations determined by genomic analysis: a descriptive study. BMC Infect Dis 2023; 23:780. [PMID: 37946111 PMCID: PMC10636837 DOI: 10.1186/s12879-023-08797-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The efficacy of antiviral drugs that neutralize antibody drugs and fight against SARS-COV-2 is reported to be attenuated by genetic mutations of the virus in vitro. When B-cell immunocompromised patients are infected with SARS-COV-2, the infection can be prolonged, and genetic mutations can occur during the course of treatment. Therefore, for refractory patients with persistent COVID-19 infection, genomic analysis was performed to obtain data on drug resistance mutations as a reference to determine which antiviral drugs and antibody therapies might be effective in their treatment. METHODS This was a descriptive analysis with no controls. Patients were diagnosed as having COVID-19, examined, and treated in the Kansai Medical University General Medical Center between January 2022 and January 2023. The subjects of the study were B-cell immunocompromised patients in whom genome analysis of SARS-CoV-2 was performed. RESULTS During the study period, 984 patients with COVID-19 were treated at our hospital. Of those, 17 refractory cases underwent genomic analysis. All 17 patients had factors related to immunodeficiency, such as malignant lymphoma or post-organ transplantation. Eleven patients started initial treatment for COVID-19 at our hospital, developed persistent infection, and underwent genomic analysis. Six patients who were initially treated for COVID-19 at other hospitals became persistently infected and were transferred to our hospital. Before COVID-19 treatment, genomic analysis showed no intrahost mutations in the NSP5, the NSP12, and the RBD regions. After COVID-19 treatment, mutations in these regions were found in 12 of 17 cases (71%). Sixteen patients survived the quarantine, but one died of sepsis. CONCLUSIONS In genomic analysis, more mutations were found to be drug-resistant after COVID-19 treatment than before COVID-19 treatment. Although it was not possible to demonstrate the usefulness of genome analysis for clinical application, the change of the treatment drug with reference to drug resistance indicated by genomic analysis may lead to good outcome of immunocompromised COVID-19 patients.
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Affiliation(s)
- Haruka Shimazu
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Daiki Wada
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan.
| | - Shuhei Maruyama
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Akira Inoue
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Masami Kashihara
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Tomoyuki Yoshihara
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Fukuki Saito
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Kazuhisa Yoshiya
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yasushi Nakamori
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, 10-15 Fumizono-Cho, Moriguchi, Osaka, 570-8507, Japan
| | - Yasuyuki Kuwagata
- Department of Emergency and Critical Care Medicine, Kansai Medical University Hospital, 2-3-1 Shinmachi, Hirakata, Osaka, 573-1191, Japan
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21
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Hedskog C, Rodriguez L, Roychoudhury P, Huang ML, Jerome KR, Hao L, Ireton RC, Li J, Perry JK, Han D, Camus G, Greninger AL, Gale M, Porter DP. Viral Resistance Analyses From the Remdesivir Phase 3 Adaptive COVID-19 Treatment Trial-1 (ACTT-1). J Infect Dis 2023; 228:1263-1273. [PMID: 37466213 PMCID: PMC10629708 DOI: 10.1093/infdis/jiad270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Remdesivir is approved for treatment of coronavirus disease 2019 (COVID-19) in nonhospitalized and hospitalized adult and pediatric patients. Here we present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resistance analyses from the phase 3 ACTT-1 randomized placebo-controlled trial conducted in adult participants hospitalized with COVID-19. METHODS Swab samples were collected at baseline and longitudinally through day 29. SARS-CoV-2 genomes were sequenced using next-generation sequencing. Phenotypic analysis was conducted directly on participant virus isolates and/or using SARS-CoV-2 subgenomic replicons expressing mutations identified in the Nsp12 target gene. RESULTS Among participants with both baseline and postbaseline sequencing data, emergent Nsp12 substitutions were observed in 12 of 31 (38.7%) and 12 of 30 (40.0%) participants in the remdesivir and placebo arms, respectively. No emergent Nsp12 substitutions in the remdesivir arm were observed in more than 1 participant. Phenotyping showed low to no change in susceptibility to remdesivir relative to wild-type Nsp12 reference for the substitutions tested: A16V (0.8-fold change in EC50), P323L + V792I (2.2-fold), C799F (2.5-fold), K59N (1.0-fold), and K59N + V792I (3.4-fold). CONCLUSIONS The similar rate of emerging Nsp12 substitutions in the remdesivir and placebo arms and the minimal change in remdesivir susceptibility among tested substitutions support a high barrier to remdesivir resistance development in COVID-19 patients. Clinical Trials Registration. NCT04280705.
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Affiliation(s)
| | | | - Pavitra Roychoudhury
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Meei-Li Huang
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Linhui Hao
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Renee C Ireton
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Jiani Li
- Gilead Sciences, Inc, Foster City, California, USA
| | | | - Dong Han
- Gilead Sciences, Inc, Foster City, California, USA
| | | | - Alexander L Greninger
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
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22
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Li Z, Lee JE, Cho N, Yoo HM. Anti-viral effect of usenamine a using SARS-CoV-2 pseudo-typed viruses. Heliyon 2023; 9:e21742. [PMID: 38027904 PMCID: PMC10656252 DOI: 10.1016/j.heliyon.2023.e21742] [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: 06/18/2023] [Revised: 09/09/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
The escalating pandemic brought about by the novel SARS-CoV-2 virus is threatening global health, and thus, it is necessary to develop effective antiviral drugs. Usenamine A is a dibenzo-furan derivative separated from lichen Usnea diffracta showing broad-spectrum activity against different viruses. We evaluate that usenamine A has antiviral effects against novel SARS-CoV-2 Delta variant pseudotyped viruses (PVs) in A549 cells. In addition, usenamine A significantly suppresses SARS-CoV-2 PV-induced mitochondrial depolarization, elevated reactive oxygen species (ROS) levels, apoptosis, and inflammation. Usenamine A also causes the SARS-CoV-2 spike protein to become less stable. Thus, usenamine A shows potential as an antiviral drug that can provide protection against COVID-19.
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Affiliation(s)
- Zijun Li
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju 61186, South Korea
| | - Joo-Eun Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju 61186, South Korea
| | - Namki Cho
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju 61186, South Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
- Department of Precision Measurement, University of Science and Technology (UST), Daejeon 34113, South Korea
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23
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Lin CH, Tam HMH, Yang CY, Hsieh FC, Wang JL, Yang CC, Hsu HW, Liu HP, Wu HY. Evolution of the coronavirus spike protein in the full-length genome and defective viral genome under diverse selection pressures. J Gen Virol 2023; 104:001920. [PMID: 37997889 PMCID: PMC10768696 DOI: 10.1099/jgv.0.001920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/28/2023] [Indexed: 11/25/2023] Open
Abstract
How coronaviruses evolve by altering the structures of their full-length genome and defective viral genome (DVG) under dynamic selection pressures has not been studied. In this study, we aimed to experimentally identify the dynamic evolutionary patterns of the S protein sequence in the full-length genome and DVG under diverse selection pressures, including persistence, innate immunity and antiviral drugs. The evolutionary features of the S protein sequence in the full-length genome and in the DVG under diverse selection pressures are as follows: (i) the number of nucleotide (nt) mutations does not necessarily increase with the number of selection pressures; (ii) certain types of selection pressure(s) can lead to specific nt mutations; (iii) the mutated nt sequence can be reverted to the wild-type nt sequence under the certain type of selection pressure(s); (iv) the DVG can also undergo mutations and evolve independently of the full-length genome; and (v) DVG species are regulated during evolution under diverse selection pressures. The various evolutionary patterns of the S protein sequence in the full-length genome and DVG identified in this study may contribute to coronaviral fitness under diverse selection pressures.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hon-Man-Herman Tam
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Feng-Cheng Hsieh
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jiun-Long Wang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan, ROC
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chun-Chun Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hsuan-Wei Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hao-Ping Liu
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
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24
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Koch EM, Du J, Dressner M, Alwasti HE, Al Taif Z, Shehab F, Mohamed AM, Ghanem A, Alhajeri A, Alawadhi A, Almoamen N, Ashoor K, Hasan S, Haghighi A, Sunyaev S, Farhat M. Demographic and Viral-Genetic Analyses of COVID-19 Severity in Bahrain Identify Local Risk Factors and a Protective Effect of Polymerase Mutations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2022.08.13.22278740. [PMID: 36032980 PMCID: PMC9413726 DOI: 10.1101/2022.08.13.22278740] [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: 11/24/2022]
Abstract
A multitude of demographic, health, and genetic factors are associated with the risk of developing severe COVID-19 following infection by the SARS-CoV-2. There is a need to perform studies across human societies and to investigate the full spectrum of genetic variation of the virus. Using data from 869 COVID-19 patients in Bahrain between March 2020 and March 2021, we analyzed paired viral sequencing and non-genetic host data to understand host and viral determinants of severe COVID-19. We estimated the effects of demographic variables specific to the Bahrain population and found that the impact of health factors are largely consistent with other populations. To extend beyond the common variants of concern in the Spike protein analyzed by previous studies, we used a viral burden approach and detected a protective effect of low-frequency missense viral mutations in the RNA-dependent RNA polymerase (Pol) gene on disease severity. Our results contribute to the survey of severe COVID-19 in diverse populations and highlight the benefits of studying rare viral mutations.
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Affiliation(s)
- Evan M. Koch
- Department of Biomedical Informatics, Harvard Medical School
| | | | | | | | - Zahra Al Taif
- Public Health Laboratories, Public Health Directorate, Bahrain Ministry of Health
| | - Fatima Shehab
- Public Health Laboratories, Public Health Directorate, Bahrain Ministry of Health
| | - Afaf Merza Mohamed
- Public Health Laboratories, Public Health Directorate, Bahrain Ministry of Health
| | - Amjad Ghanem
- Public Health Laboratories, Public Health Directorate, Bahrain Ministry of Health
| | - Amani Alhajeri
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Amna Alawadhi
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Nabeel Almoamen
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Khulood Ashoor
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Sara Hasan
- Genetic Department, Government Hospitals, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | - Alireza Haghighi
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital
- Department of Genetics, Harvard Medical School
- Broad Institute of MIT and Harvard
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital
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25
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Zhang Y, Sun Y, Xie Y, Shang W, Wang Z, Jiang H, Shen J, Xiao G, Zhang L. A viral RNA-dependent RNA polymerase inhibitor VV116 broadly inhibits human coronaviruses and has synergistic potency with 3CLpro inhibitor nirmatrelvir. Signal Transduct Target Ther 2023; 8:360. [PMID: 37735468 PMCID: PMC10514301 DOI: 10.1038/s41392-023-01587-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/28/2023] [Accepted: 08/03/2023] [Indexed: 09/23/2023] Open
Abstract
During the ongoing pandemic, providing treatment consisting of effective, low-cost oral antiviral drugs at an early stage of SARS-CoV-2 infection has been a priority for controlling COVID-19. Although Paxlovid and molnupiravir have received emergency approval from the FDA, some side effect concerns have emerged, and the possible oral agents are still limited, resulting in optimized drug development becoming an urgent requirement. An oral remdesivir derivative, VV116, has been reported to have promising antiviral effects against SARS-CoV-2 and positive therapeutic outcomes in clinical trials. However, whether VV116 has broad-spectrum anti-coronavirus activity and potential synergy with other drugs is not clear. Here, we uncovered the broad-spectrum antiviral potency of VV116 against SARS-CoV-2 variants of concern (VOCs), HCoV-OC43, and HCoV-229E in various cell lines. In vitro drug combination screening targeted RdRp and proteinase, highlighting the synergistic effect of VV116 and nirmatrelvir on HCoV-OC43 and SARS-CoV-2. When co-administrated with ritonavir, the combination of VV116 and nirmatrelvir showed significantly enhanced antiviral potency with noninteracting pharmacokinetic properties in mice. Our findings will facilitate clinical treatment with VV116 or VV116+nirmatrelvir combination to fight coronavirus infection.
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Affiliation(s)
- Yumin Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Yuan Sun
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | | | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Zhen Wang
- Lingang Laboratory, 200031, Shanghai, China
| | - Hualiang Jiang
- Lingang Laboratory, 200031, Shanghai, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Jingshan Shen
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Hubei Jiangxia Laboratory, 430200, Wuhan, China.
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26
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Gammeltoft KA, Zhou Y, Ryberg LA, Pham LV, Binderup A, Hernandez CRD, Offersgaard A, Fahnøe U, Peters GHJ, Ramirez S, Bukh J, Gottwein JM. Substitutions in SARS-CoV-2 Mpro Selected by Protease Inhibitor Boceprevir Confer Resistance to Nirmatrelvir. Viruses 2023; 15:1970. [PMID: 37766376 PMCID: PMC10536901 DOI: 10.3390/v15091970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Nirmatrelvir, which targets the SARS-CoV-2 main protease (Mpro), is the first-in-line drug for prevention and treatment of severe COVID-19, and additional Mpro inhibitors are in development. However, the risk of resistance development threatens the future efficacy of such direct-acting antivirals. To gain knowledge on viral correlates of resistance to Mpro inhibitors, we selected resistant SARS-CoV-2 under treatment with the nirmatrelvir-related protease inhibitor boceprevir. SARS-CoV-2 selected during five escape experiments in VeroE6 cells showed cross-resistance to nirmatrelvir with up to 7.3-fold increased half-maximal effective concentration compared to original SARS-CoV-2, determined in concentration-response experiments. Sequence analysis revealed that escape viruses harbored Mpro substitutions L50F and A173V. For reverse genetic studies, these substitutions were introduced into a cell-culture-infectious SARS-CoV-2 clone. Infectivity titration and analysis of genetic stability of cell-culture-derived engineered SARS-CoV-2 mutants showed that L50F rescued the fitness cost conferred by A173V. In the concentration-response experiments, A173V was the main driver of resistance to boceprevir and nirmatrelvir. Structural analysis of Mpro suggested that A173V can cause resistance by making boceprevir and nirmatrelvir binding less favorable. This study contributes to a comprehensive overview of the resistance profile of the first-in-line COVID-19 treatment nirmatrelvir and can thus inform population monitoring and contribute to pandemic preparedness.
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Affiliation(s)
- Karen Anbro Gammeltoft
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Yuyong Zhou
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Line Abildgaard Ryberg
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Long V. Pham
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Alekxander Binderup
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Carlos Rene Duarte Hernandez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Anna Offersgaard
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | | | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Judith Margarete Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Kettegård Alle 30, 2650 Hvidovre, Denmark; (K.A.G.); (Y.Z.); (L.A.R.); (L.V.P.); (A.B.); (C.R.D.H.); (A.O.); (U.F.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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27
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Mhlekude B, Postmus D, Stenzel S, Weiner J, Jansen J, Zapatero-Belinchón FJ, Olmer R, Richter A, Heinze J, Heinemann N, Mühlemann B, Schroeder S, Jones TC, Müller MA, Drosten C, Pich A, Thiel V, Martin U, Niemeyer D, Gerold G, Beule D, Goffinet C. Pharmacological inhibition of bromodomain and extra-terminal proteins induces an NRF-2-mediated antiviral state that is subverted by SARS-CoV-2 infection. PLoS Pathog 2023; 19:e1011657. [PMID: 37747932 PMCID: PMC10629670 DOI: 10.1371/journal.ppat.1011657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/07/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
Inhibitors of bromodomain and extra-terminal proteins (iBETs), including JQ-1, have been suggested as potential prophylactics against SARS-CoV-2 infection. However, molecular mechanisms underlying JQ-1-mediated antiviral activity and its susceptibility to viral subversion remain incompletely understood. Pretreatment of cells with iBETs inhibited infection by SARS-CoV-2 variants and SARS-CoV, but not MERS-CoV. The antiviral activity manifested itself by reduced reporter expression of recombinant viruses, and reduced viral RNA quantities and infectious titers in the culture supernatant. While we confirmed JQ-1-mediated downregulation of expression of angiotensin-converting enzyme 2 (ACE2) and interferon-stimulated genes (ISGs), multi-omics analysis addressing the chromatin accessibility, transcriptome and proteome uncovered induction of an antiviral nuclear factor erythroid 2-related factor 2 (NRF-2)-mediated cytoprotective response as an additional mechanism through which JQ-1 inhibits SARS-CoV-2 replication. Pharmacological inhibition of NRF-2, and knockdown of NRF-2 and its target genes reduced JQ-1-mediated inhibition of SARS-CoV-2 replication. Serial passaging of SARS-CoV-2 in the presence of JQ-1 resulted in predominance of ORF6-deficient variant, which exhibited resistance to JQ-1 and increased sensitivity to exogenously administered type I interferon (IFN-I), suggesting a minimised need for SARS-CoV-2 ORF6-mediated repression of IFN signalling in the presence of JQ-1. Importantly, JQ-1 exhibited a transient antiviral activity when administered prophylactically in human airway bronchial epithelial cells (hBAECs), which was gradually subverted by SARS-CoV-2, and no antiviral activity when administered therapeutically following an established infection. We propose that JQ-1 exerts pleiotropic effects that collectively induce an antiviral state in the host, which is ultimately nullified by SARS-CoV-2 infection, raising questions about the clinical suitability of the iBETs in the context of COVID-19.
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Affiliation(s)
- Baxolele Mhlekude
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- Virology and Innate Immunity Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dylan Postmus
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Saskia Stenzel
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - January Weiner
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Jenny Jansen
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Francisco J. Zapatero-Belinchón
- Department of Biochemistry, University of Veterinary Medicine Hannover, Hannover, Germany
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Virology & Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Ruth Olmer
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH—Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julian Heinze
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas Heinemann
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Barbara Mühlemann
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simon Schroeder
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Terry C. Jones
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Marcel A. Müller
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Pich
- Institute of Toxicology, Hannover Medical School, Core Facility Proteomics, Hannover, Germany
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), University of Bern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH—Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Daniela Niemeyer
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gisa Gerold
- Department of Biochemistry, University of Veterinary Medicine Hannover, Hannover, Germany
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Virology & Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Dieter Beule
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool United Kingdom
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28
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Grimes SL, Choi YJ, Banerjee A, Small G, Anderson-Daniels J, Gribble J, Pruijssers AJ, Agostini ML, Abu-Shmais A, Lu X, Darst SA, Campbell E, Denison MR. A mutation in the coronavirus nsp13-helicase impairs enzymatic activity and confers partial remdesivir resistance. mBio 2023; 14:e0106023. [PMID: 37338298 PMCID: PMC10470589 DOI: 10.1128/mbio.01060-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 06/21/2023] Open
Abstract
Coronaviruses (CoVs) encode nonstructural proteins 1-16 (nsps 1-16) which form replicase complexes that mediate viral RNA synthesis. Remdesivir (RDV) is an adenosine nucleoside analog antiviral that inhibits CoV RNA synthesis. RDV resistance mutations have been reported only in the nonstructural protein 12 RNA-dependent RNA polymerase (nsp12-RdRp). We here show that a substitution mutation in the nsp13-helicase (nsp13-HEL A335V) of the betacoronavirus murine hepatitis virus (MHV) that was selected during passage with the RDV parent compound confers partial RDV resistance independently and additively when expressed with co-selected RDV resistance mutations in the nsp12-RdRp. The MHV A335V substitution did not enhance replication or competitive fitness compared to WT MHV and remained sensitive to the active form of the cytidine nucleoside analog antiviral molnupiravir (MOV). Biochemical analysis of the SARS-CoV-2 helicase encoding the homologous substitution (A336V) demonstrates that the mutant protein retained the ability to associate with the core replication proteins nsps 7, 8, and 12 but had impaired helicase unwinding and ATPase activity. Together, these data identify a novel determinant of nsp13-HEL enzymatic activity, define a new genetic pathway for RDV resistance, and demonstrate the importance of surveillance for and testing of helicase mutations that arise in SARS-CoV-2 genomes. IMPORTANCE Despite the development of effective vaccines against COVID-19, the continued circulation and emergence of new variants support the need for antivirals such as RDV. Understanding pathways of antiviral resistance is essential for surveillance of emerging variants, development of combination therapies, and for identifying potential new targets for viral inhibition. We here show a novel RDV resistance mutation in the CoV helicase also impairs helicase functions, supporting the importance of studying the individual and cooperative functions of the replicase nonstructural proteins 7-16 during CoV RNA synthesis. The homologous nsp13-HEL mutation (A336V) has been reported in the GISAID database of SARS-CoV-2 genomes, highlighting the importance of surveillance of and genetic testing for nucleoside analog resistance in the helicase.
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Affiliation(s)
- Samantha L. Grimes
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Young J. Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
- Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Gabriel Small
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Jordan Anderson-Daniels
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jennifer Gribble
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrea J. Pruijssers
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, USA
| | - Maria L. Agostini
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexandra Abu-Shmais
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Xiaotao Lu
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Elizabeth Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Mark R. Denison
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, USA
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29
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Gratteri C, Ambrosio FA, Lupia A, Moraca F, Catalanotti B, Costa G, Bellocchi M, Carioti L, Salpini R, Ceccherini-Silberstein F, Frazia SL, Malagnino V, Sarmati L, Svicher V, Bryant S, Artese A, Alcaro S. Molecular and Structural Aspects of Clinically Relevant Mutations of SARS-CoV-2 RNA-Dependent RNA Polymerase in Remdesivir-Treated Patients. Pharmaceuticals (Basel) 2023; 16:1143. [PMID: 37631058 PMCID: PMC10459223 DOI: 10.3390/ph16081143] [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: 07/13/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Background: SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target to fight COVID-19, and many RdRp inhibitors nucleotide/nucleoside analogs, such as remdesivir, have been identified or are in clinical studies. However, the appearance of resistant mutations could reduce their efficacy. In the present work, we structurally evaluated the impact of RdRp mutations found at baseline in 39 patients treated with remdesivir and associated with a different degree of antiviral response in vivo. (2) Methods: A refined bioinformatics approach was applied to assign SARS-CoV-2 clade and lineage, and to define RdRp mutational profiles. In line with such a method, the same mutations were built and analyzed by combining docking and thermodynamics evaluations with both molecular dynamics and representative pharmacophore models. (3) Results: Clinical studies revealed that patients bearing the most prevalent triple mutant P323L+671S+M899I, which was present in 41% of patients, or the more complex mutational profile P323L+G671S+L838I+D738Y+K91E, which was found with a prevalence of 2.6%, showed a delayed reduced response to remdesivir, as confirmed by the increase in SARS-CoV-2 viral load and by a reduced theoretical binding affinity versus RdRp (ΔGbindWT = -122.70 kcal/mol; ΔGbindP323L+671S+M899I = -84.78 kcal/mol; ΔGbindP323L+G671S+L838I+D738Y+K91E = -96.74 kcal/mol). Combined computational approaches helped to rationalize such clinical observations, offering a mechanistic understanding of the allosteric effects of mutants on the global motions of the viral RNA synthesis machine and in the changes of the interactions patterns of remdesivir during its binding.
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Affiliation(s)
- Carmen Gratteri
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
| | - Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy;
| | - Antonio Lupia
- Dipartimento di Scienze della vita e dell’ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy;
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Federica Moraca
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Bruno Catalanotti
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Maria Bellocchi
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Luca Carioti
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Romina Salpini
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Francesca Ceccherini-Silberstein
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Simone La Frazia
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Vincenzo Malagnino
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Loredana Sarmati
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Valentina Svicher
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Sharon Bryant
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, 1070 Vienna, Austria;
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
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Takashita E, Fujisaki S, Morita H, Nagata S, Miura H, Nagashima M, Watanabe S, Takeda M, Kawaoka Y, Hasegawa H. Assessment of the frequency of SARS-CoV-2 Omicron variant escape from RNA-dependent RNA polymerase inhibitors and 3C-like protease inhibitors. Antiviral Res 2023:105671. [PMID: 37451629 DOI: 10.1016/j.antiviral.2023.105671] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The emergence and spread of antiviral-resistant SARS-CoV-2 is of great concern. In this study, we evaluated the propensity of Omicron variants to escape from RNA-dependent RNA polymerase (RdRP) inhibitors and 3C-like protease (3CLpro) inhibitors. SARS-CoV-2 Delta and Omicron variants were serially passaged in vitro in the presence of RdRP inhibitors (remdesivir and molnupiravir) and 3CLpro inhibitors (nirmatrelvir and lufotrelvir) to detect SARS-CoV-2 escape mutants. After five passages with 3CLpro inhibitors, mutant viruses that escaped from 3CLpro inhibitors emerged; however, in the presence of RdRP inhibitors all variants disappeared within 2-4 passages. Our findings suggest that the frequency of SARS-CoV-2 mutant escape from RdRP inhibitors is lower than that from 3CLpro inhibitors. We also found that Delta variants were more likely to acquire amino acid substitutions associated with resistance to 3CLpro inhibitors under the selective pressure of this drug compared with Omicron variants.
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Affiliation(s)
- Emi Takashita
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan.
| | - Seiichiro Fujisaki
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Hiroko Morita
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Shiho Nagata
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Hideka Miura
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo, 169-0073, Japan
| | - Shinji Watanabe
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
| | - Makoto Takeda
- Department of Virology Ⅲ, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan; Department of Microbiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan; Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan; Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI, 53711, USA; The University of Tokyo, Pandemic Preparedness, Infection, and Advanced Research Center, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Hideki Hasegawa
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, 208-0011, Japan
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31
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von Delft A, Hall MD, Kwong AD, Purcell LA, Saikatendu KS, Schmitz U, Tallarico JA, Lee AA. Accelerating antiviral drug discovery: lessons from COVID-19. Nat Rev Drug Discov 2023; 22:585-603. [PMID: 37173515 PMCID: PMC10176316 DOI: 10.1038/s41573-023-00692-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/15/2023]
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, a wave of rapid and collaborative drug discovery efforts took place in academia and industry, culminating in several therapeutics being discovered, approved and deployed in a 2-year time frame. This article summarizes the collective experience of several pharmaceutical companies and academic collaborations that were active in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral discovery. We outline our opinions and experiences on key stages in the small-molecule drug discovery process: target selection, medicinal chemistry, antiviral assays, animal efficacy and attempts to pre-empt resistance. We propose strategies that could accelerate future efforts and argue that a key bottleneck is the lack of quality chemical probes around understudied viral targets, which would serve as a starting point for drug discovery. Considering the small size of the viral proteome, comprehensively building an arsenal of probes for proteins in viruses of pandemic concern is a worthwhile and tractable challenge for the community.
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Affiliation(s)
- Annette von Delft
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK.
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | | | | | | | | | | | - Alpha A Lee
- PostEra, Inc., Cambridge, MA, USA.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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32
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Martinez DR, Moreira FR, Zweigart MR, Gully KL, De la Cruz G, Brown AJ, Adams LE, Catanzaro N, Yount B, Baric TJ, Mallory ML, Conrad H, May SR, Dong S, Scobey DT, Montgomery SA, Perry J, Babusis D, Barrett KT, Nguyen AH, Nguyen AQ, Kalla R, Bannister R, Bilello JP, Feng JY, Cihlar T, Baric RS, Mackman RL, Schäfer A, Sheahan TP. Efficacy of the oral nucleoside prodrug GS-5245 (Obeldesivir) against SARS-CoV-2 and coronaviruses with pandemic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546784. [PMID: 37425890 PMCID: PMC10327034 DOI: 10.1101/2023.06.27.546784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Despite the wide availability of several safe and effective vaccines that can prevent severe COVID-19 disease, the emergence of SARS-CoV-2 variants of concern (VOC) that can partially evade vaccine immunity remains a global health concern. In addition, the emergence of highly mutated and neutralization-resistant SARS-CoV-2 VOCs such as BA.1 and BA.5 that can partially or fully evade (1) many therapeutic monoclonal antibodies in clinical use underlines the need for additional effective treatment strategies. Here, we characterize the antiviral activity of GS-5245, Obeldesivir (ODV), an oral prodrug of the parent nucleoside GS-441524, which targets the highly conserved RNA-dependent viral RNA polymerase (RdRp). Importantly, we show that GS-5245 is broadly potent in vitro against alphacoronavirus HCoV-NL63, severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-related Bat-CoV RsSHC014, Middle East Respiratory Syndrome coronavirus (MERS-CoV), SARS-CoV-2 WA/1, and the highly transmissible SARS-CoV-2 BA.1 Omicron variant in vitro and highly effective as antiviral therapy in mouse models of SARS-CoV, SARS-CoV-2 (WA/1), MERS-CoV and Bat-CoV RsSHC014 pathogenesis. In all these models of divergent coronaviruses, we observed protection and/or significant reduction of disease metrics such as weight loss, lung viral replication, acute lung injury, and degradation in pulmonary function in GS-5245-treated mice compared to vehicle controls. Finally, we demonstrate that GS-5245 in combination with the main protease (Mpro) inhibitor nirmatrelvir had increased efficacy in vivo against SARS-CoV-2 compared to each single agent. Altogether, our data supports the continuing clinical evaluation of GS-5245 in humans infected with COVID-19, including as part of a combination antiviral therapy, especially in populations with the most urgent need for more efficacious and durable interventions.
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Affiliation(s)
- David R. Martinez
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Fernando R. Moreira
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mark R. Zweigart
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra L. Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriela De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Ariane J. Brown
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily E. Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas J. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael L. Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Helen Conrad
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samantha R. May
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie Dong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D. Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie A. Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | | | | | | | | | - Rao Kalla
- Gilead Sciences, Inc, Foster City, CA, USA
| | | | | | | | | | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P. Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Rapidly Emerging Antiviral Drug Development Initiative, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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33
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Gonzalez-Reiche AS, Alshammary H, Schaefer S, Patel G, Polanco J, Carreño JM, Amoako AA, Rooker A, Cognigni C, Floda D, van de Guchte A, Khalil Z, Farrugia K, Assad N, Zhang J, Alburquerque B, Sominsky LA, Gleason C, Srivastava K, Sebra R, Ramirez JD, Banu R, Shrestha P, Krammer F, Paniz-Mondolfi A, Sordillo EM, Simon V, van Bakel H. Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants. Nat Commun 2023; 14:3235. [PMID: 37270625 PMCID: PMC10239218 DOI: 10.1038/s41467-023-38867-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, direct evidence of subsequent transmission and continued stepwise adaptation is lacking. Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins. Our findings demonstrate not only that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome but also that patients with persistent infections can transmit these viral variants. Thus, there is, an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients.
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Affiliation(s)
- Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Schaefer
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gopi Patel
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jose Polanco
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Angela A Amoako
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aria Rooker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christian Cognigni
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel Floda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nima Assad
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jian Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bremy Alburquerque
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Levy A Sominsky
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan David Ramirez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Karim M, Lo CW, Einav S. Preparing for the next viral threat with broad-spectrum antivirals. J Clin Invest 2023; 133:e170236. [PMID: 37259914 PMCID: PMC10232003 DOI: 10.1172/jci170236] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
There is a large global unmet need for the development of countermeasures to combat hundreds of viruses known to cause human disease and for the establishment of a therapeutic portfolio for future pandemic preparedness. Most approved antiviral therapeutics target proteins encoded by a single virus, providing a narrow spectrum of coverage. This, combined with the slow pace and high cost of drug development, limits the scalability of this direct-acting antiviral (DAA) approach. Here, we summarize progress and challenges in the development of broad-spectrum antivirals that target either viral elements (proteins, genome structures, and lipid envelopes) or cellular proviral factors co-opted by multiple viruses via newly discovered compounds or repurposing of approved drugs. These strategies offer new means for developing therapeutics against both existing and emerging viral threats that complement DAAs.
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Affiliation(s)
- Marwah Karim
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
| | - Chieh-Wen Lo
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
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35
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Fong W, Rockett RJ, Agius JE, Chandra S, Johnson-Mckinnon J, Sim E, Lam C, Arnott A, Gall M, Draper J, Maddocks S, Chen S, Kok J, Dwyer D, O'Sullivan M, Sintchenko V. SABRes: in silico detection of drug resistance conferring mutations in subpopulations of SARS-CoV-2 genomes. BMC Infect Dis 2023; 23:303. [PMID: 37158832 PMCID: PMC10165565 DOI: 10.1186/s12879-023-08236-6] [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: 09/16/2022] [Accepted: 04/08/2023] [Indexed: 05/10/2023] Open
Abstract
The emergence of resistance to antiviral drugs increasingly used to treat SARS-CoV-2 infections has been recognised as a significant threat to COVID-19 control. In addition, some SARS-CoV-2 variants of concern appear to be intrinsically resistant to several classes of these antiviral agents. Therefore, there is a critical need for rapid recognition of clinically relevant polymorphisms in SARS-CoV-2 genomes associated with significant reduction of drug activity in virus neutralisation experiments. Here we present SABRes, a bioinformatic tool, which leverages on expanding public datasets of SARS-CoV-2 genomes and allows detection of drug resistance mutations in consensus genomes as well as in viral subpopulations. We have applied SABRes to detect resistance-conferring mutations in 25,197 genomes generated over the course of the SARS-CoV-2 pandemic in Australia and identified 299 genomes containing resistance conferring mutations to the five antiviral therapeutics that retain effectiveness against currently circulating strains of SARS-CoV-2 - Sotrovimab, Bebtelovimab, Remdesivir, Nirmatrelvir and Molnupiravir. These genomes accounted for a 1.18% prevalence of resistant isolates discovered by SABRes, including 80 genomes with resistance conferring mutations found in viral subpopulations. Timely recognition of these mutations within subpopulations is critical as these mutations can provide an advantage under selective pressure and presents an important step forward in our ability to monitor SARS-CoV-2 drug resistance.
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Affiliation(s)
- Winkie Fong
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia.
| | - Rebecca J Rockett
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Jessica E Agius
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Shona Chandra
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
| | - Jessica Johnson-Mckinnon
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Eby Sim
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Connie Lam
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Alicia Arnott
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Mailie Gall
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Jenny Draper
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Sharon Chen
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Jen Kok
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Dominic Dwyer
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Matthew O'Sullivan
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
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Khadilkar A, Bunch ZL, Wagoner J, Ravindran V, Oda JM, Vidar WS, Clark TN, Manwill PK, Todd DA, Barr SA, Olinger LK, Fink SL, Strangman WK, Linington RG, MacMillan JB, Cech NB, Polyak SJ. Modulation of in Vitro SARS-CoV-2 Infection by Stephania tetrandra and Its Alkaloid Constituents. JOURNAL OF NATURAL PRODUCTS 2023; 86:1061-1073. [PMID: 37043739 PMCID: PMC10108733 DOI: 10.1021/acs.jnatprod.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Indexed: 05/05/2023]
Abstract
Botanical natural products have been widely consumed for their purported usefulness against COVID-19. Here, six botanical species from multiple sources and 173 isolated natural product compounds were screened for blockade of wild-type (WT) SARS-CoV-2 infection in human 293T epithelial cells overexpressing ACE-2 and TMPRSS2 protease (293TAT). Antiviral activity was demonstrated by an extract from Stephania tetrandra. Extract fractionation, liquid chromatography-mass spectrometry (LC-MS), antiviral assays, and computational analyses revealed that the alkaloid fraction and purified alkaloids tetrandrine, fangchinoline, and cepharanthine inhibited WT SARS-CoV-2 infection. The alkaloids and alkaloid fraction also inhibited the delta variant of concern but not WT SARS-CoV-2 in VeroAT cells. Membrane permeability assays demonstrate that the alkaloids are biologically available, although fangchinoline showed lower permeability than tetrandrine. At high concentrations, the extract, alkaloid fractions, and pure alkaloids induced phospholipidosis in 293TAT cells and less so in VeroAT cells. Gene expression profiling during virus infection suggested that alkaloid fraction and tetrandrine displayed similar effects on cellular gene expression and pathways, while fangchinoline showed distinct effects on cells. Our study demonstrates a multifaceted approach to systematically investigate the diverse activities conferred by complex botanical mixtures, their cell-context specificity, and their pleiotropic effects on biological systems.
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Affiliation(s)
- Aswad Khadilkar
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95964, United States
| | - Zoie L. Bunch
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Jessica Wagoner
- Department
of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington 98195,United States
| | - Vandana Ravindran
- Oslo
Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Oslo 0313, Norway
| | - Jessica M. Oda
- Department
of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington 98195,United States
| | - Warren S. Vidar
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Trevor N. Clark
- Department
of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Preston K. Manwill
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Daniel A. Todd
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Sarah A. Barr
- Department
of Chemistry and Biochemistry, University
of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Lauren K. Olinger
- Department
of Biology and Marine Biology, University
of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Susan L. Fink
- Department
of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington 98195,United States
| | - Wendy K. Strangman
- Department
of Chemistry and Biochemistry, University
of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Roger G. Linington
- Department
of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - John B. MacMillan
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95964, United States
| | - Nadja B. Cech
- Department
of Chemistry and Biochemistry, University
of North Carolina, Greensboro, North Carolina 27412, United States
| | - Stephen J. Polyak
- Department
of Laboratory Medicine and Pathology, University
of Washington, Seattle, Washington 98195,United States
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37
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Payen SH, Gorzalski A, Siao DD, Pandori M, Verma SC, Rossetto CC. Analysis of SARS-CoV-2 variants from patient specimens in Nevada from October 2020 to August 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 111:105434. [PMID: 37059256 PMCID: PMC10098042 DOI: 10.1016/j.meegid.2023.105434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
In early 2020, the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population quickly developed into a global pandemic. SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19) which has a broad range of respiratory illnesses. As the virus circulates, it acquires nucleotide changes. These mutations are potentially due to the inherent differences in the selection pressures within the human population compared to the original zoonotic reservoir of SARS-CoV-2 and formerly naïve humans. The acquired mutations will most likely be neutral, but some may have implications for viral transmission, disease severity and resistance to therapies or vaccines. This is a follow-up study from our early report (Hartley et al. J Genet Genomics. 01202021;48(1):40-51) which detected a rare variant (nsp12, RdRp P323F) circulating within Nevada in mid 2020 at high frequency. The primary goals of the current study were to determine the phylogenetic relationship of the SARS-CoV-2 genomes within Nevada and to determine if there are any unusual variants within Nevada compared to the current database of SARS-CoV-2 sequences. Whole genome sequencing and analysis of SARS-CoV-2 from 425 positively identified nasopharyngeal/nasal swab specimens were performed from October 2020 to August 2021 to determine any variants that could result in potential escape from current therapeutics. Our analysis focused on nucleotide mutations that generated amino acid variations in the viral Spike (S) protein, Receptor binding domain (RBD) and the RNA-dependent RNA-polymerase (RdRp) complex. The data indicate that SARS-CoV-2 sequences from Nevada did not contain any unusual variants that had not been previously reported. Additionally, we did not detect the previously identified the RdRp P323F variant in any of the samples. This suggests that the rare variant we detected before was only able to circulate because of the stay-at-home orders and semi-isolation experience during the early months of the pandemic. IMPORTANCE: SARS-COV-2 continues to circulate in the human population. In this study, SARS-CoV-2 positive nasopharyngeal/nasal swab samples were used for whole genome sequencing to determine the phylogenetic relationship of SARS-CoV-2 sequences within Nevada from October 2020 to August 2021. The resulting data is being added to a continually growing database of SARS-CoV-2 sequences that will be important for understanding the transmission and evolution of the virus as it spreads around the globe.
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Affiliation(s)
- Shannon Harger Payen
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno
| | | | | | - Mark Pandori
- School of Medicine, University of Nevada, Reno; Nevada State Public Health Lab
| | - Subhash C Verma
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno
| | - Cyprian C Rossetto
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno.
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38
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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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39
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Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, Katzourakis A. The evolution of SARS-CoV-2. Nat Rev Microbiol 2023; 21:361-379. [PMID: 37020110 DOI: 10.1038/s41579-023-00878-2] [Citation(s) in RCA: 301] [Impact Index Per Article: 301.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
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Affiliation(s)
- Peter V Markov
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
- London School of Hygiene & Tropical Medicine, University of London, London, UK.
| | - Mahan Ghafari
- Big Data Institute, University of Oxford, Oxford, UK
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos I Stilianakis
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
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40
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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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41
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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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42
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Hamad M, AlKhamach DMH, Alsayadi LM, Sarhan SA, Saeed BQ, Sokovic M, Ben Hadda T, Soliman SSM. Alpha to Omicron (Variants of Concern): Mutation Journey, Vaccines, and Therapy. Viral Immunol 2023; 36:83-100. [PMID: 36695729 DOI: 10.1089/vim.2022.0122] [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: 01/26/2023] Open
Abstract
Coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initially emerged in December 2019 and has subsequently expanded globally, leading to the ongoing pandemic. The extensive spread of various SARS-CoV-2 variants possesses a serious public health threat. An extensive literature search along with deep analysis was performed to describe and evaluate the characteristics of SARS-CoV-2 variants of concern in relation to the effectiveness of the current vaccines and therapeutics. The obtained results showed that several significant mutations have evolved during the COVID-19 pandemic. The developed variants and their various structural mutations can compromise the effectiveness of several vaccines, escape the neutralizing antibodies, and limit the efficiency of available therapeutics. Furthermore, deep analysis of the available data enables the prediction of the future impact of virus mutations on the ongoing pandemic along with the selection of appropriate vaccines and therapeutics.
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Affiliation(s)
- Mohamad Hamad
- College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Dana M H AlKhamach
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | | | | | | | - Marina Sokovic
- Institute for Biological Research "Siniša Stanković," National Institute of the Republic of Serbia, University of Belgrade, Beograd, Serbia
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Sameh S M Soliman
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
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43
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Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform. iScience 2023; 26:105944. [PMID: 36644320 PMCID: PMC9822553 DOI: 10.1016/j.isci.2023.105944] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/07/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Reliable, easy-to-handle phenotypic screening platforms are needed for the identification of anti-SARS-CoV-2 compounds. Here, we present caspase 3/7 activity as a readout for monitoring the replication of SARS-CoV-2 isolates from different variants, including a remdesivir-resistant strain, and of other coronaviruses in numerous cell culture models, independently of cytopathogenic effect formation. Compared to other models, the Caco-2 subline Caco-2-F03 displayed superior performance. It possesses a stable SARS-CoV-2 susceptibility phenotype and does not produce false-positive hits due to drug-induced phospholipidosis. A proof-of-concept screen of 1,796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of phosphoglycerate dehydrogenase (PHGDH), CDC like kinase 1 (CLK-1), and colony stimulating factor 1 receptor (CSF1R). The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the hexokinase II (HK2) inhibitor 2-deoxy-D-glucose, which is in clinical development for COVID-19. In conclusion, caspase 3/7 activity detection in SARS-CoV-2-infected Caco-2-F03 cells provides a simple phenotypic high-throughput screening platform for SARS-CoV-2 drug candidates that reduces false-positive hits.
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44
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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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45
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Shannon A, Canard B. Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2. Antiviral Res 2023; 210:105501. [PMID: 36567022 PMCID: PMC9773703 DOI: 10.1016/j.antiviral.2022.105501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase for incorporation into the viral RNA genome. Incorporated analogues can either 'kill' (terminate) synthesis, or 'corrupt' (genetically or chemically) the RNA. Against coronaviruses, the use of NAs has been further complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities. Here, we describe the mechanism of action of four promising anti-COVID-19 NAs; remdesivir, molnupiravir, favipiravir and bemnifosbuvir. Their distinct mechanisms of action best exemplify the concept of 'killers' and 'corruptors'. We review available data regarding their ability to be incorporated and excised, and discuss the specific structural features that dictate their overall potency, toxicity, and mutagenic potential. This should guide the synthesis of novel analogues, lend insight into the potential for resistance mutations, and provide a rational basis for upcoming combinations therapies.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.
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46
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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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47
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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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48
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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. Nature 2023; 613:558-564. [PMID: 36351451 PMCID: PMC9849135 DOI: 10.1038/s41586-022-05514-2] [Citation(s) in RCA: 169] [Impact Index Per Article: 169.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/02/2022] [Indexed: 11/10/2022]
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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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hiroshi Mohri
- 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
| | - Bruce Culbertson
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Medical Scientist Training Program, 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
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - 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
| | - Medini K Annavajhala
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yicheng Guo
- 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
| | - Zizhang Sheng
- 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
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, 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
| | - 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
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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49
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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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50
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Varricchio C, Mathez G, Pillonel T, Bertelli C, Kaiser L, Tapparel C, Brancale A, Cagno V. 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] [Key Words] [MESH Headings] [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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Affiliation(s)
- Carmine Varricchio
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff, King Edward VII Avenue, Cardiff, UK
| | - Gregory Mathez
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, University of Geneva, Geneva, Switzerland; Center for Emerging Viruses, Geneva University Hospitals, 1205, Geneva, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva, 1206, Geneva, Switzerland
| | - Andrea Brancale
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff, King Edward VII Avenue, Cardiff, UK
| | - Valeria Cagno
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland.
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