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Alagarsamy V, Solomon VR, Murugesan S, Sundar PS, Muzaffar-Ur-Rehman MD, Chandu A, Aishwarya AD, Narendhar B, Sulthana MT, Ravikumar V. In Silico Screening of Some Active Phytochemicals to Identify Promising Inhibitors Against SARS-CoV-2 Targets. Curr Drug Discov Technol 2024; 21:73-89. [PMID: 37861016 DOI: 10.2174/0115701638243222230920051050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND There are very few small-molecule drug candidates developed against SARS-CoV-2 that have been revealed since the epidemic began in November 2019. The typical medicinal chemistry discovery approach requires more than a decade of the year of painstaking research and development and a significant financial guarantee, which is not feasible in the challenge of the current epidemic. OBJECTIVE This current study proposes to find and identify the most effective and promising phytomolecules against SARS-CoV-2 in six essential proteins (3CL protease, Main protease, Papain- Like protease, N-protein RNA binding domain, RNA-dependent RNA polymerase, and Spike receptor binding domain target through in silico screening of 63 phytomolecules from six different Ayurveda medicinal plants. METHODS The phytomolecules and SARS-CoV-2 proteins were taken from public domain databases such as PubChem and RCSB Protein Data Bank. For in silico screening, the molecular interactions, binding energy, and ADMET properties were investigated. RESULTS The structure-based molecular docking reveals some molecules' greater affinity towards the target than the co-crystal ligand. Our results show that tannic acid, cyanidin-3-rutinoside, zeaxanthin, and carbolactone are phytomolecules capable of inhibiting SARS-CoV-2 target proteins in the least energy conformations. Tannic acid had the least binding energy of -8.8 kcal/mol, which is better than the binding energy of its corresponding co-crystal ligand (-7.5 kcal/mol) against 3 CL protease. Also, it has shown the least binding energy of -9.9 kcal/mol with a more significant number of conventional hydrogen bond interactions against the RdRp target. Cyanidin-3-rutinoside showed binding energy values of -8.8 and -7.6 kcal/mol against Main protease and Papain-like protease, respectively. Zeaxanthin was the top candidate in the N protein RBD with a binding score of - 8.4 kcal/mol, which is slightly better when compared to a co-crystal ligand (-8.2 kcal/mol). In the spike, carbolactone was the suitable candidate with the binding energy of -7.2 kcal/mol and formed a conventional hydrogen bond and two hydrophobic interactions. The best binding affinity-scored phytomolecules were selected for the MD simulations studies. CONCLUSION The present in silico screening study suggested that active phytomolecules from medicinal plants could inhibit SARS-CoV-2 targets. The elite docked compounds with drug-like properties have a harmless ADMET profile, which may help to develop promising COVID-19 inhibitors.
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Affiliation(s)
- V Alagarsamy
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - V Raja Solomon
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - S Murugesan
- Department of Pharmacy, BITS Pilani, Pilani Campus, Pilani, 333031, India
| | - P Shyam Sundar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | | | - A Chandu
- Department of Pharmacy, BITS Pilani, Pilani Campus, Pilani, 333031, India
| | - A Dharshini Aishwarya
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - B Narendhar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - M T Sulthana
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - V Ravikumar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy - 502 294, Gr. Hyderabad, India
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Coste AT, Egli A, Schrenzel J, Nickel B, Zbinden A, Lienhard R, Dumoulin A, Risch M, Greub G. IVDR: Analysis of the Social, Economic, and Practical Consequences of the Application of an Ordinance of the In Vitro Diagnostic Ordinance in Switzerland. Diagnostics (Basel) 2023; 13:2910. [PMID: 37761277 PMCID: PMC10529212 DOI: 10.3390/diagnostics13182910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/04/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
IVDR regulation represents a major challenge for diagnostic microbiology laboratories. IVDR complicates a broad range of aspects and poses a risk given the high diversity of pathogens (including rare but highly virulent microbes) and the large variety of samples submitted for analysis. The regular emergence of new pathogens (including Echovirus E-11, Adenovirus 41, Monkeypox virus, Alongshan virus, and Enterovirus D68, as recent examples in Europe in the post SARS-CoV-2 era) is another factor that makes IVDR regulation risky, because its detrimental effect on production of in-house tests will negatively impact knowledge and expertise in the development of new diagnostic tests. Moreover, such regulations negatively impact the availability of diagnostic tests, especially for neglected pathogens, and has a detrimental effect on the overall costs of the tests. The increased regulatory burden of IVDR may thereby pose an important risk for public health. Taken together, it will have a negative impact on the financial balance of diagnostic microbiology laboratories (especially small ones). The already-high standards of quality management of all ISO-accredited and Swissmedic-authorized laboratories render IVDR law of little value, at least in Switzerland, while tremendously increasing the regulatory burden and associated costs. Eventually, patients will need to pay for diagnostic assays outside of the framework of their insurance in order to obtain a proper diagnostic assessment, which may result in social inequity. Thus, based on the risk assessment outlined above, the coordinated commission for clinical microbiology proposes adjusting the IvDO ordinance by (i) introducing an obligation to be ISO 15189 accredited and (ii) not implementing the IvDO 2028 milestone.
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Affiliation(s)
- Alix T. Coste
- Institute of Microbiology, University of Lausanne & University Hospital Center, 1011 Lausanne, Switzerland;
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland; (A.E.); (A.Z.)
| | - Jacques Schrenzel
- Bacteriology Laboratory, Service of Laboratory Medicine, Department of Diagnostic, Geneva University Hospitals, 1211 Geneva, Switzerland;
| | - Beatrice Nickel
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland;
- University of Basel, 4002 Basel, Switzerland
| | - Andrea Zbinden
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland; (A.E.); (A.Z.)
| | - Reto Lienhard
- ADMed Microbiologie Laboratory, 2300 La Chaux-de-Fonds, Switzerland;
| | - Alexis Dumoulin
- Department of Infectious Diseases, Institut Central des Hôpitaux, Hôpital du Valais, 1950 Sion, Switzerland;
| | - Martin Risch
- Dr Risch Medical Laboratory, Wuhrstrasse 14, 9490 Vaduz, Switzerland;
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne & University Hospital Center, 1011 Lausanne, Switzerland;
- Infectious Disease Service, University of Lausanne & University Hospital Center, 1011 Lausanne, Switzerland
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3
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Hawkins SFC, Guest PC. Multiplex Quantitative Polymerase Chain Reaction Test to Identify SARS-CoV-2 Variants. Methods Mol Biol 2022; 2511:67-78. [PMID: 35838952 DOI: 10.1007/978-1-0716-2395-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is a routinely used method for detection and quantitation of gene expression in real time. This is achieved through the incorporation and measurement of fluorescent reporter probes in the amplified cDNA strands, since the fluorescent signals increase as the reaction progresses. The availability of multiple probes which fluoresce at different wavelengths allows for multiplexing as this gives rise to amplicons with unique fluorescent signatures. Here we describe a method using the Inhibitor-Tolerant RT-qPCR kit, developed by Meridian Bioscience kit which allows simultaneous real-time quantitation of the UK, South Africa, and Brazil SARS-CoV-2 variants.
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Affiliation(s)
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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Chavda VP, Vuppu S, Mishra T, Kamaraj S, Patel AB, Sharma N, Chen ZS. Recent review of COVID-19 management: diagnosis, treatment and vaccination. Pharmacol Rep 2022; 74:1120-1148. [PMID: 36214969 PMCID: PMC9549062 DOI: 10.1007/s43440-022-00425-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 02/06/2023]
Abstract
The idiopathic Coronavirus disease 2019 (COVID-19) pandemic outbreak caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reached global proportions; the World Health Organization (WHO) declared it as a public health emergency during the month of January 30, 2020. The major causes of the rise of new variants of SARS-CoV-2 are genetic mutations and recombination. Some of the variants with high infection and transmission rates are termed as variants of concern (VOCs) like currently Omicron variants. Pregnant women, aged people, and immunosuppressed and compromised patients constitute the most susceptible human population to the SARS-CoV-2 infection, especially to the new evolving VOCs. To effectively manage the pathological condition of infection, the focus should be directed towards prevention and prophylactic approach. In this narrative review, we aimed to analyze the current scenario of COVID-19 management and discuss the treatment and prevention strategies. We also focused on the complications prevalent during the COVID-19 and post-COVID period and to discuss the novel approaches developed for mitigation of the global pandemic. We have also emphasized on the COVID-19 management approaches for the special population including children, pregnant women, aged groups, and immunocompromised patients. We conclude that the advancements in therapeutic and pharmacological domains have provided opportunities to develop and design novel diagnosis, treatment, and prevention strategies. New advanced techniques such as RT-LAMP, RT-qPCR, High-Resolution Computed Tomography, etc., efficiently diagnose patients with SARS-CoV-2 infection. In the case of treatment options, new drugs like paxlovid, combinations of β-lactum drugs and molnupiravir are found to be effective against even the new emerging variants. In addition, vaccination is an essential approach to prevent the infection or to reduce its severity. Vaccines for against COVID-19 from Comirnaty by Pfizer-BioNTech, SpikeVax by Moderna, and Vaxzevria by Oxford-AstraZeneca are approved and used widely. Similarly, numerous vaccines have been developed with different percentages of effectiveness against VOCs. New developments like nanotechnology and AI can be beneficial in providing an efficient and reliable solution for the suppression of SARS-CoV-2. Public health concerns can be efficiently treated by a unified scientific approach, public engagement, and better diagnosis.
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Affiliation(s)
- Vivek P. Chavda
- grid.419037.80000 0004 1765 7930Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat India
| | - Suneetha Vuppu
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, 632014 Tamil Nadu India
| | - Toshika Mishra
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, 632014 Tamil Nadu India
| | - Sathvika Kamaraj
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, 632014 Tamil Nadu India
| | - Aayushi B. Patel
- grid.419037.80000 0004 1765 7930Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat India
| | - Nikita Sharma
- grid.412813.d0000 0001 0687 4946Department of Biotechnology, Science, Innovation, and Society Research Lab 115, Hexagon (SMV), Vellore Institute of Technology, Vellore, 632014 Tamil Nadu India
| | - Zhe-Sheng Chen
- grid.264091.80000 0001 1954 7928Department of Pharmaceutical Science, College of Pharmacy and Health Sciences, St. John’s University, New York, NY 11439 USA
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Heo ML, Jang YM. Development and Validation of the Infection Prevention Behavior Scale of Individuals (IPBS-I) for the General Population. J Multidiscip Healthc 2021; 14:2791-2802. [PMID: 34675528 PMCID: PMC8502068 DOI: 10.2147/jmdh.s334154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/15/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose This study aimed to develop a scale for measuring infection prevention behavior of individuals and to verify its validity and reliability for the general population. Patients and Methods The scale items were selected using a literature review on the chain of infection and its content validity. There were 297 study participants, all of whom provided informed consent. Data were collected online from September 3 to September 8, 2020, using Google Survey in Korea. The scale's construct validity was verified through exploratory and confirmatory factor analyses, criterion validity was Pearson's Correlation, and reliability was tested using Cronbach's alpha. Results Twelve items and three factors were selected after a factor and an exploratory factor analysis of 29 scale items. The three factors were pathogen blocking, transmission blocking, and immunity enhancement. A confirmatory factor analysis validated the model goodness of fit, and the convergent validity and discriminant validity of the scale were verified. The correlation coefficient with a scale for respiratory infection prevention practice was 0.69, thereby confirming the criterion validity of the scale. The reliability of the final scale (Cronbach's alpha) was 0.86. Conclusion This scale is reflective of the social features of the Korean adult population, and it is easy and concise to be administered to general public, making it useful for subsequent studies on infection prevention.
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Affiliation(s)
- Myoung-Lyun Heo
- Department of Nursing Science, Jeonju University, Jeonju-si, Jeollabuk-do, South Korea
| | - Yang-Min Jang
- Department of Nursing Science, Shinsung University, Dangjin, Chungcheongnam-do, South Korea
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Bogiel T, Rzepka M, Depka D. Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection-Results Questioning Previous Observations. Diagnostics (Basel) 2021; 11:1839. [PMID: 34679537 PMCID: PMC8534906 DOI: 10.3390/diagnostics11101839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 is a new virus from the Coronaviridae family and its rapid spread is now the most important medical problem worldwide. Currently used tests vary in the number and selection of SARS-CoV-2 target genes. Meanwhile, the choice of the appropriate target gene may be important in terms of a reliable detection of a viral RNA. As some researchers questioned the sensitivity of the monogenic VIASURE SARS-CoV-2 S gene Real Time PCR Detection Kit (CerTest Biotec, Zaragoza, Spain) in mid-2020, the aim of the study was to evaluate the usefulness of this kit, used along with the BD MAX™ System (Becton Dickinson, East Rutherford, NJ, USA), and compare the results with two-gene Bosphore Novel Coronavirus (2019-nCoV) Detection Kit v1 (Anatolia Diagnostics and Biotechnology Products Inc., Istanbul, Turkey). Both tests were carried out on 306 nasopharyngeal/oropharyngeal swabs. The consistent results (72 positive and 225 negative results found simultaneously in both kits) were obtained for 297 (97.1%) samples altogether, while discrepancies between the results of the evaluated tests were observed for nine (2.9%) specimens. There were no statistically significant differences between the method used and the frequency of positive results. Both tests, targeted at detecting one and two genes, are effective in SARS-CoV-2 RNA detection.
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Affiliation(s)
- Tomasz Bogiel
- Microbiology Department, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 9 Maria Skłodowska-Curie Street, 85-094 Bydgoszcz, Poland; (M.R.); (D.D.)
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Fiorillo L, Meto A, Cicciù F, De Stefano R. An Eventual Sars-CoV-2 Infection Prevention Protocol in the Medical Setting and Dental Office. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:2593. [PMID: 33807646 PMCID: PMC7967356 DOI: 10.3390/ijerph18052593] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/12/2022]
Abstract
The current Coronavirus disease 2019 (COVID-19) pandemic has affected the entire world population, and in particular the medical-health field, especially dentistry [...].
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Affiliation(s)
- Luca Fiorillo
- Department of Biomedical and Dental Sciences, Morphological and Functional Images, School of Dentistry, University of Messina, Policlinico G. Martino, Via Consolare Valeria, 98100 Messina, Italy
- Multidisciplinary Department of Medical-Surgical and Odontostomatological Specialties, University of Campania “Luigi Vanvitelli”, 80121 Naples, Italy
| | - Aida Meto
- Department of Dental Therapy, Faculty of Dental Medicine, University of Medicine, 1005 Tirana, Albania;
| | - Francesca Cicciù
- Unità Operativa di Patologia Clinica, ARNAS Garibaldi Centro, 95123 Catania, Italy;
| | - Rosa De Stefano
- Department of Biomedical and Dental Sciences, Morphological and Functional Images, University of Messina, 98100 Messina, Italy;
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Hashimoto T, Sawano T, Ozaki A, Tsubokura M, Tsuchiya T. Need for more proactive use of pharmacists in the COVID-19 pandemic following lessons learnt from the Great East Japan Earthquake. J Glob Health 2020; 10:020397. [PMID: 33274060 PMCID: PMC7696243 DOI: 10.7189/jogh.10.020397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Toyoaki Sawano
- Department of Surgery, Sendai City Medical Center, Sendai, Japan.,Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Akihiko Ozaki
- Department of Breast Surgery, Jyoban Hospital of Tokiwa Foundation, Iwaki, Fukushima, Japan
| | - Masaharu Tsubokura
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Takashi Tsuchiya
- Department of Surgery, Sendai City Medical Center, Sendai, Japan
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Srivastava V, Yadav A, Sarkar P. Molecular Docking and ADMET Study of Bioactive Compounds of Glycyrrhiza glabra Against Main Protease of SARS-CoV2. ACTA ACUST UNITED AC 2020; 49:2999-3007. [PMID: 33078096 PMCID: PMC7556787 DOI: 10.1016/j.matpr.2020.10.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/03/2020] [Indexed: 12/23/2022]
Abstract
Recent pandemic situation of COVID-19 is caused due to SARS-CoV2 and almost all the countries of the world have been affected by this highly contagious virus. Main protease (Mpro) of this virus is a highly attractive drug target among various other enzymes due to its ability to process poly-protein that is the translated product of the SARS-CoV2 RNA. The present study demonstrates molecular docking study of Glycyrrhiza glabra (Gg) active compounds such as Glycyrrhizic acid (GA), Liquiritigenin (L) and Glabridin (G) against the Mpro. Docking studies shows that these active compounds bind strongly with some of the amino acid residues in the active site of Mpro and inhibits the enzyme strongly. GA, L, and G are proposed to be strong inhibitors of the enzyme and the amino acids: His41, Gly143, Gln189, Glu 166, Cys 145, Thr25, Asn142, Met49, Cys44, Thr45 and pro168 present in the active site of Mpro were shown to make non-covalent interaction with these compounds. In silico ADMET properties prediction also shows that Gg active compounds had good solubility, absorption, permeation, non-toxic, and non– carcinogenic characteristics. Our finding concludes that all of the three active compounds of Gg have the potential to be strong inhibitors for Mpro of SARS-CoV2 but glycyrrhizic acid has a high binding affinity and a good ADMET properties than the other two.
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Affiliation(s)
- Vivek Srivastava
- Department of Chemistry and Biochemistry, School of Basic Sciences and Research, Sharda University, Greater Noida-201308, U.P, India
| | - Ankush Yadav
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi-110062, India
| | - Paratpar Sarkar
- Department of Chemistry and Biochemistry, School of Basic Sciences and Research, Sharda University, Greater Noida-201308, U.P, India
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Clinical Case: SARS-CoV-2 Reactivation After a Heavy Workout. ACTA MEDICA BULGARICA 2020. [DOI: 10.2478/amb-2020-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
We present a clinical case of a patient with reactivation of SARS-CoV-2 infection after strenuous exercise in the gym. Reactivation of the virus was confirmed after detecting SARS-CoV-2 in a nasopharyngeal swab sample using real-time polymerase chain reaction (PCR). The clinical symptoms of the patient – fever and shortness of breath, as well as the presence of IgM antibodies further confirmed the diagnosis. The subjective complaints of persistent shortness of breath for more than a few weeks were noted.
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