1
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Wong CKH, Lau JJ, Au ICH, Lau KTK, Hung IFN, Peiris M, Leung GM, Wu JT. Optimal timing of nirmatrelvir/ritonavir treatment after COVID-19 symptom onset or diagnosis: target trial emulation. Nat Commun 2023; 14:8377. [PMID: 38104114 PMCID: PMC10725470 DOI: 10.1038/s41467-023-43706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023] Open
Abstract
Reports of symptomatic rebound and/or test re-positivity among COVID-19 patients following the standard five-day treatment course of nirmatrelvir/ritonavir have sparked debates regarding optimal treatment timing and dosage. It is unclear whether initiating nirmatrelvir/ritonavir immediately after symptom onset would improve clinical outcomes and/or lead to post-treatment viral burden rebound due to inadequate viral clearance during treatment. Here we show that, by emulating a randomized target trial using real-world electronic medical record data from all 87,070 adult users of nirmatrelvir/ritonavir in Hong Kong between 16th March 2022 and 15th January 2023, early initiation of nirmatrelvir/ritonavir treatment (0 to 1 days after symptom onset or diagnosis) significantly reduced the incidence of 28-day all-cause mortality and hospitalization compared to delayed initiation (2 or more days) (absolute risk reduction [ARR]: 1.50% (95% confidence interval 1.17-1.80%); relative risk [RR]: 0.77 (0.73, 0.82)), but may be associated with a significant elevated risk of viral burden rebound (ARR: -1.08% (-1.55%, -0.46%)), although the latter estimates were associated with high uncertainty due to limited sample sizes. As such, patients should continue to initiate nirmatrelvir/ritonavir early after symptom onset or diagnosis to better protect against the more serious outcomes of hospitalization and mortality.
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Affiliation(s)
- Carlos K H Wong
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Family Medicine and Primary Care, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Vaccine Confidence Project, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Jonathan J Lau
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ivan C H Au
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kristy T K Lau
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ivan F N Hung
- Infectious Diseases Division, Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong SAR, China
| | - Gabriel M Leung
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Joseph T Wu
- Laboratory of Data Discovery for Health (D24H), Hong Kong SAR, China.
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
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2
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Liu Z, Li J, Pei S, Lu Y, Li C, Zhu J, Chen R, Wang D, Sun J, Chen K. An updated review of epidemiological characteristics, immune escape, and therapeutic advances of SARS-CoV-2 Omicron XBB.1.5 and other mutants. Front Cell Infect Microbiol 2023; 13:1297078. [PMID: 38156316 PMCID: PMC10752979 DOI: 10.3389/fcimb.2023.1297078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023] Open
Abstract
The rapid evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to the emergence of new variants with different genetic profiles, with important implications for public health. The continued emergence of new variants with unique genetic features and potential changes in biological properties poses significant challenges to public health strategies, vaccine development, and therapeutic interventions. Omicron variants have attracted particular attention due to their rapid spread and numerous mutations in key viral proteins. This review aims to provide an updated and comprehensive assessment of the epidemiological characteristics, immune escape potential, and therapeutic advances of the SARS-CoV-2 Omicron XBB.1.5 variant, as well as other variants.
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Affiliation(s)
- Zongming Liu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiaxuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Shanshan Pei
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- School of Pharmacy, Beihua University, Jilin, China
| | - Ying Lu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Chaonan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiajie Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Ruyi Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Di Wang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jingbo Sun
- School of Pharmacy, Beihua University, Jilin, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
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3
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Bei ZC, Yu H, Wang H, Li Q, Wang B, Zhang D, Xu L, Zhao L, Dong S, Song Y. Orthogonal dual reporter-based gain-of-signal assay for probing SARS-CoV-2 3CL protease activity in living cells: inhibitor identification and mutation investigation. Emerg Microbes Infect 2023; 12:2211688. [PMID: 37144395 PMCID: PMC10187092 DOI: 10.1080/22221751.2023.2211688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/03/2023] [Indexed: 05/06/2023]
Abstract
ABSTRACTThe main protease (3-chymotrypsin-like protease, 3CLpro) of SARS-CoV-2 has become a focus of anti-coronavirus research. Despite efforts, drug development targeting 3CLpro has been hampered by limitations in the currently available activity assays. Additionally, the emergence of 3CLpro mutations in circulating SARS-CoV-2 variants has raised concerns about potential resistance. Both emphasize the need for a more reliable, sensitive, and facile 3CLpro assay. Here, we report an orthogonal dual reporter-based gain-of-signal assay for measuring 3CLpro activity in living cells. It builds on the finding that 3CLpro induces cytotoxicity and reporter expression suppression, which can be rescued by its inhibitor or mutation. This assay circumvents most limitations in previously reported assays, especially false positives caused by nonspecific compounds and signal interference from test compounds. It is also convenient and robust for high throughput screening of compounds and comparing the drug susceptibilities of mutants. Using this assay, we screened 1789 compounds, including natural products and protease inhibitors, with 45 compounds that have been reported to inhibit SARS-CoV-2 3CLpro among them. Except for the approved drug PF-07321332, only five of these inhibit 3CLpro in our assays: GC376; PF-00835231; S-217622; Boceprevir; and Z-FA-FMK. The susceptibilities of seven 3CLpro mutants prevalent in circulating variants to PF-07321332, S-217622, and GC376 were also assessed. Three mutants were identified as being less susceptible to PF-07321322 (P132H) and S-217622 (G15S, T21I). This assay should greatly facilitate the development of novel 3CLpro-targeted drugs and the monitoring of the susceptibility of emerging SARS-CoV-2 variants to 3CLpro inhibitors.
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Affiliation(s)
- Zhu-Chun Bei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Huanhuan Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
- The Affiliated AnNing First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People’s Republic of China
| | - Hong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Qingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
- Clinical Laboratory, Chinese People’s Liberation Army, Taiyuan, People’s Republic of China
| | - Baogang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Dongna Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Likun Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Liangliang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Shuwei Dong
- The Affiliated AnNing First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People’s Republic of China
| | - Yabin Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
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4
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Yang F, Tran TNA, Howerton E, Boni MF, Servadio JL. Benefits of near-universal vaccination and treatment access to manage COVID-19 burden in the United States. BMC Med 2023; 21:321. [PMID: 37620926 PMCID: PMC10463609 DOI: 10.1186/s12916-023-03025-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND As we continue the fourth year of the COVID-19 epidemic, SARS-CoV-2 infections still cause high morbidity and mortality in the United States. During 2020-2022, COVID-19 was one of the leading causes of death in the United States and by far the leading cause among infectious diseases. Vaccination uptake remains low despite this being an effective burden reducing intervention. The development of COVID-19 therapeutics provides hope for mitigating severe clinical outcomes. This modeling study examines combined strategies of vaccination and treatment to reduce the burden of COVID-19 epidemics over the next decade. METHODS We use a validated mathematical model to evaluate the reduction of incident cases, hospitalized cases, and deaths in the United States through 2033 under various levels of vaccination and treatment coverage. We assume that future seasonal transmission patterns for COVID-19 will be similar to those of influenza virus and account for the waning of infection-induced immunity and vaccine-induced immunity in a future with stable COVID-19 dynamics. Due to uncertainty in the duration of immunity following vaccination or infection, we consider three exponentially distributed waning rates, with means of 365 days (1 year), 548 days (1.5 years), and 730 days (2 years). We also consider treatment failure, including rebound frequency, as a possible treatment outcome. RESULTS As expected, universal vaccination is projected to eliminate transmission and mortality. Under current treatment coverage (13.7%) and vaccination coverage (49%), averages of 81,000-164,600 annual reported deaths, depending on duration of immunity, are expected by the end of this decade. Annual mortality in the United States can be reduced below 50,000 per year with 52-80% annual vaccination coverage and below 10,000 annual deaths with 59-83% annual vaccination coverage, depending on duration of immunity. Universal treatment reduces hospitalizations by 88.6% and deaths by 93.1% under current vaccination coverage. A reduction in vaccination coverage requires a comparatively larger increase in treatment coverage in order for hospitalization and mortality levels to remain unchanged. CONCLUSIONS Adopting universal vaccination and universal treatment goals in the United States will likely lead to a COVID-19 mortality burden below 50,000 deaths per year, a burden comparable to that of influenza virus.
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Affiliation(s)
- Fuhan Yang
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Thu Nguyen-Anh Tran
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Emily Howerton
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Maciej F Boni
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Joseph L Servadio
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
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5
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Qiu C, Wu Z, Liu X, Zhang Q, Wu L, Ye X, Zhou J, Shi J, Jiang X. Efficacy and safety of Nirmatrelvir/Ritonavir for treating the Omicron variant of COVID-19. Front Med (Lausanne) 2023; 10:1161193. [PMID: 37521354 PMCID: PMC10373876 DOI: 10.3389/fmed.2023.1161193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/30/2023] [Indexed: 08/01/2023] Open
Abstract
Objective To evaluate the efficacy and safety of Nirmatrelvir/Ritonavir in the treatment of the Omicron variant of coronavirus disease 2019 (COVID-19). Methods Data from 58 patients who were infected with the Omicron variant of COVID-19 were retrospectively collected. The patients were divided into two groups according to the treatment regimen they received. Patients in both groups were given Lianhua Qingwen capsules orally, three times/day, 6 g/time. The study group was given Nirmatrelvir 300 mg/Ritonavir 100 mg orally, q12h, for 5 days, and the control group was not given any antiviral drugs. The two groups were compared in terms of the change in computed tomography (CT) values of COVID-19 nucleic acid, the negative conversion time of COVID-19 RNA, hospitalization time, adverse drug reactions and COVID-19 nucleic acid re-positive tests. Results The time to increase the CT values in the study group was faster than that in the control group, and the CT values in the study group were significantly larger than in the control group on days four and seven (p < 0.05); The negative conversion time in the study group was shorter than the control group (Z = -2.424, p = 0.015), and the hospitalization time was also shorter (Z = -2.603, p = 0.009). There were no statistically significant adverse drug reactions during hospitalization in both groups (χ2 = 2.747, p = 0.097). None of the study group tested re-positive for SARS-CoV-2 nucleic acid after discharge. Conclusion The efficacy of Nirmatrelvir/Ritonavir in the treatment of the Omicron variant of COVID-19 was positive and had good tolerance in patients.
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Affiliation(s)
| | | | | | | | | | | | | | - Jichan Shi
- Department of Infection, Wenzhou Central Hospital, Dingli Clinical College of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiangao Jiang
- Department of Infection, Wenzhou Central Hospital, Dingli Clinical College of Wenzhou Medical University, Wenzhou, Zhejiang, China
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6
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Pagliano P, Spera A, Sellitto C, Scarpati G, Folliero V, Piazza O, Franci G, Conti V, Ascione T. Preclinical discovery and development of nirmatrelvir/ritonavir combinational therapy for the treatment of COVID-19 and the lessons learned from SARS-COV-2 variants. Expert Opin Drug Discov 2023; 18:1301-1311. [PMID: 37614103 DOI: 10.1080/17460441.2023.2248879] [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: 03/25/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023]
Abstract
INTRODUCTION Nirmatrelvir/ritonavir (Paxlovid®) represent an oral antiviral therapy approved for the treatment of COVID-19. Extensive in vitro and in vivo studies have reported the promising activity of nirmatrelvir/ritonavir against numerous emerging viruses. This combination consists of nirmatrelvir, a protease reversible inhibitor of coronavirus 3CLpro mainly metabolized by cytochrome P450 (CYP)3A4, and ritonavir, an inhibitor of the CYP3A isoforms that enhances the efficacy of nirmatrelvir by fixing its suboptimal pharmacokinetic properties. AREAS COVERED This review comprehensively examines the efficacy of nirmatrelvir/ritonavir through rigorous analysis of in vitro and in vivo studies. Moreover, it thoroughly assesses its safety, tolerability, pharmacokinetics, and antiviral efficacy against SARS-COV-2 infection, based on the main pre-authorization randomized controlled trials. EXPERT OPINION Nirmatrelvir/ritonavir has a good tolerability profile. Its administration during the early stages of mild-to-moderate COVID-19 holds potential benefits, as it can help prevent the onset of an aberrant immune response that could lead to pulmonary and extra-pulmonary complications. However, its drug - drug interactions can be a factor limiting its use, at least in populations on some chronic therapies, along with the risk of infection relapse after treatment.
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Affiliation(s)
- Pasquale Pagliano
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Infectious Diseases, University of Salerno, Baronissi, Italy
| | - Annamaria Spera
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Infectious Diseases, University of Salerno, Baronissi, Italy
| | - Carmine Sellitto
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Pharmacology, University of Salerno, Baronissi, Italy
| | - Giuliana Scarpati
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Anesthesiology, University of Salerno, Baronissi, Italy
| | - Veronica Folliero
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Unit of Microbiology, University of Salerno, Baronissi, Italy
| | - Ornella Piazza
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Anesthesiology, University of Salerno, Baronissi, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Unit of Microbiology, University of Salerno, Baronissi, Italy
| | - Valeria Conti
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", Unit of Pharmacology, University of Salerno, Baronissi, Italy
| | - Tiziana Ascione
- Department of Medicine, Service of Infectious Diseases, Cardarelli Hospital, Naples, Italy
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7
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Huijghebaert S, Parviz S, Rabago D, Baxter A, Chatterjee U, Khan FR, Fabbris C, Poulas K, Hsu S. Saline nasal irrigation and gargling in COVID-19: a multidisciplinary review of effects on viral load, mucosal dynamics, and patient outcomes. Front Public Health 2023; 11:1161881. [PMID: 37397736 PMCID: PMC10312243 DOI: 10.3389/fpubh.2023.1161881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
With unrelenting SARS-CoV-2 variants, additional COVID-19 mitigation strategies are needed. Oral and nasal saline irrigation (SI) is a traditional approach for respiratory infections/diseases. As a multidisciplinary network with expertise/experience with saline, we conducted a narrative review to examine mechanisms of action and clinical outcomes associated with nasal SI, gargling, spray, or nebulization in COVID-19. SI was found to reduce SARS-CoV-2 nasopharyngeal loads and hasten viral clearance. Other mechanisms may involve inhibition of viral replication, bioaerosol reduction, improved mucociliary clearance, modulation of ENaC, and neutrophil responses. Prophylaxis was documented adjunctive to personal protective equipment. COVID-19 patients experienced significant symptom relief, while overall data suggest lower hospitalization risk. We found no harm and hence recommend SI use, as safe, inexpensive, and easy-to-use hygiene measure, complementary to hand washing or mask-wearing. In view of mainly small studies, large well-controlled or surveillance studies can help to further validate the outcomes and to implement its use.
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Affiliation(s)
| | - Shehzad Parviz
- Medstar Health, Brooke Grove Rehabilitation Village, Sandy Spring, MD, United States
- Infectious Disease, Adventist Healthcare, White Oak Medical Center, Silver Spring, MD, United States
| | - David Rabago
- Departments of Family and Community Medicine and Public Health Sciences, Penn State College of Medicine, Pennsylvania, PA, United States
| | - Amy Baxter
- Department of Emergency Medicine, Augusta University, Augusta, GA, United States
| | - Uday Chatterjee
- Department of Paediatric Surgery, Park Medical Research and Welfare Society, Kolkata, West Bengal, India
| | - Farhan R. Khan
- Department of Surgery, Aga Khan University, Karachi, Pakistan
| | | | | | - Stephen Hsu
- Department of Oral Biology, Augusta University, Augusta, GA, United States
- Department of Oral Health and Diagnostic Sciences, Augusta University, Augusta, GA, United States
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8
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Fumagalli V, Di Lucia P, Ravà M, Marotta D, Bono E, Grassi S, Donnici L, Cannalire R, Stefanelli I, Ferraro A, Esposito F, Pariani E, Inverso D, Montesano C, Delbue S, Perlman S, Tramontano E, De Francesco R, Summa V, Guidotti LG, Iannacone M. Nirmatrelvir treatment of SARS-CoV-2-infected mice blunts antiviral adaptive immune responses. EMBO Mol Med 2023; 15:e17580. [PMID: 36946379 PMCID: PMC10165354 DOI: 10.15252/emmm.202317580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Abstract
Alongside vaccines, antiviral drugs are becoming an integral part of our response to the SARS-CoV-2 pandemic. Nirmatrelvir-an orally available inhibitor of the 3-chymotrypsin-like cysteine protease-has been shown to reduce the risk of progression to severe COVID-19. However, the impact of nirmatrelvir treatment on the development of SARS-CoV-2-specific adaptive immune responses is unknown. Here, by using mouse models of SARS-CoV-2 infection, we show that nirmatrelvir administration blunts the development of SARS-CoV-2-specific antibody and T cell responses. Accordingly, upon secondary challenge, nirmatrelvir-treated mice recruited significantly fewer memory T and B cells to the infected lungs and mediastinal lymph nodes, respectively. Together, the data highlight a potential negative impact of nirmatrelvir treatment with important implications for clinical management and might help explain the virological and/or symptomatic relapse after treatment completion reported in some individuals.
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Affiliation(s)
- Valeria Fumagalli
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Pietro Di Lucia
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Micol Ravà
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Davide Marotta
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Elisa Bono
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Stefano Grassi
- Pathology UnitIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Lorena Donnici
- INGM ‐ Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”MilanItaly
| | - Rolando Cannalire
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Irina Stefanelli
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Anastasia Ferraro
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell'AmbienteCittadella Universitaria di MonserratoCagliariItaly
| | - Elena Pariani
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
| | - Donato Inverso
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | | | - Serena Delbue
- Department of Biomedical, Surgical and Dental SciencesUniversity of MilanMilanItaly
| | - Stanley Perlman
- Department of Microbiology and ImmunologyUniversity of IowaIowa CityIAUSA
- Department of PediatricsUniversity of IowaIowa CityIAUSA
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'AmbienteCittadella Universitaria di MonserratoCagliariItaly
| | - Raffaele De Francesco
- INGM ‐ Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”MilanItaly
- Department of Pharmacological and Biomolecular SciencesUniversity of MilanMilanItaly
| | - Vincenzo Summa
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Luca G Guidotti
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Matteo Iannacone
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
- Experimental Imaging CenterIRCCS San Raffaele Scientific InstituteMilanItaly
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9
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Treating COVID-19: Targeting the Host Response, Not the Virus. Life (Basel) 2023; 13:life13030712. [PMID: 36983871 PMCID: PMC10054780 DOI: 10.3390/life13030712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 03/09/2023] Open
Abstract
In low- and middle-income countries (LMICs), inexpensive generic drugs like statins, ACE inhibitors, and ARBs, especially if used in combination, might be the only practical way to save the lives of patients with severe COVID-19. These drugs will already be available in all countries on the first pandemic day. Because they target the host response to infection instead of the virus, they could be used to save lives during any pandemic. Observational studies show that inpatient statin treatment reduces 28–30-day mortality but randomized controlled trials have failed to show this benefit. Combination treatment has been tested for antivirals and dexamethasone but, with the exception of one observational study in Belgium, not for inexpensive generic drugs. Future pandemic research must include testing combination generic drug treatments that could be used in LMICs.
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10
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Yang F, Tran TNA, Howerton E, Boni MF, Servadio JL. Benefits of near-universal vaccination and treatment access to manage COVID-19 burden in the United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.08.23285658. [PMID: 36798204 PMCID: PMC9934803 DOI: 10.1101/2023.02.08.23285658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Background As we enter the fourth year of the COVID-19 pandemic, SARS-CoV-2 infections still cause high morbidity and mortality in the United States. During 2020-2022, COVID-19 was one of the leading causes of death in the United States and by far the leading cause among infectious diseases. Vaccination uptake remains low despite this being an effective burden reducing intervention. The development of COVID-19 therapeutics provides hope for mitigating severe clinical outcomes. This modeling study examines combined strategies of vaccination and treatment to reduce the burden of COVID-19 epidemics over the next decade. Methods We use a validated mathematical model to evaluate the reduction of incident cases, hospitalized cases, and deaths in the United States through 2033 under various levels of vaccination and treatment coverage. We assume that future seasonal transmission patterns for COVID-19 will be similar to those of influenza virus. We account for the waning of infection-induced immunity and vaccine-induced immunity in a future with stable COVID-19 dynamics. Due to uncertainty in the duration of immunity following vaccination or infection, we consider two exponentially-distributed waning rates, with means of 365 days (one year) and 548 days (1.5 years). We also consider treatment failure, including rebound frequency, as a possible treatment outcome. Results As expected, universal vaccination is projected to eliminate transmission and mortality. Under current treatment coverage (13.7%) and vaccination coverage (49%), averages of 89,000 annual deaths (548-day waning) and 120,000 annual deaths (365-day waning) are expected by the end of this decade. Annual mortality in the United States can be reduced below 50,000 per year with >81% annual vaccination coverage, and below 10,000 annual deaths with >84% annual vaccination coverage. Universal treatment reduces hospitalizations by 88% and deaths by 93% under current vaccination coverage. A reduction in vaccination coverage requires a comparatively larger increase in treatment coverage in order for hospitalization and mortality levels to remain unchanged. Conclusions Adopting universal vaccination and universal treatment goals in the United States will likely lead to a COVID-19 mortality burden below 50,000 deaths per year, a burden comparable to that of influenza virus.
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Affiliation(s)
- Fuhan Yang
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, United States
| | - Thu Nguyen-Anh Tran
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, United States
| | - Emily Howerton
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, United States
| | - Maciej F Boni
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, United States
| | - Joseph L Servadio
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, United States
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Lan S, Neilsen G, Slack RL, Cantara WA, Castaner AE, Lorson ZC, Lulkin N, Zhang H, Lee J, Cilento ME, Tedbury PR, Sarafianos SG. Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.12.31.522389. [PMID: 36656782 PMCID: PMC9844013 DOI: 10.1101/2022.12.31.522389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The antiviral component of Paxlovid, nirmatrelvir (NIR), forms a covalent bond with Cys145 of SARS-CoV-2 nsp5. To explore NIR resistance we designed mutations to impair binding of NIR over substrate. Using 12 Omicron (BA.1) and WA.1 SARS-CoV-2 replicons, cell-based complementation and enzymatic assays, we showed that in both strains, E166V imparted high NIR resistance (∼55-fold), with major decrease in WA1 replicon fitness (∼20-fold), but not BA.1 (∼2-fold). WA1 replicon fitness was restored by L50F. These differences may contribute to a potentially lower barrier to resistance in Omicron than WA1. E166V is rare in untreated patients, albeit more prevalent in paxlovid-treated EPIC-HR clinical trial patients. Importantly, NIR-resistant replicons with E166V or E166V/L50F remained susceptible to a) the flexible GC376, and b) PF-00835231, which forms additional interactions. Molecular dynamics simulations show steric clashes between the rigid and bulky NIR t-butyl and β-branched V166 distancing the NIR warhead from its Cys145 target. In contrast, GC376, through "wiggling and jiggling" accommodates V166 and still covalently binds Cys145. PF-00835231 uses its strategically positioned methoxy-indole to form a β-sheet and overcome E166V. Drug design based on strategic flexibility and main chain-targeting may help develop second-generation nsp5-targeting antivirals efficient against NIR-resistant viruses.
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Padhi AK, Tripathi T. Hotspot residues and resistance mutations in the nirmatrelvir-binding site of SARS-CoV-2 main protease: Design, identification, and correlation with globally circulating viral genomes. Biochem Biophys Res Commun 2022; 629:54-60. [PMID: 36113178 PMCID: PMC9450486 DOI: 10.1016/j.bbrc.2022.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/15/2022]
Abstract
Shortly after the onset of the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has acquired numerous variations in its intracellular proteins to adapt quickly, become more infectious, and ultimately develop drug resistance by mutating certain hotspot residues. To keep the emerging variants at bay, including Omicron and subvariants, FDA has approved the antiviral nirmatrelvir for mild-to-moderate and high-risk COVID-19 cases. Like other viruses, SARS-CoV-2 could acquire mutations in its main protease (Mpro) to adapt and develop resistance against nirmatrelvir. Employing a unique high-throughput protein design technique, the hotspot residues, and signatures of adaptation of Mpro having the highest probability of mutating and rendering nirmatrelvir ineffective were identified. Our results show that ∼40% of the designed mutations in Mpro already exist in the globally circulating SARS-CoV-2 lineages and several predicted mutations. Moreover, several high-frequency, designed mutations were found to be in corroboration with the experimentally reported nirmatrelvir-resistant mutants and are naturally occurring. Our work on the targeted design of the nirmatrelvir-binding site offers a comprehensive picture of potential hotspot sites and resistance mutations in Mpro and is thus crucial in comprehending viral adaptation, robust antiviral design, and surveillance of evolving Mpro variations.
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India; Regional Director's Office, Indira Gandhi National Open University, Regional Centre Kohima, Kenuozou, Kohima, 797001, India.
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