1
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Huang S, Perry A, Sanchez Parra C, Gonzalez Torriente A, Ghumman H, Charkowick S, Colon J, Heide M, Jaglal M, Mhaskar R, Rico JF. Incidence of Thrombosis in COVID-19 Patients Compared to Non-COVID-19 Sepsis Patients in the Intensive Care Unit. J Clin Med 2024; 13:2974. [PMID: 38792515 PMCID: PMC11121895 DOI: 10.3390/jcm13102974] [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: 11/12/2023] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Background/Objectives: The hypercoagulable state associated with COVID-19 infection is associated with adverse outcomes and mortality. Studies have also demonstrated high rates of venous thromboembolism (VTE) events among patients with sepsis. We aimed to evaluate how the increase in thrombotic events in critically ill patients with COVID-19 infection compares to that of critically ill patients with non-COVID-19 sepsis. Methods: A chart review was performed of patients 18 years or older admitted to the intensive care unit (ICU) at Tampa General Hospital between 1 January 2020 and 31 December 2020 diagnosed with COVID-19 or sepsis secondary to other pathogens. Non-COVID-19 sepsis patients and COVID-19 patients were propensity-matched 3:1 on the Charlson Comorbidity Index. Multivariate analyses adjusting for confounding were conducted to report odds ratio (OR) and 95% confidence intervals (95% CIs) of predictors for thrombotic events and overall mortality. Results: After propensity score matching, 492 sepsis patients and 164 COVID-19 patients were included in the analysis. COVID-19 patients were significantly older (p = 0.021) and showed higher BMI (p < 0.001) than sepsis patients. COVID-19 patients did not show significantly higher odds of thrombosis after adjustment for confounders (OR 0.85, 95% CI 0.42-1.72), but had significantly lower odds of mortality than sepsis patients (OR 0.33, 95% CI 0.16-0.66). Conclusions: Our results suggest that further study is required to lower the rate of VTE in COVID-19 and non-COVID-19 sepsis patients admitted to the ICU; it is also reasonable to consider similar thromboembolism practices between these two patient groups.
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Affiliation(s)
- Sherri Huang
- Department of Internal Medicine and Pediatrics, University of South Florida, Tampa, FL 33606, USA
| | - Ashley Perry
- Department of Internal Medicine and Pediatrics, University of South Florida, Tampa, FL 33606, USA
| | - Carlos Sanchez Parra
- Department of Internal Medicine and Pediatrics, University of South Florida, Tampa, FL 33606, USA
- Division of Pediatric Cardiology, Texas Children’s Hospital, Houston, TX 77030, USA
| | | | - Haider Ghumman
- Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Shaun Charkowick
- Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Joshua Colon
- Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - McKenzi Heide
- Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Michael Jaglal
- Department of Hematology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Department of Hematology and Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Rahul Mhaskar
- Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Juan Felipe Rico
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL 33606, USA
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2
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Das T, Sikdar S, Chowdhury MHU, Nyma KJ, Adnan M. SARS-CoV-2 prevalence in domestic and wildlife animals: A genomic and docking based structural comprehensive review. Heliyon 2023; 9:e19345. [PMID: 37662720 PMCID: PMC10474441 DOI: 10.1016/j.heliyon.2023.e19345] [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: 01/22/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/05/2023] Open
Abstract
The SARS-CoV-2 virus has been identified as the infectious agent that led to the COVID-19 pandemic, which the world has seen very recently. Researchers have linked the SARS-CoV-2 outbreak to bats for the zoonotic spread of the virus to humans. Coronaviruses have a crown-like shape and positive-sense RNA nucleic acid. It attaches its spike glycoprotein to the host angiotensin-converting enzyme 2 (ACE2) receptor. Coronavirus genome comprises 14 ORFs and 27 proteins, spike glycoprotein being one of the most critical proteins for viral pathogenesis. Many mammals and reptiles, including bats, pangolins, ferrets, snakes, and turtles, serve as the principal reservoirs for this virus. But many experimental investigations have shown that certain domestic animals, including pigs, chickens, dogs, cats, and others, may also be able to harbor this virus, whether they exhibit any symptoms. These animals act as reservoirs for SARS-CoV, facilitating its zoonotic cross-species transmission to other species, including humans. In this review, we performed a phylogenetic analysis with multiple sequence alignment and pairwise evolutionary distance analysis, which revealed the similarity of ACE2 receptors in humans, chimpanzees, domestic rabbits, house mice, and golden hamsters. Pairwise RMSD analysis of the spike protein from some commonly reported SARS-CoV revealed that bat and pangolin coronavirus shared the highest structural similarity with human coronavirus. In a further experiment, molecular docking confirmed a higher affinity of pig, bat, and pangolin coronavirus spike proteins' affinity to the human ACE2 receptor. Such comprehensive structural and genomic analysis can help us to forecast the next likely animal source of these coronaviruses that may infect humans. To combat these zoonotic illnesses, we need a one health strategy that considers the well-being of people and animals and the local ecosystem.
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Affiliation(s)
- Tuhin Das
- Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Suranjana Sikdar
- Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Md. Helal Uddin Chowdhury
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram, 4331, Bangladesh
| | | | - Md. Adnan
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, 84112, United States
- Department of Pharmacy, International Islamic University Chittagong, Chattogram, 4318, Bangladesh
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3
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Zhang Y, Clarke SP, Wu H, Li W, Zhou C, Lin K, Wang J, Wang J, Liang Y, Wang X, Wang L. A comprehensive overview on the transmission, pathogenesis, diagnosis, treatment, and prevention of SARS-CoV-2. J Med Virol 2023; 95:e28776. [PMID: 37212261 DOI: 10.1002/jmv.28776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) is a single positive-strand RNA virus that is responsible for the current pandemic that the world has been facing since 2019. The primary route of transmission of SARS-CoV-2 is through respiratory tract transmission. However, other transmission routes such as fecal-oral, vertical transmission, and aerosol-eye also exist. In addition, it has been found that the pathogenesis of this virus involves the binding of the virus's S protein to its host cell surface receptor angiotensin-converting enzyme 2, which results in the subsequent membrane fusion that is required for SARS-CoV-2 to replicate and complete its entire life. The clinical symptoms of patients infected with SARS-CoV-2 can range from asymptomatic to severe. The most common symptoms seen include fever, dry cough, and fatigue. Once these symptoms are observed, a nucleic acid test is done using reverse transcription-polymerase chain reaction. This currently serves as the main confirmatory tool for COVID-19. Despite the fact that no cure has been found for SARS-CoV-2, prevention methods such as vaccines, specific facial mask, and social distancing have proven to be quite effective. It is imperative to have a complete understanding of the transmission and pathogenesis of this virus. To effectively develop new drugs as well as diagnostic tools, more knowledge about this virus would be needed.
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Affiliation(s)
- Yiting Zhang
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | | | - Huanwu Wu
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Wenli Li
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Chang Zhou
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Kang Lin
- Department of Basic Medical Sciences, Morphological Experimental Center, Anhui Medical University, Hefei, Anhui, China
| | - Jiawen Wang
- Department of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Jinzhi Wang
- Department of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Ying Liang
- Department of The Second Clinical School of Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Xin Wang
- Department of Chemistry, Anhui Medical University, Hefei, Anhui, China
| | - Linding Wang
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
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4
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Rudiansyah M, Jasim SA, Mohammad Pour ZG, Athar SS, Jeda AS, Doewes RI, Jalil AT, Bokov DO, Mustafa YF, Noroozbeygi M, Karampoor S, Mirzaei R. Coronavirus disease 2019 (COVID-19) update: From metabolic reprogramming to immunometabolism. J Med Virol 2022; 94:4611-4627. [PMID: 35689351 PMCID: PMC9350347 DOI: 10.1002/jmv.27929] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/22/2022] [Accepted: 06/09/2022] [Indexed: 12/15/2022]
Abstract
The field of immunometabolism investigates and describes the effects of metabolic rewiring in immune cells throughout activation and the fates of these cells. Recently, it has been appreciated that immunometabolism plays an essential role in the progression of viral infections, cancer, and autoimmune diseases. Regarding COVID‐19, the aberrant immune response underlying the progression of diseases establishes two major respiratory pathologies, including acute respiratory distress syndrome (ARDS) or pneumonia‐induced acute lung injury (ALI). Both innate and adaptive immunity (T cell‐based) were impaired in the course of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. Current findings have deciphered that macrophages (innate immune cells) are involved in the inflammatory response seen in COVID‐19. It has been demonstrated that immune system cells can change metabolic reprogramming in some conditions, including autoimmune diseases, cancer, and infectious disease, including COVID‐19. The growing findings on metabolic reprogramming in COVID‐19 allow an exploration of metabolites with immunomodulatory properties as future therapies to combat this hyperinflammatory response. The elucidation of the exact role and mechanism underlying this metabolic reprograming in immune cells could help apply more precise approaches to initial diagnosis, prognosis, and in‐hospital therapy. This report discusses the latest findings from COVID‐19 on host metabolic reprogramming and immunometabolic responses.
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Affiliation(s)
- Mohammad Rudiansyah
- Division of Nephrology & Hypertension, Department of Internal Medicine, Faculty of Medicine, Universitas Lambung Mangkurat/Ulin Hospital, Banjarmasin, Indonesia
| | - Saade Abdalkareem Jasim
- Medical Laboratory Techniques Department, Al-Maarif University College, Al-Anbar-Ramadi, Iraq
| | | | - Sara Sohrabi Athar
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran.,Department of Human Nutrition, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Ali Salimi Jeda
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rumi Iqbal Doewes
- Faculty of Sport, Universitas Sebelas Maret, Kentingan, Surakarta, Indonesia
| | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla, Iraq
| | - D O Bokov
- Institute of Pharmacy, Sechenov First Moscow State Medical University, Moscow, Russian Federation.,Laboratory of Food Chemistry, Federal Research Center of Nutrition, Biotechnology and Food Safety, Moscow, Russian Federation
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, Iraq
| | - Mina Noroozbeygi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sajad Karampoor
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.,Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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5
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Emergence of SARS-CoV-2 New Variants and Their Clinical Significance. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:7336309. [PMID: 35669528 PMCID: PMC9167142 DOI: 10.1155/2022/7336309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/17/2022] [Accepted: 04/28/2022] [Indexed: 12/23/2022]
Abstract
COVID-19 is a respiration-related disease caused by SARS-CoV-2 and was identified in China's Wuhan city. More than 223 countries are affected by the disease worldwide. The new variants of the COVID-19 virus are causing problems, from average to life-threatening pneumonia and acute respiratory distress syndrome (ARDS). Presently, there are 170 vaccine candidates, out of which 10 have been approved by the WHO for vaccination, such as Ad26.COV2.S, Pfizer/BioNTech, COVISHIELD, Covovax, Moderna, KoviVac, and some other vaccines to combat the deadly SARS-CoV-2 infection. From all these vaccines, Pfizer/BioNTech and Moderna are showing the highest efficacy against COVID-19. These vaccines are highly efficient against COVID-19 disease, but their potentiality against new variants remains a question. COVID-19 vaccines are highly effective at preventing severe illnesses, hospitalizations, and death. The antibodies elicited by earlier infection or vaccination are the key for possible protection against SARS-CoV-2. The problem has been exacerbated by new information from Africa on the origins of the novel contagious SARS-CoV-2 strain. These new strains occur due to unique mutations in the spike protein, which modify SARS-CoV-2 transmission and infection capabilities, limiting the efficacy of the COVID-19 vaccination. Hence, there is a need to find a potential vaccine against it.
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6
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Chung DR. Responses against infectious disease pandemics: a narrative review on COVID-19. PRECISION AND FUTURE MEDICINE 2021. [DOI: 10.23838/pfm.2021.00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Currently, the world is facing the coronavirus disease 2019 (COVID-19) pandemic. With this, an emerging infectious disease pandemic in the absence of effective antiviral agents and vaccines for a novel virus is no different from the 1918 influenza pandemic, which became a great disaster for humankind. We also experienced a global lockdown with a stringent implementation of social distancing, which is a first for mankind living in the present day, and has led to enormous economic damage and restrictions on individual freedom. The microorganism that will cause the next pandemic may be a highly fatal avian influenza virus, another coronavirus, or a completely different microorganism. This COVID-19 pandemic is an enormous lesson for humankind and is tantamount to a vaccine in preparation for the next pandemic. Important and urgent undertakings were given to each country in terms of complementing laws and regulations for a stronger and more resilient healthcare system, such as investment in research and development for new rapid diagnostic technologies, vaccines, new therapeutic agents, among others.
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7
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Li C, He Q, Qian H, Liu J. Overview of the pathogenesis of COVID-19 (Review). Exp Ther Med 2021; 22:1011. [PMID: 34345293 PMCID: PMC8311250 DOI: 10.3892/etm.2021.10444] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/21/2021] [Indexed: 01/08/2023] Open
Abstract
At present, the pathogenesis of the novel coronavirus disease 2019 (COVID-19) has not been fully elucidated. Clinical and experimental findings from studies investigating COVID-19 have suggested that the immune-inflammatory response has a crucial role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The present article aimed to systematically review the available literature on the pathogenesis of COVID-19. Severe COVID-19 is characterized by organ dysfunction, hypercytokinemia and lymphopenia. It is assumed that the direct cytopathological damage of host cells and the dysregulated immune response caused by SARS-CoV-2 may be the primary underlying mechanisms of COVID-19. Based on the published literature, this review attempts to provide an integrated view of the immunological mechanisms and the potential pathogenesis of COVID-19, providing an in-depth summary of the host-pathogen interaction and host immune responses. It is of great importance to elucidate the possible pathogenesis of COVID-19 to determine the direction of future research.
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Affiliation(s)
- Chao Li
- Department of Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215001, P.R. China
| | - Qifang He
- Department of Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215001, P.R. China
| | - Hebu Qian
- Department of Critical Care Medicine, Suzhou Ninth People's Hospital, The Affiliated Wujiang Hospital of Nantong University, Suzhou, Jiangsu 215001, P.R. China
| | - Jun Liu
- Department of Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215001, P.R. China
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8
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Beeraka NM, Tulimilli SV, Karnik M, Sadhu SP, Pragada RR, Aliev G, Madhunapantula SV. The Current Status and Challenges in the Development of Vaccines and Drugs against Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2). BIOMED RESEARCH INTERNATIONAL 2021; 2021:8160860. [PMID: 34159203 PMCID: PMC8168478 DOI: 10.1155/2021/8160860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 04/16/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection causes coronavirus disease-19 (COVID-19), which is characterized by clinical manifestations such as pneumonia, lymphopenia, severe acute respiratory distress, and cytokine storm. S glycoprotein of SARS-CoV-2 binds to angiotensin-converting enzyme II (ACE-II) to enter into the lungs through membrane proteases consequently inflicting the extensive viral load through rapid replication mechanisms. Despite several research efforts, challenges in COVID-19 management still persist at various levels that include (a) availability of a low cost and rapid self-screening test, (b) lack of an effective vaccine which works against multiple variants of SARS-CoV-2, and (c) lack of a potent drug that can reduce the complications of COVID-19. The development of vaccines against SARS-CoV-2 is a complicated process due to the emergence of mutant variants with greater virulence and their ability to invoke intricate lung pathophysiology. Moreover, the lack of a thorough understanding about the virus transmission mechanisms and complete pathogenesis of SARS-CoV-2 is making it hard for medical scientists to develop a better strategy to prevent the spread of the virus and design a clinically viable vaccine to protect individuals from being infected. A recent report has tested the hypothesis of T cell immunity and found effective when compared to the antibody response in agammaglobulinemic patients. Understanding SARS-CoV-2-induced changes such as "Th-2 immunopathological variations, mononuclear cell & eosinophil infiltration of the lung and antibody-dependent enhancement (ADE)" in COVID-19 patients provides key insights to develop potential therapeutic interventions for immediate clinical management. Therefore, in this review, we have described the details of rapid detection methods of SARS-CoV-2 using molecular and serological tests and addressed different therapeutic modalities used for the treatment of COVID-19 patients. In addition, the current challenges against the development of vaccines for SARS-CoV-2 are also briefly described in this article.
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Affiliation(s)
- Narasimha M. Beeraka
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
- Sechenov First Moscow State Medical University (Sechenov University), St. Trubetskaya, 8, Bld. 2, Moscow 119991, Russia
| | - SubbaRao V. Tulimilli
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
| | - Medha Karnik
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
| | - Surya P. Sadhu
- AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, 530003 Andhra Pradesh, India
| | - Rajeswara Rao Pragada
- AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, 530003 Andhra Pradesh, India
| | - Gjumrakch Aliev
- Sechenov First Moscow State Medical University (Sechenov University), St. Trubetskaya, 8, Bld. 2, Moscow 119991, Russia
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, Moscow Region 142432, Russia
- Research Institute of Human Morphology, 3Tsyurupy Street, Moscow 117418, Russia
- GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX 78229, USA
| | - SubbaRao V. Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
- Special Interest Group in Cancer Biology and Cancer Stem Cells (SIG-CBCSC), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysore, 570015 Karnataka, India
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9
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Khursheed A, Jain V, Rasool A, Rather MA, Malik NA, Shalla AH. Molecular scaffolds from mother nature as possible lead compounds in drug design and discovery against coronaviruses: A landscape analysis of published literature and molecular docking studies. Microb Pathog 2021; 157:104933. [PMID: 33984466 PMCID: PMC8110334 DOI: 10.1016/j.micpath.2021.104933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 12/23/2022]
Abstract
The recent outbreak of viral infection and its transmission has highlighted the importance of its slowdown for the safeguard of public health, globally. The identification of novel drugs and efficient therapies against these infectious viruses is need of the hour. The eruption of COVID-19 is caused by a novel acute respiratory syndrome virus SARS-CoV-2 which has taken the whole world by storm as it has transformed into a global pandemic. This lethal syndrome is a global health threat to general public which has already affected millions of people. Despite the development of some potential vaccines and repurposed drugs by some Pharma companies, this health emergency needs more attention due to the less efficacy of these vaccines coupled with the emergence of novel and resistant strains of SARS-CoV-2. Due to enormous structural diversity and biological applications, natural products are considered as a wonderful source of drugs for such diseases. Natural product based drugs constitute a substantial proportion of the pharmaceutical market particularly in the therapeutic areas of infectious diseases and oncology. The naturally occurring bioactive antiviral phytochemicals including alkaloids, flavonoids and peptides have been subjected to virtual screening against COVID-19. Since there is no specific medicine available for the treatment of Covid-19, designing new drugs using in silico methods plays an all important role to find that magic bullet which can target this lethal virus. The in silico method is not only quick but economical also when compared to the other conventional methods which are hit and trial methods. Based on this in silico approach, various natural products have been recently identified which might have a potential to inhibit COVID-19 outbreak. These natural products have been shown by these docking studies to interact with the spike protein of the novel coronavirus. This spike protein has been shown to bind to a transmembrane protein called Angiotensin converting enzyme 2 (ACE2), this protein acts as a receptor for the viral spike protein. This comprehensive review article anticipates providing a summary of the authentic and peer reviewed published literature about the potential of natural metabolites that can be developed into possible lead compounds against this new threat of Covid-19. Main focus of the article will be to highlight natural sources of potential anti-coronavirus molecules, mechanism of action, docking studies and the target proteins as well as their toxicity profiles. This review article intends to provide a starting point for the research endeavors that are needed for the design and development of drugs based on pure natural products, their synthetic or semi-synthetic derivatives and standardized plant extracts. This review article will be highly helpful for scientists who are working or intend to work on antiviral drugs from natural sources.
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Affiliation(s)
- Aadil Khursheed
- Department of Chemistry, Madhyanchal Professional University, Ratibad, Bhopal, 462044, Madhya Pradesh, India
| | - Vikrant Jain
- Department of Chemistry, Madhyanchal Professional University, Ratibad, Bhopal, 462044, Madhya Pradesh, India
| | - Ajaz Rasool
- Department of Zoology, University of Kashmir, Srinagar, 190006, India
| | - Manzoor A Rather
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India.
| | - Nisar Ahmad Malik
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India
| | - Aabid Hussain Shalla
- Department of Chemistry, Islamic University of Science and Technology, Awanti Pora, 192122, Jammu and Kashmir, India
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10
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Spratt AN, Gallazzi F, Quinn TP, Lorson CL, Sönnerborg A, Singh K. Coronavirus helicases: attractive and unique targets of antiviral drug-development and therapeutic patents. Expert Opin Ther Pat 2021; 31:339-350. [PMID: 33593200 PMCID: PMC8074651 DOI: 10.1080/13543776.2021.1884224] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction: Coronaviruses encode a helicase that is essential for viral replication and represents an excellent antiviral target. However, only a few coronavirus helicase inhibitors have been patented. These patents include drug-like compound SSYA10-001, aryl diketo acids (ADK), and dihydroxychromones. Additionally, adamantane-derived bananins, natural flavonoids, one acrylamide derivative [(E)-3-(furan-2-yl)-N-(4-sulfamoylphenyl)acrylamide], a purine derivative (7-ethyl-8-mercapto-3-methyl-3,7-dihydro-1 H-purine-2,6-dione), and a few bismuth complexes. The IC50 of patented inhibitors ranges between 0.82 μM and 8.95 μM, depending upon the assays used. Considering the urgency of clinical interventions against Coronavirus Disease-19 (COVID-19), it is important to consider developing antiviral portfolios consisting of small molecules. Areas covered: This review examines coronavirus helicases as antiviral targets, and the potential of previously patented and experimental compounds to inhibit the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) helicase. Expert opinion: Small molecule coronavirus helicase inhibitors represent attractive pharmacological modalities for the treatment of coronaviruses such as SARS-CoV and SARS-CoV-2. Rightfully so, the current emphasis is focused upon the development of vaccines. However, vaccines may not work for everyone and broad-based adoption of vaccinations is an increasingly challenging societal endeavor. Therefore, it is important to develop additional pharmacological antivirals against the highly conserved coronavirus helicases to broadly protect against this and subsequent coronavirus epidemics.
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Affiliation(s)
- Austin N Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Fabio Gallazzi
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Thomas P Quinn
- cDepartment of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,dDepartment of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- eDivision of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,fDepartment of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,gSanctum Therapeutics Corporation, Sunnyvale, CA, USA
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11
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Beig Parikhani A, Bazaz M, Bamehr H, Fereshteh S, Amiri S, Salehi-Vaziri M, Arashkia A, Azadmanesh K. The Inclusive Review on SARS-CoV-2 Biology, Epidemiology, Diagnosis, and Potential Management Options. Curr Microbiol 2021; 78:1099-1114. [PMID: 33638671 PMCID: PMC7913045 DOI: 10.1007/s00284-021-02396-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/07/2021] [Indexed: 12/18/2022]
Abstract
A novel coronavirus member was reported in Wuhan City, Hubei Province, China, at the end of the year 2019. Initially, the infection spread locally, affecting the Wuhan people, and then expanded rapidly throughout the world. On 11 March 2020, the World Health Organization (WHO) proclaimed it a global pandemic. The virus is a new strain most closely related to a bat coronavirus (RaTG13) which was not previously discovered in humans and is now formally known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus disease 2019 (COVID-19) is the disease syndrome that the SARS-CoV-2 virus triggers. It is suggested that SARS-CoV-2 can be transmitted through aerosols, direct/indirect contact, and also during medical procedures and specimen handling. The infection is characterized by isolated flu-like symptoms, but there may be specific signs of fever, fatigue, cough, and shortness of breath, as well as the loss of smell and breathing difficulty. Within this report, we tried to review the most current scientific literature published by January 2021 on various aspects of the outbreak, including virus structure, pathogenesis, clinical presentation, epidemiology, diagnostic approaches, potential therapeutics and vaccines, and prospects. We hope this article makes a beneficial impact on public education to better deal with the SARS-CoV-2 crisis and push a step forward in the near term towards its prevention and control.
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Affiliation(s)
- Arezoo Beig Parikhani
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Masoume Bazaz
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Hadi Bamehr
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Shahin Amiri
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mostafa Salehi-Vaziri
- Department of Arboviruses and Viral Hemorrhagic Fevers, Pasteur Institute of Iran, Tehran, Iran
- Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Arash Arashkia
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.
- Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
| | - Kayhan Azadmanesh
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
- Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
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12
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Zhang E, Lequesne E, Rohs A, Frankle WG. Suspected Recurrence of Symptomatic COVID-19: Management During Inpatient Psychiatric Treatment. J Psychiatr Pract 2021; 27:137-144. [PMID: 33656821 PMCID: PMC8043330 DOI: 10.1097/pra.0000000000000534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The widespread prevalence of coronavirus disease 2019 (COVID-19) means that inpatient psychiatric units will necessarily manage patients who have COVID-19 that is comorbid with acute psychiatric symptoms. We report a case of recurrence of respiratory symptoms and positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription-polymerase chain reaction (RT-PCR) testing in a patient on an inpatient psychiatric unit occurring 42 days after the initial positive SARS-CoV-2 RT-PCR test, 38 days after initial symptom resolution, and 30 days after the first of 3 negative SARS-CoV-2 RT-PCR tests. Over the course of the admission, the patient was safely initiated on clozapine. Recent literature on COVID-19's potential recurrence and neuropsychiatric effects is reviewed and implications for the management of COVID-19 on inpatient psychiatric units are discussed. In the era of COVID-19 and our still-developing understanding of this illness, psychiatrists' role as advocates and collaborators in our patients' physical health care has become even more critical.
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13
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Molaei S, Dadkhah M, Asghariazar V, Karami C, Safarzadeh E. The immune response and immune evasion characteristics in SARS-CoV, MERS-CoV, and SARS-CoV-2: Vaccine design strategies. Int Immunopharmacol 2021; 92:107051. [PMID: 33429331 PMCID: PMC7522676 DOI: 10.1016/j.intimp.2020.107051] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 01/25/2023]
Abstract
The worldwide outbreak of SARS-CoV-2, severe acute respiratory syndrome coronavirus 2 as a novel human coronavirus, was the worrying news at the beginning of 2020. Since its emergence complicated more than 870,000 individuals and led to more than 43,000 deaths worldwide. Considering to the potential threat of a pandemic and transmission severity of it, there is an urgent need to evaluate and realize this new virus's structure and behavior and the immunopathology of this disease to find potential therapeutic protocols and to design and develop effective vaccines. This disease is able to agitate the response of the immune system in the infected patients, so ARDS, as a common consequence of immunopathological events for infections with Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, and SARS-CoV-2, could be the main reason for death. Here, we summarized the immune response and immune evasion characteristics in SARS-CoV, MERS-CoV, and SARS-CoV-2 and therapeutic and prophylactic strategies with a focus on vaccine development and its challenges.
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Affiliation(s)
- Soheila Molaei
- Deputy of Research & Technology, Ardabil University of Medical Sciences, Ardabil, Iran; Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Masoomeh Dadkhah
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran; Department of Pharmacology, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Vahid Asghariazar
- Deputy of Research & Technology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Chiman Karami
- Department of Microbiology, Parasitology, and Immunology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Elham Safarzadeh
- Department of Microbiology, Parasitology, and Immunology, Ardabil University of Medical Sciences, Ardabil, Iran.
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14
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Mirzaei R, Mohammadzadeh R, Mahdavi F, Badrzadeh F, Kazemi S, Ebrahimi M, Soltani F, Kazemi S, Jeda AS, Darvishmotevalli M, Yousefimashouf R, Keyvani H, Karampoor S. Overview of the current promising approaches for the development of an effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine. Int Immunopharmacol 2020; 88:106928. [PMID: 32862110 PMCID: PMC7444935 DOI: 10.1016/j.intimp.2020.106928] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by the novel coronavirus called SARS-CoV-2. There is a gap in our understanding regarding the immunopathogenesis of COVID-19. However, many clinical trials are underway across the world for screening effective drugs against COVID-19. Nevertheless, currently, no proven effective therapies for this virus exists. The vaccines are deemed as a significant part of disease prevention for emerging viral diseases, since, in several cases, other therapeutic choices are limited or non-existent, or that diseases result in such an accelerated clinical worsening that the efficacy of treatments is restricted. Therefore, effective vaccines against COVID-19 are urgently required to overcome the tremendous burden of mortality and morbidity correlated with SARS-CoV-2. In this review, we will describe the latest evidence regarding outstanding vaccine approaches and the challenges for vaccine production.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Rokhsareh Mohammadzadeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farzad Mahdavi
- Department of Medical Parasitology and Mycology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fariba Badrzadeh
- Faculty of Medicine, Golestan University of Medical Sciences, Golestan, Iran
| | - Sheida Kazemi
- Students' Seientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Ebrahimi
- Department of Environmental Health, School of Health, Guilan University of Medical Sciences, Rasht, Iran
| | - Fatemeh Soltani
- Health Safety and Environment Management Department, Azad University, Ahvaz Branch, Ahvaz, Iran
| | - Sima Kazemi
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Salimi Jeda
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Darvishmotevalli
- Research Center For Health, Safety And Environment (RCHSE), Alborz University of Medical Sciences, Karaj, Iran
| | - Rasoul Yousefimashouf
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Sajad Karampoor
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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15
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Olotu FA, Omolabi KF, Soliman MES. Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain. INFORMATICS IN MEDICINE UNLOCKED 2020; 21:100451. [PMID: 33083517 PMCID: PMC7561517 DOI: 10.1016/j.imu.2020.100451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/11/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023] Open
Abstract
The systematic entry of SARS-CoV-2 into host cells, as mediated by its Spike (S) protein, is highly essential for pathogenicity in humans. Hence, targeting the viral entry mechanisms remains a major strategy for COVID-19 treatment. Although recent efforts have focused on the direct inhibition of S-protein receptor-binding domain (RBD) interactions with human angiotensin-converting enzyme 2 (hACE2), allosteric targeting remains an unexplored possibility. Therefore, in this study, for the first time, we employed an integrative meta-analytical approach to investigate the allosteric inhibitory mechanisms of SARS-CoV-2 S-protein and its association with hACE2. Findings revealed two druggable sites (Sites 1 and 2) located at the N-terminal domain (NTD) and S2 regions of the protein. Two high-affinity binders; ZINC3939013 (Fosaprepitant - Site 1) and ZINC27990463 (Lomitapide - Site 2) were discovered via site-directed high-throughput screening against a library of ~1500 FDA approved drugs. Interestingly, we observed that allosteric binding of both compounds perturbed the prefusion S-protein conformations, which in turn, resulted in unprecedented hACE2 displacement from the RBD. Estimated ΔG binds for both compounds were highly favorable due to high-affinity interactions at the target sites. In addition, Site 1 residues; R190, H207, K206 and K187, I101, R102, I119, F192, L226, V126 and W104 were identified for their crucial involvement in the binding and stability of ZINC3939013. Likewise, energy contributions of Q957, N953, Q954, L303, Y313, Q314, L858, V952, N953, and A956 corroborated their importance to ZINC27990463 binding at the predicted Site 2. We believe these findings would pave way for the structure-based discovery of allosteric SARS-CoV-2 S-protein inhibitors for COVID-19 treatment.
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Affiliation(s)
- Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Kehinde F Omolabi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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16
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Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs. Pathogens 2020; 9:pathogens9050320. [PMID: 32357471 PMCID: PMC7281371 DOI: 10.3390/pathogens9050320] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKU1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and the newest SARS-CoV-2 (the causative agent of COVID-19) lead to severe and deadly diseases with mortality rates ranging between ~1 to 35% depending on factors such as age and pre-existing conditions. Despite continuous global health threats to humans, there are no approved vaccines or drugs targeting human CoVs, and the recent outbreak of COVID-19 emphasizes an urgent need for therapeutic interventions. Using computational and bioinformatics tools, here we present the feasibility of reported broad-spectrum RNA polymerase inhibitors as anti- SARS-CoV-2 drugs targeting its main RNA polymerase, suggesting that investigational and approved nucleoside RNA polymerase inhibitors have potential as anti-SARS-CoV-2 drugs. However, we note that it is also possible for SARS-CoV-2 to evolve and acquire drug resistance mutations against these nucleoside inhibitors.
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17
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Morse JS, Lalonde T, Xu S, Liu WR. Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV. Chembiochem 2020; 21:730-738. [PMID: 32022370 PMCID: PMC7162020 DOI: 10.1002/cbic.202000047] [Citation(s) in RCA: 495] [Impact Index Per Article: 123.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Indexed: 11/08/2022]
Abstract
With the current trajectory of the 2019-nCoV outbreak unknown, public health and medicinal measures will both be needed to contain spreading of the virus and to optimize patient outcomes. Although little is known about the virus, an examination of the genome sequence shows strong homology with its better-studied cousin, SARS-CoV. The spike protein used for host cell infection shows key nonsynonymous mutations that might hamper the efficacy of previously developed therapeutics but remains a viable target for the development of biologics and macrocyclic peptides. Other key drug targets, including RNA-dependent RNA polymerase and coronavirus main proteinase (3CLpro), share a strikingly high (>95 %) homology to SARS-CoV. Herein, we suggest four potential drug candidates (an ACE2-based peptide, remdesivir, 3CLpro-1 and a novel vinylsulfone protease inhibitor) that could be used to treat patients suffering with the 2019-nCoV. We also summarize previous efforts into drugging these targets and hope to help in the development of broad-spectrum anti-coronaviral agents for future epidemics.
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Affiliation(s)
- Jared S. Morse
- The Texas A&M Drug Discovery LaboratoryDepartment of ChemistryTexas A&M UniversityCollege StationTX77843USA
| | - Tyler Lalonde
- The Texas A&M Drug Discovery LaboratoryDepartment of ChemistryTexas A&M UniversityCollege StationTX77843USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery LaboratoryDepartment of ChemistryTexas A&M UniversityCollege StationTX77843USA
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery LaboratoryDepartment of ChemistryTexas A&M UniversityCollege StationTX77843USA
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18
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Morse JS, Lalonde T, Xu S, Liu W. Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020. [PMID: 32511285 DOI: 10.26434/chemrxiv.11728983.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
With the current trajectory of the 2019-nCoV outbreak unknown, public health and medicinal measures will both be needed to contain spreading of the virus and to optimize patient outcomes. While little is known about the virus, an examination of the genome sequence shows strong homology with its more well-studied cousin, SARS-CoV. The spike protein used for host cell infection shows key nonsynonymous mutations which may hamper efficacy of previously developed therapeutics but remains a viable target for the development of biologics and macrocyclic peptides. Other key drug targets, including RdRp and 3CLpro, share a strikingly high (>95%) homology to SARS-CoV. Herein, we suggest 4 potential drug candidates (an ACE2-based peptide, remdesivir, 3CLpro-1 and a novel vinylsulfone protease inhibitor) that can be used to treat patients suffering with the 2019-nCoV. We also summarize previous efforts into drugging these targets and hope to help in the development of broad spectrum anti-coronaviral agents for future epidemics.
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19
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Morse JS, Lalonde T, Xu S, Liu WR. Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:11728983. [PMID: 32511285 PMCID: PMC7251965 DOI: 10.26434/chemrxiv.11728983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Revised: 01/27/2020] [Indexed: 01/06/2023]
Abstract
With the current trajectory of the 2019-nCoV outbreak unknown, public health and medicinal measures will both be needed to contain spreading of the virus and to optimize patient outcomes. While little is known about the virus, an examination of the genome sequence shows strong homology with its more well-studied cousin, SARS-CoV. The spike protein used for host cell infection shows key nonsynonymous mutations which may hamper efficacy of previously developed therapeutics but remains a viable target for the development of biologics and macrocyclic peptides. Other key drug targets, including RdRp and 3CLpro, share a strikingly high (>95%) homology to SARS-CoV. Herein, we suggest 4 potential drug candidates (an ACE2-based peptide, remdesivir, 3CLpro-1 and a novel vinylsulfone protease inhibitor) that can be used to treat patients suffering with the 2019-nCoV. We also summarize previous efforts into drugging these targets and hope to help in the development of broad spectrum anti-coronaviral agents for future epidemics.
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Affiliation(s)
- Jared S. Morse
- The Texas A&M Drug Discovery Laboratory, Department of
Chemistry, Texas A&M University, College Station, Texas 77843, United
States
| | - Tyler Lalonde
- The Texas A&M Drug Discovery Laboratory, Department of
Chemistry, Texas A&M University, College Station, Texas 77843, United
States
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of
Chemistry, Texas A&M University, College Station, Texas 77843, United
States
| | - Wenshe R. Liu
- The Texas A&M Drug Discovery Laboratory, Department of
Chemistry, Texas A&M University, College Station, Texas 77843, United
States
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20
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Lineage A Betacoronavirus NS2 Proteins and the Homologous Torovirus Berne pp1a Carboxy-Terminal Domain Are Phosphodiesterases That Antagonize Activation of RNase L. J Virol 2017; 91:JVI.02201-16. [PMID: 28003490 DOI: 10.1128/jvi.02201-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/13/2016] [Indexed: 01/22/2023] Open
Abstract
Viruses in the family Coronaviridae, within the order Nidovirales, are etiologic agents of a range of human and animal diseases, including both mild and severe respiratory diseases in humans. These viruses encode conserved replicase and structural proteins as well as more diverse accessory proteins, encoded in the 3' ends of their genomes, that often act as host cell antagonists. We previously showed that 2',5'-phosphodiesterases (2',5'-PDEs) encoded by the prototypical Betacoronavirus, mouse hepatitis virus (MHV), and by Middle East respiratory syndrome-associated coronavirus antagonize the oligoadenylate-RNase L (OAS-RNase L) pathway. Here we report that additional coronavirus superfamily members, including lineage A betacoronaviruses and toroviruses infecting both humans and animals, encode 2',5'-PDEs capable of antagonizing RNase L. We used a chimeric MHV system (MHVMut) in which exogenous PDEs were expressed from an MHV backbone lacking the gene for a functional NS2 protein, the endogenous RNase L antagonist. With this system, we found that 2',5'-PDEs encoded by the human coronavirus HCoV-OC43 (OC43; an agent of the common cold), human enteric coronavirus (HECoV), equine coronavirus (ECoV), and equine torovirus Berne (BEV) are enzymatically active, rescue replication of MHVMut in bone marrow-derived macrophages, and inhibit RNase L-mediated rRNA degradation in these cells. Additionally, PDEs encoded by OC43 and BEV rescue MHVMut replication and restore pathogenesis in wild-type (WT) B6 mice. This finding expands the range of viruses known to encode antagonists of the potent OAS-RNase L antiviral pathway, highlighting its importance in a range of species as well as the selective pressures exerted on viruses to antagonize it.IMPORTANCE Viruses in the family Coronaviridae include important human and animal pathogens, including the recently emerged viruses severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and Middle East respiratory syndrome-associated coronavirus (MERS-CoV). We showed previously that two viruses within the genus Betacoronavirus, mouse hepatitis virus (MHV) and MERS-CoV, encode 2',5'-phosphodiesterases (2',5'-PDEs) that antagonize the OAS-RNase L pathway, and we report here that these proteins are furthermore conserved among additional coronavirus superfamily members, including lineage A betacoronaviruses and toroviruses, suggesting that they may play critical roles in pathogenesis. As there are no licensed vaccines or effective antivirals against human coronaviruses and few against those infecting animals, identifying viral proteins contributing to virulence can inform therapeutic development. Thus, this work demonstrates that a potent antagonist of host antiviral defenses is encoded by multiple and diverse viruses within the family Coronaviridae, presenting a possible broad-spectrum therapeutic target.
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21
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Wang YS, Chang CK, Hou MH. Crystallographic analysis of the N-terminal domain of Middle East respiratory syndrome coronavirus nucleocapsid protein. Acta Crystallogr F Struct Biol Commun 2015; 71:977-80. [PMID: 26249685 PMCID: PMC4528927 DOI: 10.1107/s2053230x15010146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/26/2015] [Indexed: 02/23/2023] Open
Abstract
The N-terminal domain of the nucleocapsid protein from Middle East respiratory syndrome coronavirus (MERS-CoV NP-NTD) contains many positively charged residues and has been identified to be responsible for RNA binding during ribonucleocapsid formation by the virus. In this study, the crystallization and crystallographic analysis of MERS-CoV NP-NTD (amino acids 39-165), with a molecular weight of 14.7 kDa, are reported. MERS-CoV NP-NTD was crystallized at 293 K using PEG 3350 as a precipitant and a 94.5% complete native data set was collected from a cooled crystal at 77 K to 2.63 Å resolution with an overall Rmerge of 9.6%. The crystals were monoclinic and belonged to space group P21, with unit-cell parameters a = 35.60, b = 109.64, c = 91.99 Å, β = 101.22°. The asymmetric unit contained four MERS-CoV NP-NTD molecules.
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Affiliation(s)
- Yong-Sheng Wang
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hon Hou
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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22
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Chihrin S, Loutfy MR. Overview of antiviral and anti-inflammatory treatment for severe acute respiratory syndrome. Expert Rev Anti Infect Ther 2014; 3:251-62. [PMID: 15918782 DOI: 10.1586/14787210.3.2.251] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In 2003, an outbreak of a novel respiratory virus exploded from mainland China into an international issue, catching the world by surprise. The ensuing challenges to hospital and public health workers rose to a level never before seen in healthcare, in part due to the unknown nature of the disease, the fear of the human-to-human transmission and the significant media involvement. A new coronavirus was identified as the causative agent and named the severe acute respiratory syndrome-associated virus. A number of antiviral and anti-inflammatory treatment strategies were explored during the epidemic, with varying success. Following the epidemic, in vitro antiviral analyses of numerous compounds have been conducted. This review summarizes treatment agents assessed during and after the 2003 severe acute respiratory syndrome outbreak, with the aim of guiding future decision makers should the virus return.
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Affiliation(s)
- Stephen Chihrin
- University of Western Ontario , Faculty of Medicine, London, Ontario, Canada
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23
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Liang FY, Lin LC, Ying TH, Yao CW, Tang TK, Chen YW, Hou MH. Immunoreactivity characterisation of the three structural regions of the human coronavirus OC43 nucleocapsid protein by Western blot: implications for the diagnosis of coronavirus infection. J Virol Methods 2012; 187:413-20. [PMID: 23174159 PMCID: PMC7112824 DOI: 10.1016/j.jviromet.2012.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 10/15/2012] [Accepted: 11/08/2012] [Indexed: 01/25/2023]
Abstract
Previous studies have reported that a prokaryotic-expressed recombinant nucleocapsid protein (NP) is a suitable reagent for the epidemiological screening of coronavirus infection. In this study, soluble recombinant human coronavirus OC43 (HCoV-OC43) NP was produced to examine the antigenicity of the HCoV-OC43 NP of betacoronavirus. Using the purified recombinant NP as an antigen, a polyclonal antibody from rabbit serum with specificity for HCoV-OC43 NP was generated; this antibody reacts specifically with HCoV-OC43 NP and does not cross-react with other human CoV NPs (including those of SARS-CoV and HCoV-229E) by Western blot. Sera from 26 young adults, 17 middle-aged and elderly patients with respiratory infection, and 15 cord blood samples were also tested. Strong reactivity to the NPs of HCoV-OC43 was observed in 96%, 82%, and 93% of the serum samples from the young adults, respiratory patients, and cord blood samples, respectively. To identify the immunoreactivities of the three structural regions of the NP that are recognised by the rabbit polyclonal antibody and human serum, the antigenicities of three protein fragments, including the N-terminal domain (aa 1-173), the central-linker region (aa 174-300), and the C-terminal domain (aa 301-448), were evaluated by Western blot. The rabbit polyclonal antibody demonstrated greater immunoreactivity to the central-linker region and the C-terminal domain than to the N-terminal domain. Three different patterns for the immunoreactivities of the three structural regions of HCoV-OC43 NP were observed in human serum, suggesting variability in the immune responses that occur during HCoV-OC43 infection in humans. The central-linker region of the NP appeared to be the most highly immunoreactive region for all three patterns observed. The goal of this study was to offer insight into the design of diagnostic tools for HCoV infection.
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Affiliation(s)
- Fang-Ying Liang
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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Chen IJ, Chou CC, Liu CL, Lee CC, Kan LS, Hou MH. Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of human coronavirus OC43 nucleocapsid protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:815-8. [PMID: 20606281 PMCID: PMC2898469 DOI: 10.1107/s1744309110017616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Accepted: 05/13/2010] [Indexed: 11/25/2022]
Abstract
The N-terminal domain of nucleocapsid protein from human coronavirus OC43 (HCoV-OC43 N-NTD) mostly contains positively charged residues and has been identified as being responsible for RNA binding during ribonucleocapsid formation in the coronavirus. In this study, the crystallization and preliminary crystallographic analysis of HCoV-OC43 N-NTD (amino acids 58-195) with a molecular weight of 20 kDa are reported. HCoV-OC43 N-NTD was crystallized at 293 K using PEG 1500 as a precipitant and a 99.9% complete native data set was collected to 1.7 A resolution at 100 K with an overall R(merge) of 5.0%. The crystals belonged to the hexagonal space group P6(5), with unit-cell parameters a = 81.57, c = 42.87 A. Solvent-content calculations suggest that there is likely to be one subunit of N-NTD in the asymmetric unit.
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Affiliation(s)
- I-Jung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
| | - Chia-Cheng Chou
- National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan
| | - Chia-Ling Liu
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Lou-Sing Kan
- Institute of Bioengineering, Tatung University, Taipei 104, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hon Hou
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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Mardani K, Noormohammadi AH, Ignjatovic J, Browning GF. Naturally occurring recombination between distant strains of infectious bronchitis virus. Arch Virol 2010; 155:1581-6. [PMID: 20574643 PMCID: PMC7086740 DOI: 10.1007/s00705-010-0731-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 06/14/2010] [Indexed: 11/29/2022]
Abstract
New variants of infectious bronchitis virus (IBV) have emerged in Australia despite its geographical isolation and intensive vaccination programs. In the present study, the 3′ terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The comparison revealed that recombination between classical and novel IBVs was responsible for the emergence of the new variant. It was concluded that novel IBVs, which have not been detected since 1993, and which are phylogenically more distant from classical IBVs than turkey coronaviruses, might still be circulating and contributing to the evolution of IBV in Australia.
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Affiliation(s)
- Karim Mardani
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Urmia University, Urmia, West Azarbaijan, Iran.
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Affiliation(s)
- Brigitte A Wevers
- Master Biomedical Sciences, Department of Medical Microbiology, VU University Amsterdam, Faculty of Earth and Life Sciences, Amsterdam, The Netherlands
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Abstract
In this review, the current state of vaccine development against human severe acute respiratory syndrome (SARS) coronavirus, focusing on recently published data is assessed. We discuss which strategies have been assessed immunologically and which have been evaluated in SARS coronavirus challenge models. We discuss inactivated vaccines, virally and bacterially vectored vaccines, recombinant protein and DNA vaccines, as well as the use of attenuated vaccines. Data regarding the correlates of protection, animal models and the available evidence regarding potential vaccine enhancement of SARS disease are discussed. While there is much evidence that various vaccine strategies against SARS are safe and immunogenic, vaccinated animals still display significant disease upon challenge. Current data suggest that intranasal vaccination may be crucial and that new or combination strategies may be required for good protective efficacy against SARS in humans.
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Affiliation(s)
- Rachel L Roper
- Brody School of Medicine, Department of Microbiology & Immunology, East Carolina University, Greenville, NC 27834, USA.
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Bright KR, Sicairos-Ruelas EE, Gundy PM, Gerba CP. Assessment of the Antiviral Properties of Zeolites Containing Metal Ions. FOOD AND ENVIRONMENTAL VIROLOGY 2009; 1:37. [PMCID: PMC7091263 DOI: 10.1007/s12560-008-9006-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 12/11/2008] [Indexed: 05/20/2023]
Abstract
The antiviral properties of zeolite (sodium aluminosilicate) powders amended with metal ions were assessed using human coronavirus 229E, feline infectious peritonitis virus (FIPV), and feline calicivirus F-9. Zeolites containing silver and silver/copper caused significant reductions of coronavirus 229E after 1 h in suspension. The silver/copper combination yielded a >5.13-log10 reduction within 24 h. It was also the most effective (>3.18-log10) against FIPV after 4 h. Other formulations were ineffective against FIPV. On plastic coupons with incorporated silver/copper-zeolites, >1.7-log10 and >3.8-log10 reductions were achieved for coronavirus 229E and feline calicivirus within 24 h, respectively. Silver/copper zeolite reduced titers of all viruses tested, suggesting that it may be effective against related pathogens of interest [i.e., SARS coronavirus, other coronaviruses, human norovirus (calicivirus)]. Of note, it was effective against both enveloped and nonenveloped viruses. Metal-zeolites could therefore possibly be used in applications to reduce virus contamination of fomites and thus the spread of viral diseases.
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Affiliation(s)
- Kelly R. Bright
- Department of Soil, Water and Environmental Science, The University of Arizona, Building 38, Room 429, Tucson, AZ 85721 USA
| | - Enue E. Sicairos-Ruelas
- Department of Soil, Water and Environmental Science, The University of Arizona, Building 38, Room 429, Tucson, AZ 85721 USA
| | - Patricia M. Gundy
- Department of Soil, Water and Environmental Science, The University of Arizona, Building 38, Room 429, Tucson, AZ 85721 USA
| | - Charles P. Gerba
- Department of Soil, Water and Environmental Science, The University of Arizona, Building 38, Room 429, Tucson, AZ 85721 USA
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29
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Ariaans MP, van de Haar PM, Hensen EJ, Vervelde L. Infectious Bronchitis Virus induces acute interferon-gamma production through polyclonal stimulation of chicken leukocytes. Virology 2008; 385:68-73. [PMID: 19070879 PMCID: PMC7103388 DOI: 10.1016/j.virol.2008.11.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 09/29/2008] [Accepted: 11/10/2008] [Indexed: 01/13/2023]
Abstract
Infectious Bronchitis Virus, a member of the Coronaviridae, is a respiratory pathogen in poultry. We found that in vitro stimulation with IBV resulted in ChIFN-gamma production in splenocytes of both infected birds and uninfected birds. The non-specific stimulation did not occur when other avian viruses or other coronaviruses were used or when mammalian cells were stimulated with IBV. Inactivation of IBV reduced ChIFN-gamma production, but ChIFN-gamma remained elevated compared to unstimulated cells. An increase in ChIFN-gamma mRNA was detected in splenocytes from IBV-infected and uninfected chickens as early as 1 h after stimulation with IBV. These results indicate that IBV acts as a polyclonal stimulus, inducing a rapid production of IFN-gamma even without previous exposure to the virus.
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Affiliation(s)
- Mark P Ariaans
- Department of Infectious Diseases and Immunology, Utrecht University, The Netherlands
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30
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Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. J Virol 2008; 83:1823-36. [PMID: 19052085 DOI: 10.1128/jvi.01781-08] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1"-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.
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31
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See RH, Petric M, Lawrence DJ, Mok CPY, Rowe T, Zitzow LA, Karunakaran KP, Voss TG, Brunham RC, Gauldie J, Finlay BB, Roper RL. Severe acute respiratory syndrome vaccine efficacy in ferrets: whole killed virus and adenovirus-vectored vaccines. J Gen Virol 2008; 89:2136-2146. [PMID: 18753223 DOI: 10.1099/vir.0.2008/001891-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although the 2003 severe acute respiratory syndrome (SARS) outbreak was controlled, repeated transmission of SARS coronavirus (CoV) over several years makes the development of a SARS vaccine desirable. We performed a comparative evaluation of two SARS vaccines for their ability to protect against live SARS-CoV intranasal challenge in ferrets. Both the whole killed SARS-CoV vaccine (with and without alum) and adenovirus-based vectors encoding the nucleocapsid (N) and spike (S) protein induced neutralizing antibody responses and reduced viral replication and shedding in the upper respiratory tract and progression of virus to the lower respiratory tract. The vaccines also diminished haemorrhage in the thymus and reduced the severity and extent of pneumonia and damage to lung epithelium. However, despite high neutralizing antibody titres, protection was incomplete for all vaccine preparations and administration routes. Our data suggest that a combination of vaccine strategies may be required for effective protection from this pathogen. The ferret may be a good model for SARS-CoV infection because it is the only model that replicates the fever seen in human patients, as well as replicating other SARS disease features including infection by the respiratory route, clinical signs, viral replication in upper and lower respiratory tract and lung damage.
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Affiliation(s)
- Raymond H See
- University of British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada
| | - Martin Petric
- University of British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada
| | - David J Lawrence
- University of British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada
| | - Catherine P Y Mok
- University of British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada
| | - Thomas Rowe
- Southern Research Institute, Birmingham, AL 35205, USA
| | - Lois A Zitzow
- Southern Research Institute, Birmingham, AL 35205, USA
| | - Karuna P Karunakaran
- University of British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada
| | - Thomas G Voss
- Southern Research Institute, Birmingham, AL 35205, USA
| | - Robert C Brunham
- University of British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada
| | - Jack Gauldie
- Departments of Pathology and Molecular Medicine and Biology, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - B Brett Finlay
- Michael Smith Laboratories and Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Rachel L Roper
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC 27834, USA
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32
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Martin JE, Louder MK, Holman LA, Gordon IJ, Enama ME, Larkin BD, Andrews CA, Vogel L, Koup RA, Roederer M, Bailer RT, Gomez PL, Nason M, Mascola JR, Nabel GJ, Graham BS. A SARS DNA vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a Phase I clinical trial. Vaccine 2008; 26:6338-43. [PMID: 18824060 PMCID: PMC2612543 DOI: 10.1016/j.vaccine.2008.09.026] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 08/14/2008] [Accepted: 09/02/2008] [Indexed: 01/19/2023]
Abstract
Background The severe acute respiratory syndrome (SARS) virus is a member of the Coronaviridae (CoV) family that first appeared in the Guangdong Province of China in 2002 and was recognized as an emerging infectious disease in March 2003. Over 8000 cases and 900 deaths occurred during the epidemic. We report the safety and immunogenicity of a SARS DNA vaccine in a Phase I human study. Methods A single-plasmid DNA vaccine encoding the Spike (S) glycoprotein was evaluated in 10 healthy adults. Nine subjects completed the 3 dose vaccination schedule and were evaluated for vaccine safety and immune responses. Immune response was assessed by intracellular cytokine staining (ICS), ELISpot, ELISA, and neutralization assays. Results The vaccine was well tolerated. SARS-CoV-specific antibody was detected by ELISA in 8 of 10 subjects and neutralizing antibody was detected in all subjects who received 3 doses of vaccine. SARS-CoV-specific CD4+ T-cell responses were detected in all vaccinees, and CD8+ T-cell responses in ∼20% of individuals. Conclusions The VRC SARS DNA vaccine was well tolerated and produced cellular immune responses and neutralizing antibody in healthy adults.
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Affiliation(s)
- Julie E Martin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, MSC-2610, Bethesda, MD 20892-3017, USA
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33
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Serrano P, Johnson MA, Almeida MS, Horst R, Herrmann T, Joseph JS, Neuman BW, Subramanian V, Saikatendu KS, Buchmeier MJ, Stevens RC, Kuhn P, Wüthrich K. Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus. J Virol 2007; 81:12049-60. [PMID: 17728234 PMCID: PMC2168779 DOI: 10.1128/jvi.00969-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
This paper describes the structure determination of nsp3a, the N-terminal domain of the severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural protein 3. nsp3a exhibits a ubiquitin-like globular fold of residues 1 to 112 and a flexibly extended glutamic acid-rich domain of residues 113 to 183. In addition to the four beta-strands and two alpha-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a feature that has not previously been observed in these proteins. Nuclear magnetic resonance chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA. Structural similarities with proteins involved in various cell-signaling pathways indicate possible roles of nsp3a in viral infection and persistence.
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Affiliation(s)
- Pedro Serrano
- Department of Molecular Biology, MB-44, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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34
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Stertz S, Reichelt M, Spiegel M, Kuri T, Martínez-Sobrido L, García-Sastre A, Weber F, Kochs G. The intracellular sites of early replication and budding of SARS-coronavirus. Virology 2007; 361:304-15. [PMID: 17210170 PMCID: PMC7103305 DOI: 10.1016/j.virol.2006.11.027] [Citation(s) in RCA: 283] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 09/07/2006] [Accepted: 11/16/2006] [Indexed: 01/12/2023]
Abstract
In this study, we analyzed the replication and budding sites of severe acute respiratory syndrome coronavirus (SARS-CoV) at early time points of infection. We detected cytoplasmic accumulations containing the viral nucleocapsid protein, viral RNA and the non-structural protein nsp3. Using EM techniques, we found that these putative viral replication sites were associated with characteristic membrane tubules and double membrane vesicles that most probably originated from ER cisternae. In addition to its presence at the replication sites, N also accumulated in the Golgi region and colocalized with the viral spike protein. Immuno-EM revealed that budding occurred at membranes of the ERGIC (ER–Golgi intermediate compartment) and the Golgi region as early as 3 h post infection, demonstrating that SARS-CoV replicates surprisingly fast. Our data suggest that SARS-CoV establishes replication complexes at ER-derived membranes. Later on, viral nucleocapsids have to be transported to the budding sites in the Golgi region where the viral glycoproteins accumulate and particle formation occurs.
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Affiliation(s)
- Silke Stertz
- Department of Virology, University of Freiburg, D-79008 Freiburg, Germany
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35
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Liu M, Gu C, Wu J, Zhu Y. Amino acids 1 to 422 of the spike protein of SARS associated coronavirus are required for induction of cyclooxygenase-2. Virus Genes 2006; 33:309-17. [PMID: 16991002 PMCID: PMC7088811 DOI: 10.1007/s11262-005-0070-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 12/12/2005] [Indexed: 02/07/2023]
Abstract
The causative agent of severe acute respiratory syndrome (SARS) has been identified as SARS-associated coronavirus (SARS-CoV). To evaluate the molecular mechanisms involved in the viral infection, in this study, we investigated the role of SARS-CoV Spike (S) protein in the regulation of cyclooxygenase-2 (COX-2). Expression of COX-2 stimulated by the S protein was verified by RT-PCR and western blot assay. To explore the relationship between S and COX-2, we constructed a series of plasmids containing truncated N-terminal fragments of the SARS-CoV S gene (designated from Sa to Si), which encoded truncated S proteins, and investigated whether these truncated proteins could induce effective expression of COX-2 in 293T cells. Our results showed that S(d) that encoded a truncated S protein with 422 amino acid residues (from 1 to 422 aa), a part of 672 amino-acid S1 subunit is crucial for the induction of COX-2 expression. Immunofluorescence examinations also give the evidence that these N terminal 422 amino acids of the S protein were also required for the correct localization of the protein. We also compared S protein sequences of SARS-CoV isolated during the SARS break with that from palm civets, a possible source of SARS-CoV found in humans. S protein residues (344, 360), which mutated in the epitome from palm civet to human being were characterized in 3D modeling of 252-375 amino acid fragment. Collectively, these results indicate that S protein of SARS-CoV induces the expression of COX-2 and an N-terminal fragment of the Spike protein is crucial for the induction. Our finding may provide clue for the induction of inflammation by SARS-CoV and cast insight into the severity of the SARS epidemic.
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Affiliation(s)
- Mo Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072 P. R. China
| | - Chunfang Gu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072 P. R. China
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072 P. R. China
| | - Ying Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072 P. R. China
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36
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Weiss SR, Navas-Martin S. Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. Microbiol Mol Biol Rev 2006; 69:635-64. [PMID: 16339739 PMCID: PMC1306801 DOI: 10.1128/mmbr.69.4.635-664.2005] [Citation(s) in RCA: 739] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Coronaviruses are a family of enveloped, single-stranded, positive-strand RNA viruses classified within the Nidovirales order. This coronavirus family consists of pathogens of many animal species and of humans, including the recently isolated severe acute respiratory syndrome coronavirus (SARS-CoV). This review is divided into two main parts; the first concerns the animal coronaviruses and their pathogenesis, with an emphasis on the functions of individual viral genes, and the second discusses the newly described human emerging pathogen, SARS-CoV. The coronavirus part covers (i) a description of a group of coronaviruses and the diseases they cause, including the prototype coronavirus, murine hepatitis virus, which is one of the recognized animal models for multiple sclerosis, as well as viruses of veterinary importance that infect the pig, chicken, and cat and a summary of the human viruses; (ii) a short summary of the replication cycle of coronaviruses in cell culture; (iii) the development and application of reverse genetics systems; and (iv) the roles of individual coronavirus proteins in replication and pathogenesis. The SARS-CoV part covers the pathogenesis of SARS, the developing animal models for infection, and the progress in vaccine development and antiviral therapies. The data gathered on the animal coronaviruses continue to be helpful in understanding SARS-CoV.
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Affiliation(s)
- Susan R Weiss
- Department of Microbiology, University of Pennsylvania School of Medicine, 36th Street and Hamilton Walk, Philadelphia, Pennsylvania 19104-6076, USA.
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37
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Weiss SR, Navas-Martin S. Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. Microbiol Mol Biol Rev 2005. [PMID: 16339739 DOI: 10.1128/mmbr.69.4.635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
Coronaviruses are a family of enveloped, single-stranded, positive-strand RNA viruses classified within the Nidovirales order. This coronavirus family consists of pathogens of many animal species and of humans, including the recently isolated severe acute respiratory syndrome coronavirus (SARS-CoV). This review is divided into two main parts; the first concerns the animal coronaviruses and their pathogenesis, with an emphasis on the functions of individual viral genes, and the second discusses the newly described human emerging pathogen, SARS-CoV. The coronavirus part covers (i) a description of a group of coronaviruses and the diseases they cause, including the prototype coronavirus, murine hepatitis virus, which is one of the recognized animal models for multiple sclerosis, as well as viruses of veterinary importance that infect the pig, chicken, and cat and a summary of the human viruses; (ii) a short summary of the replication cycle of coronaviruses in cell culture; (iii) the development and application of reverse genetics systems; and (iv) the roles of individual coronavirus proteins in replication and pathogenesis. The SARS-CoV part covers the pathogenesis of SARS, the developing animal models for infection, and the progress in vaccine development and antiviral therapies. The data gathered on the animal coronaviruses continue to be helpful in understanding SARS-CoV.
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Affiliation(s)
- Susan R Weiss
- Department of Microbiology, University of Pennsylvania School of Medicine, 36th Street and Hamilton Walk, Philadelphia, Pennsylvania 19104-6076, USA.
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38
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Pendleton AR, Machamer CE. Differential localization and turnover of infectious bronchitis virus 3b protein in mammalian versus avian cells. Virology 2005; 345:337-45. [PMID: 16298409 PMCID: PMC7111863 DOI: 10.1016/j.virol.2005.09.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Revised: 09/15/2005] [Accepted: 09/22/2005] [Indexed: 12/24/2022]
Abstract
Infectious bronchitis virus (IBV) 3b protein is highly conserved among group 3 coronaviruses, suggesting that it is important for infection. A previous report (Virology 2003, 311:16-27) indicated that transfected IBV 3b localized to the nucleus in mammalian cells using a vaccinia-virus expression system. Although we confirmed these findings, we observed cytoplasmic localization of IBV 3b with apparent exclusion from the nucleus in avian cells (IBV normally infects chickens). IBV 3b was virtually undetectable by microscopy in mammalian cells transfected without vaccinia virus and in IBV-infected mammalian cells because of a greatly reduced half-life in these cells. A proteasome inhibitor stabilized IBV 3b in mammalian cells, but had little effect on IBV 3b in avian cells, suggesting that rapid turnover of IBV 3b in mammalian cells is proteasome-dependent while turnover in avian cells may be proteasome-independent. Our results highlight the importance of using cells derived from the natural host when studying coronavirus non-structural proteins.
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Affiliation(s)
- Amanda R Pendleton
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
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39
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Bivas-Benita M, Ottenhoff THM, Junginger HE, Borchard G. Pulmonary DNA vaccination: concepts, possibilities and perspectives. J Control Release 2005; 107:1-29. [PMID: 16054263 PMCID: PMC7114572 DOI: 10.1016/j.jconrel.2005.05.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 05/27/2005] [Indexed: 12/20/2022]
Abstract
Mucosal immunity establishes the first line of defence against pathogens entering the body via mucosal surfaces. Besides eliciting both local and systemic immunity, mucosal vaccination strategies that are non-invasive in nature may increase patient compliance and reduce the need for vaccine application by trained personnel. A relatively new concept is mucosal immunization using DNA vaccines. The advantages of DNA vaccines, such as the opportunity to combine the genetic information of various antigen epitopes and stimulatory cytokines, the enhanced stability and ease of production make this class of vaccines attractive and suitable for mucosal application. In contrast to the area of intranasal vaccination, only a few recent studies have focused on pulmonary immunization and the involvement of the pulmonary immune system in eliciting protective immune responses against inhaled pathogens. This review focuses on DNA vaccine delivery to the lung as a promising approach to prevent pulmonary-associated diseases caused by inhaled pathogens. Attractive immunological features of the lung as a site for immunization, the mechanisms of action of DNA vaccines and the pulmonary application of such vaccines using novel delivery systems will be discussed. We also examine pulmonary diseases prone to prevention or therapeutical intervention by application of DNA vaccines.
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Affiliation(s)
- Maytal Bivas-Benita
- Leiden/Amsterdam Center for Drug Research, Division of Pharmaceutical Technology, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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40
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Navas-Martin S, Hingley ST, Weiss SR. Murine coronavirus evolution in vivo: functional compensation of a detrimental amino acid substitution in the receptor binding domain of the spike glycoprotein. J Virol 2005; 79:7629-40. [PMID: 15919915 PMCID: PMC1143675 DOI: 10.1128/jvi.79.12.7629-7640.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Murine coronavirus A59 strain causes mild to moderate hepatitis in mice. We have previously shown that mutants of A59, unable to induce hepatitis, may be selected by persistent infection of primary glial cells in vitro. These in vitro isolated mutants encoded two amino acids substitutions in the spike (S) gene: Q159L lies in the putative receptor binding domain of S, and H716D, within the cleavage signal of S. Here, we show that hepatotropic revertant variants may be selected from these in vitro isolated mutants (Q159L-H716D) by multiple passages in the mouse liver. One of these mutants, hr2, was chosen for more in-depth study based on a more hepatovirulent phenotype. The S gene of hr2 (Q159L-R654H-H716D-E1035D) differed from the in vitro isolates (Q159L-H716D) in only 2 amino acids (R654H and E1035D). Using targeted RNA recombination, we have constructed isogenic recombinant MHV-A59 viruses differing only in these specific amino acids in S (Q159L-R654H-H716D-E1035D). We demonstrate that specific amino acid substitutions within the spike gene of the hr2 isolate determine the ability of the virus to cause lethal hepatitis and replicate to significantly higher titers in the liver compared to wild-type A59. Our results provide compelling evidence of the ability of coronaviruses to rapidly evolve in vivo to highly virulent phenotypes by functional compensation of a detrimental amino acid substitution in the receptor binding domain of the spike glycoprotein.
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MESH Headings
- Amino Acid Substitution
- Animals
- Coronavirus Infections/pathology
- Coronavirus Infections/physiopathology
- Coronavirus Infections/virology
- Evolution, Molecular
- Hepatitis, Viral, Animal/pathology
- Hepatitis, Viral, Animal/physiopathology
- Hepatitis, Viral, Animal/virology
- Liver/pathology
- Liver/virology
- Male
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Mice, Inbred C57BL
- Murine hepatitis virus/genetics
- Murine hepatitis virus/pathogenicity
- Receptors, Virus/metabolism
- Recombination, Genetic
- Specific Pathogen-Free Organisms
- Spike Glycoprotein, Coronavirus
- Viral Envelope Proteins/chemistry
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
- Virulence
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Affiliation(s)
- Sonia Navas-Martin
- Department of Microbiology, University of Pennsylvania, School of Medicine, 36th Street and Hamilton Walk, Philadelphia, PA 19104-6076, USA.
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Pendleton AR, Machamer CE. Infectious bronchitis virus 3a protein localizes to a novel domain of the smooth endoplasmic reticulum. J Virol 2005; 79:6142-51. [PMID: 15857999 PMCID: PMC1091725 DOI: 10.1128/jvi.79.10.6142-6151.2005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All coronaviruses possess small open reading frames (ORFs) between structural genes that have been hypothesized to play important roles in pathogenesis. Infectious bronchitis virus (IBV) ORF 3a is one such gene. It is highly conserved among group 3 coronaviruses, suggesting that it has an important function in infection. IBV 3a protein is expressed in infected cells but is not detected in virions. Sequence analysis predicted that IBV 3a was a membrane protein; however, only a fraction behaved like an integral membrane protein. Microscopy and immunoprecipitation studies demonstrated that IBV 3a localized to the cytoplasm in a diffuse pattern as well as in sharp puncta in both infected and transfected cells. These puncta did not overlap cellular organelles or other punctate structures. Confocal microscopy demonstrated that IBV 3a puncta lined up along smooth endoplasmic reticulum (ER) tubules and, in a significant number of instances, were partially surrounded by these tubules. Our results suggest that IBV 3a is partially targeted to a novel domain of the smooth ER.
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