51
|
Tehrani H, Darnahal M, Nadji S, Haghighi S. COVID-19 re-infection or persistent infection in patient with acute myeloid leukaemia M3: a mini review. New Microbes New Infect 2020; 39:100830. [PMID: 33425365 PMCID: PMC7777517 DOI: 10.1016/j.nmni.2020.100830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 12/21/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has affected more than 40 million people worldwide. Some patients had episodes of symptom recurrence after the first episode of infection with variable intervals. There are multiple issues and hypotheses about re-infection or re-activation of the virus, especially in immunocompromised patients. In this paper, we present details of an individual with a recent history of COVID-19 who proceeded to acute myeloid leukaemia M3 and immunosuppression by chemotherapy, then we review some recently published articles about possible re-infection or re-activation.
Collapse
Affiliation(s)
- H.A. Tehrani
- Department of Haematology and Medical Oncology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M. Darnahal
- Department of Haematology and Medical Oncology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S.A. Nadji
- Virology Research Center, National Research Institute for Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S. Haghighi
- Department of Haematology and Medical Oncology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Corresponding author: S. Haghighi, Department of Haematology and Medical Oncology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
52
|
Picarazzi F, Vicenti I, Saladini F, Zazzi M, Mori M. Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge. Molecules 2020; 25:E5695. [PMID: 33287144 PMCID: PMC7730706 DOI: 10.3390/molecules25235695] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) is an essential enzyme for the viral replication process, catalyzing the viral RNA synthesis using a metal ion-dependent mechanism. In recent years, RdRp has emerged as an optimal target for the development of antiviral drugs, as demonstrated by recent approvals of sofosbuvir and remdesivir against Hepatitis C virus (HCV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively. In this work, we overview the main sequence and structural features of the RdRp of emerging RNA viruses such as Coronaviruses, Flaviviruses, and HCV, as well as inhibition strategies implemented so far. While analyzing the structural information available on the RdRp of emerging RNA viruses, we provide examples of success stories such as for HCV and SARS-CoV-2. In contrast, Flaviviruses' story has raised attention about how the lack of structural details on catalytically-competent or ligand-bound RdRp strongly hampers the application of structure-based drug design, either in repurposing and conventional approaches.
Collapse
Affiliation(s)
- Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
| |
Collapse
|
53
|
Nambou K, Anakpa M. Deciphering the co-adaptation of codon usage between respiratory coronaviruses and their human host uncovers candidate therapeutics for COVID-19. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104471. [PMID: 32707288 PMCID: PMC7374176 DOI: 10.1016/j.meegid.2020.104471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) has caused thousands of deaths worldwide and has become an urgent public health concern. The extraordinary interhuman transmission of this disease has urged scientists to examine the various facets of its pathogenic agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, based on publicly available genomic data, we analyzed the codon usage co-adaptation profiles of SARS-CoV-2 and other respiratory coronaviruses (CoVs) with their human host, identified CoV-responsive human genes and their functional roles on the basis of both the relative synonymous codon usage (RSCU)-based correlation of viral genes with human genes and differential gene expression analysis, and predicted potential drugs for COVID-19 treatment based on these genes. The relatively high codon adaptation index (CAI) values (>0.70) signposted the gene expressivity efficiency of CoVs in human. The ENc-GC3 plot indicated that SARS-CoV-2 genome was under strict selection pressure while SARS-CoV and MERS-CoV were under selection and mutational pressures. The RSCU-based correlation analysis indicated that the viral genomes shared similar codons with a panoply of human genes. The merging of RSCU-based correlation data and SARS-CoV-2-responsive differentially expressed genes allowed the identification of human genes potentially affected by SARS-CoV-2 infection. Functional enrichment analysis indicated that these genes were enriched in biological processes and pathways related to host response to viral infection and immune response. Using the drug-gene interaction database, we screened a list of drugs that could target these genes as potential COVID-19 therapeutics. Our findings not only will contribute in vaccine development but also provide a useful set of drugs that could guide practitioners in strategical monitoring of COVID-19. We recommend practitioners to scrupulously screen this list of predicted drugs in order to authenticate those qualified for treating COVID-19 symptoms.
Collapse
Affiliation(s)
- Komi Nambou
- Shenzhen Nambou1 Biotech, 506, Block B, West Silicon Valley, 5010 Baoan Avenue, Baoan District, Shenzhen, China.
| | - Manawa Anakpa
- Key Laboratory of Trustworthy Distributed Computing and Service, Ministry of Education, School of Sofware, Beijing University of Posts and Telecommunications, 10 Xitucheng Road, Haidian District, Beijing 100876, China
| |
Collapse
|
54
|
Klenov A, Hudak KA. Facile method of curing toxicity in large viral genomes by high-throughput identification and removal of cryptic promoters. J Virol Methods 2020; 287:113993. [PMID: 33068704 DOI: 10.1016/j.jviromet.2020.113993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023]
Abstract
Infectious plant virus clones are challenging to construct and manipulate due to the presence of cryptic promoter sequences that induce toxicity in bacteria. Common methods to overcome toxicity include intron insertion to interrupt toxic open reading frames and the use of Rhizobium or yeast species that do not recognize the same cryptic promoters. Unfortunately, intron insertion must be attempted on a trial and error basis within full-length clones and may change the infection characteristics of the virus. We have developed a facile method that can detect multiple cryptic bacterial promoters within large virus genomes. These promoters can then be silenced to obtain infectious clones that can be manipulated in E. coli. Our strategy relies on the generation of a viral library which is cloned upstream of either an eGFP open reading frame for low-throughput analysis or chloramphenicol for next generation sequencing. Pokeweed mosaic virus (PkMV), a 9.5 Kb ssRNA potyvirus, was used as a proof of concept. We found 16 putative promoter regions within 150-250 bp library fragments throughout the PkMV genome. 5'RACE allowed identification of the promoter sequence within each fragment, and subsequent silencing produced infectious clones. Our results indicate that cryptic promoters are ubiquitous within large viral genomes and that promoter screening is a desirable first step when constructing a viral clone. Our method can be applied to large plant and animal viruses as well as any DNA sequence for which low level of background transcriptional activity is required.
Collapse
|
55
|
Mahapatra S, Chandra P. Clinically practiced and commercially viable nanobio engineered analytical methods for COVID-19 diagnosis. Biosens Bioelectron 2020; 165:112361. [PMID: 32729494 PMCID: PMC7834411 DOI: 10.1016/j.bios.2020.112361] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/16/2020] [Accepted: 06/02/2020] [Indexed: 01/05/2023]
Abstract
The recent outbreak of the coronavirus disease (COVID-19) has left the world clueless. As the WHO declares this new contagion as a pandemic on the 11th of March 2020, the alarming rate of the spawn of the disease in such a short period has disarranged the globe. Standing against this situation researchers are strenuously searching for the key traits responsible for this pandemic. As knowledge regarding the dynamics and host-path interaction of COVID-19 causing Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently unknown, the formulation of strategies concerning antiviral treatment, vaccination, and epidemiological control stands crucial. Before designing adequate therapeutic strategies, it is extremely essential to diagnose the disease at the outset as early detection can have a greater impact on building health system capacity. Hence, a comprehensive review of strategies for COVID-19 diagnosis is essential in this existing global situation. In this review, sequentially, we have provided the clinical details along with genetic and proteomic biomarkers related to COVID-19. The article systematically enlightens a clear overview of the clinically adopted techniques for the detection of COVID-19 including oligonucleotide-based molecular detection, Point-of-Care immunodiagnostics, radiographical analysis/sensing system, and newly developed biosensing prototypes having commercial viability. The commercial kits/analytical methods based-sensing strategies have also been tabulated categorically. The critical insights on the developer, commercial brand name, detection methods, technical operational details, detection time, clinical specimen, status, the limit of detection/detection ability have been discussed comprehensively. We believe that this review may provide scientists, clinicians and healthcare manufacturers valuable information regarding the most recent developments/approaches towards COVID-19 diagnosis.
Collapse
Affiliation(s)
- Supratim Mahapatra
- Laboratory of Bio-Physio Sensors and Nanobioengineering, School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Varanasi, Uttar Pradesh 221005, India
| | - Pranjal Chandra
- Laboratory of Bio-Physio Sensors and Nanobioengineering, School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Varanasi, Uttar Pradesh 221005, India.
| |
Collapse
|
56
|
Arafkas M, Khosrawipour T, Kocbach P, Zielinski K, Schubert J, Mikolajczyk A, Celinska M, Khosrawipour V. Current meta-analysis does not support the possibility of COVID-19 reinfections. J Med Virol 2020; 93:1599-1604. [PMID: 32897549 DOI: 10.1002/jmv.26496] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) reinfections could be a major aggravating factor in this current pandemic, as this would further complicate potential vaccine development and help to maintain worldwide virus pockets. To investigate this critical question, we conducted a clinical meta-analysis including all available currently reported cases of potential COVID-19 reinfections. We searched for all peer-reviewed articles in the search engine of the National Center for Biotechnology Information. While there are over 30,000 publications on COVID-19, only about 15 specifically target the subject of COVID-19 reinfections. Available patient data in these reports was analyzed for age, gender, time of reported relapse after initial infection and persistent COVID-19 positive polymerase chain reaction (PCR) results. Following the first episode of infection, cases of clinical relapse are reported at 34 (mean) ± 10.5 days after full recovery. Patients with clinical relapse have persisting positive COVID-19 PCR testing results until 39 ± 9 days following initial positive testing. For patients without clinical relapse, positive testing was reported up to 54 ± 24 days. There were no reports of any clinical reinfections after a 70-day period following initial infection.
Collapse
Affiliation(s)
- Mohamed Arafkas
- Department of Plastic Surgery, St. Petrus Hospital, Wuppertal, Germany
| | - Tanja Khosrawipour
- Department of Surgery, University of California, Irvine, California, USA.,Department of Surgery (A), University Hospital of Duesseldorf, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Piotr Kocbach
- Division of Infectious diseases, University of Warmia and Mazury, Olszytn, Poland
| | | | - Justyna Schubert
- Department of Food Hygiene and Consumer Health Protection, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Agata Mikolajczyk
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Sciencess, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Maria Celinska
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Sciencess, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Veria Khosrawipour
- Department of Surgery, University of California, Irvine, California, USA
| |
Collapse
|
57
|
Rabaan AA, Al-Ahmed SH, Sah R, Al-Tawfiq JA, Haque S, Harapan H, Arteaga-Livias K, Aldana DKB, Kumar P, Dhama K, Rodriguez-Morales AJ. Genomic Epidemiology and Recent Update on Nucleic Acid-Based Diagnostics for COVID-19. CURRENT TROPICAL MEDICINE REPORTS 2020; 7:113-119. [PMID: 32989413 PMCID: PMC7513458 DOI: 10.1007/s40475-020-00212-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2020] [Indexed: 01/22/2023]
Abstract
Purpose of the Review The SARS-CoV-2 genome has been sequenced and the data is made available in the public domain. Molecular epidemiological investigators have utilized this information to elucidate the origin, mode of transmission, and contact tracing of SARS-CoV-2. The present review aims to highlight the recent advancements in the molecular epidemiological studies along with updating recent advancements in the molecular (nucleic acid based) diagnostics for COVID-19, the disease caused by SARS-CoV-2. Recent Findings Epidemiological studies with the integration of molecular genetics principles and tools are now mainly focused on the elucidation of molecular pathology of COVID-19. Molecular epidemiological studies have discovered the mutability of SARS-CoV-2 which is of utmost importance for the development of therapeutics and vaccines for COVID-19. The whole world is now participating in the race for development of better and rapid diagnostics and therapeutics for COVID-19. Several molecular diagnostic techniques have been developed for accurate and precise diagnosis of COVID-19. Summary Novel genomic techniques have helped in the understanding of the disease pathology, origin, and spread of COVID-19. The whole genome sequence established in the initial days of the outbreak has enabled to identify the virus taxonomy. Several rapid, accurate, and sensitive diagnostic methods have been developed; those are based on the principle of detecting SARS-CoV-2 nucleic acids in clinical samples. Most of these molecular diagnostics are based on RT-PCR principle.
Collapse
Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Shamsah H Al-Ahmed
- Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia
| | - Ranjit Sah
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Harapan Harapan
- Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia.,Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia.,Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia
| | - Kovy Arteaga-Livias
- Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco, Peru.,Universidad Científica del Sur, Lima, Peru
| | - D Katterine Bonilla Aldana
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda Colombia.,Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda Colombia
| | - Pawan Kumar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122 India
| | - Alfonso J Rodriguez-Morales
- Universidad Científica del Sur, Lima, Peru.,Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda Colombia.,Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda Colombia.,Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda Colombia
| |
Collapse
|
58
|
Tizaoui K, Zidi I, Lee KH, Ghayda RA, Hong SH, Li H, Smith L, Koyanagi A, Jacob L, Kronbichler A, Shin JI. Update of the current knowledge on genetics, evolution, immunopathogenesis, and transmission for coronavirus disease 19 (COVID-19). Int J Biol Sci 2020; 16:2906-2923. [PMID: 33061805 PMCID: PMC7545713 DOI: 10.7150/ijbs.48812] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/23/2020] [Indexed: 01/08/2023] Open
Abstract
In December 2019, an acute respiratory disease caused by novel species of coronavirus (SARS-CoV-2), emerged in China and has spread throughout the world. On 11th March 2020, the World Health Organization (WHO) officially declared coronavirus disease 19 (COVID-19) a pandemic, severe coronavirus-mediated human disease. Based on genomic and phylogenetic studies, SARS-CoV-2 might originate from bat coronaviruses and infects humans directly or through intermediate zoonotic hosts. However, the exact origin or the host intermediate remains unknown. Genetically, SARS-CoV-2 is similar to several existing coronaviruses, particularly SARS-CoV, but differs by silent and non-silent mutations. The virus uses different transmission routes and targets cells and tissues with angiotensin-converting enzyme 2 (ACE2) protein, which makes it contagious. COVID-19 shares both the main clinical features and excessive/dysregulated cell responses with the two previous Middle East respiratory syndrome coronavirus (MERS) and severe acute respiratory syndrome coronavirus (SARS) epidemics. In this review, we provide an update of the current knowledge on the COVID-19 pandemic. Gaining a deeper understanding of SARS-CoV-2 structure, transmission routes, and molecular responses, will assist in the prevention and control of COVID-19 outbreaks in the future.
Collapse
Affiliation(s)
- Kalthoum Tizaoui
- Laboratory Microorganismes and Active Biomolecules, Sciences Faculty of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Ines Zidi
- Laboratory Microorganismes and Active Biomolecules, Sciences Faculty of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ramy Abou Ghayda
- Division of Urology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston MA, USA
| | - Sung Hwi Hong
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston MA, USA
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Han Li
- University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Lee Smith
- The Cambridge Centre for Sport and Exercise Science, Anglia Ruskin University, Cambridge, CB1 1PT, UK
| | - Ai Koyanagi
- Research and Development Unit, Parc Sanitari Sant Joan de Déu, CIBERSAM, 08830 Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Louis Jacob
- Research and Development Unit, Parc Sanitari Sant Joan de Déu, CIBERSAM, 08830 Barcelona, Spain
- Faculty of Medicine, University of Versailles Saint-Quentin-en-Yvelines, 78000 Versailles, France
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck 6020, Austria
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
59
|
Hadi J, Dunowska M, Wu S, Brightwell G. Control Measures for SARS-CoV-2: A Review on Light-Based Inactivation of Single-Stranded RNA Viruses. Pathogens 2020; 9:E737. [PMID: 32911671 PMCID: PMC7558314 DOI: 10.3390/pathogens9090737] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 is a single-stranded RNA virus classified in the family Coronaviridae. In this review, we summarize the literature on light-based (UV, blue, and red lights) sanitization methods for the inactivation of ssRNA viruses in different matrixes (air, liquid, and solid). The rate of inactivation of ssRNA viruses in liquid was higher than in air, whereas inactivation on solid surfaces varied with the type of surface. The efficacy of light-based inactivation was reduced by the presence of absorptive materials. Several technologies can be used to deliver light, including mercury lamp (conventional UV), excimer lamp (UV), pulsed-light, and light-emitting diode (LED). Pulsed-light technologies could inactivate viruses more quickly than conventional UV-C lamps. Large-scale use of germicidal LED is dependent on future improvements in their energy efficiency. Blue light possesses virucidal potential in the presence of exogenous photosensitizers, although femtosecond laser (ultrashort pulses) can be used to circumvent the need for photosensitizers. Red light can be combined with methylene blue for application in medical settings, especially for sanitization of blood products. Future modelling studies are required to establish clearer parameters for assessing susceptibility of viruses to light-based inactivation. There is considerable scope for improvement in the current germicidal light-based technologies and practices.
Collapse
Affiliation(s)
- Joshua Hadi
- AgResearch Ltd., Hopkirk Research Institute, Cnr University Ave and Library Road, Massey University, Palmerston North 4442, New Zealand; (J.H.); (S.W.)
| | - Magdalena Dunowska
- School of Veterinary Science, Massey University Manawatu (Turitea) Tennent Drive, Palmerston North 4474, New Zealand;
| | - Shuyan Wu
- AgResearch Ltd., Hopkirk Research Institute, Cnr University Ave and Library Road, Massey University, Palmerston North 4442, New Zealand; (J.H.); (S.W.)
| | - Gale Brightwell
- AgResearch Ltd., Hopkirk Research Institute, Cnr University Ave and Library Road, Massey University, Palmerston North 4442, New Zealand; (J.H.); (S.W.)
- New Zealand Food Safety Science and Research Centre, Massey University Manawatu (Turitea) Tennent Drive, Palmerston North 4474, New Zealand
| |
Collapse
|
60
|
Ahmed Z, Zeeshan S, Foran DJ, Kleinman LC, Wondisford FE, Dong X. Integrative clinical, genomics and metabolomics data analysis for mainstream precision medicine to investigate COVID-19. ACTA ACUST UNITED AC 2020. [DOI: 10.1136/bmjinnov-2020-000444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite significant scientific and medical discoveries, the genetics of novel infectious diseases like COVID-19 remains far from understanding. SARS-CoV-2 is a single-stranded RNA respiratory virus that causes COVID-19 by binding to the ACE2 receptor in the lung and other organs. Understanding its clinical presentation and metabolomic and genetic profile will lead to the discovery of diagnostic, prognostic and predictive biomarkers, which may lead to more effective medical therapy. It is important to investigate correlations and overlap between reported diagnoses of a patient with COVID-19 in clinical data with identified germline and somatic mutations, and highly expressed genes from genomics data analysis. Timely model clinical, genomics and metabolomics data to find statistical patterns across millions of features to identify underlying biological pathways, modifiable risk factors and actionable information that supports early detection and prevention of COVID-19, and development of new therapies for better patient care. Next, ensuring security reconcile noise, need to build and train machine learning prognostic models to find actionable information that supports early detection and prevention of COVID-19. Based on the myriad data, applying appropriate machine learning algorithms to stratify patients, understand scenarios, optimise decision-making, identify high-risk rare variants (including ACE2, TMPRSS2) and making medically relevant predictions. Innovative and intelligent solutions are required to improve the traditional symptom-driven practice, and allow earlier interventions using predictive diagnostics and tailor better personalised treatments, when confronted with the challenges of pandemic situations.
Collapse
|
61
|
Dos Santos CC, Zehnbauer BA, Trahtemberg U, Marshall J. Molecular Diagnosis of Coronavirus Disease 2019. Crit Care Explor 2020; 2:e0184. [PMID: 33063040 PMCID: PMC7515613 DOI: 10.1097/cce.0000000000000184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To review molecular diagnostics for coronavirus disease 2019. The world is in the midst of a coronavirus disease 2019 pandemic. Containing the spread of the severe acute respiratory distress coronavirus is critical. Instrumental to the future success is the ability to reliably and reproducibly detect this inciting pathogen to inform public health containment policies and treatment decisions. DATA SOURCES Molecular diagnostics focusing on molecular detection methodologies for detection of the virus and the presence of the disease. STUDY SELECTION Narrative review. DATA EXTRACTION Literature, PubMed, Scopus, and official government documents. DATA SYNTHESIS Diagnosing severe acute respiratory syndrome coronavirus is done through real-time reverse transcriptase-polymerase chain reaction tests, cell culture, and serology. For patients, diagnostics are an integral part of a full medical history, physical examinations, blood tests, and diagnostic imaging. CONCLUSIONS Here, we review current approaches to the molecular diagnosis of coronavirus disease 2019.
Collapse
Affiliation(s)
- Claudia C Dos Santos
- Keenan Research Center for Biomedical Research, Unity Health Toronto, Toronto, ON, Canada
- Interdepartmental Division of Critical Care and Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | | | - Uriel Trahtemberg
- Keenan Research Center for Biomedical Research, Unity Health Toronto, Toronto, ON, Canada
| | - John Marshall
- Keenan Research Center for Biomedical Research, Unity Health Toronto, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
62
|
Lukiw WJ, Pogue A, Hill JM. SARS-CoV-2 Infectivity and Neurological Targets in the Brain. Cell Mol Neurobiol 2020; 42:217-224. [PMID: 32840758 PMCID: PMC7445393 DOI: 10.1007/s10571-020-00947-7] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/14/2020] [Indexed: 01/08/2023]
Abstract
The gateway for invasion by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into human host cells is via the angiotensin-converting enzyme 2 (ACE2) transmembrane receptor expressed in multiple immune and nonimmune cell types. SARS-CoV-2, that causes coronavirus disease 2019 (COVID-19; CoV-19) has the unusual capacity to attack many different types of human host cells simultaneously via novel clathrin- and caveolae-independent endocytic pathways, becoming injurious to diverse cells, tissues and organ systems and exploiting any immune weakness in the host. The elicitation of this multipronged attack explains in part the severity and extensive variety of signs and symptoms observed in CoV-19 patients. To further our understanding of the mechanism and pathways of SARS-CoV-2 infection and susceptibility of specific cell- and tissue-types and organ systems to SARS-CoV-2 attack in this communication we analyzed ACE2 expression in 85 human tissues including 21 different brain regions, 7 fetal tissues and 8 controls. Besides strong ACE2 expression in respiratory, digestive, renal-excretory and reproductive cells, high ACE2 expression was also found in the amygdala, cerebral cortex and brainstem. The highest ACE2 expression level was found in the pons and medulla oblongata in the human brainstem, containing the medullary respiratory centers of the brain, and may in part explain the susceptibility of many CoV-19 patients to severe respiratory distress.
Collapse
Affiliation(s)
- Walter J Lukiw
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112‑2272, USA.
- Alchem Biotech Research, Toronto, ON, M5S 1A8, Canada.
- Department of Neurology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112‑2272, USA.
- Department of Ophthalmology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112‑2272, USA.
- Department of Neuroscience, Neurology and Ophthalmology, Bollinger Professor of Alzheimer's Disease, LSU Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, 2020 Gravier Street, Suite 904, New Orleans, LA, 70112-2272, USA.
| | - Aileen Pogue
- Alchem Biotech Research, Toronto, ON, M5S 1A8, Canada
| | - James M Hill
- Neuroscience Center, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112‑2272, USA
- Department of Ophthalmology, Louisiana State University School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112‑2272, USA
- Department of Pharmacology, LSU Health Science Center, New Orleans, LA, 70112‑2272, USA
- Department of Microbiology, LSU Health Science Center, New Orleans, LA, 70112‑2272, USA
| |
Collapse
|
63
|
Zhang L, Guo H. Biomarkers of COVID-19 and technologies to combat SARS-CoV-2. ADVANCES IN BIOMARKER SCIENCES AND TECHNOLOGY 2020; 2:1-23. [PMID: 33511330 PMCID: PMC7435336 DOI: 10.1016/j.abst.2020.08.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
Due to the unprecedented public health crisis caused by COVID-19, our first contribution to the newly launching journal, Advances in Biomarker Sciences and Technology, has abruptly diverted to focus on the current pandemic. As the number of new COVID-19 cases and deaths continue to rise steadily around the world, the common goal of healthcare providers, scientists, and government officials worldwide has been to identify the best way to detect the novel coronavirus, named SARS-CoV-2, and to treat the viral infection - COVID-19. Accurate detection, timely diagnosis, effective treatment, and future prevention are the vital keys to management of COVID-19, and can help curb the viral spread. Traditionally, biomarkers play a pivotal role in the early detection of disease etiology, diagnosis, treatment and prognosis. To assist myriad ongoing investigations and innovations, we developed this current article to overview known and emerging biomarkers for SARS-CoV-2 detection, COVID-19 diagnostics, treatment and prognosis, and ongoing work to identify and develop more biomarkers for new drugs and vaccines. Moreover, biomarkers of socio-psychological stress, the high-technology quest for new virtual drug screening, and digital applications are described.
Collapse
Key Words
- ACE2, Angiotensin-converting enzyme 2
- ACEI, Angiotensin-converting enzyme inhibitor
- AI, Artificial intelligence
- AIOD-CRISPR, All-In-One Dual CRISPR-Cas12a
- ARB, Angiotensin receptor blocker
- ARDS, Acute respiratory distress syndrome
- COVID
- COVID-19, Coronavirus disease 2019
- CQ, Chloroquine
- CT, Computed tomography
- Coronavirus
- DC, Dendritic cell
- Detection
- Diagnosis
- ELISA, Enzyme-linked immunosorbent assay
- EUA, Emergency use authorization
- FDA, U.S. Food and Drug Administration
- GenOMICC, Genetics of Mortality in Critical Care
- HCQ, Hydroxychloroquine
- LFAs, Lateral flow assays
- LSPR, Localized surface plasmon resonance
- MERS, Middle East respiratory syndrome
- ML, Machine learning
- NIAID, U.S. National Institute of Allergy and Infectious Diseases
- NIH, National Institutes of Health
- PAC-MAN, Prophylactic Antiviral CRISPR in huMAN cells
- PCR, Polymerase chain reaction
- PCT, Procalcitonin
- Prevention
- Prognosis
- RT-PCR, Reverse transcription polymerase chain reaction
- SARS, Severe acute respiratory syndrome
- SARS-CoV-2, SARS coronavirus type 2
- SaaS, Software as a Service
- TCM, Traditional Chinese medicine
- Treatment
- UCB, University of California Berkeley
- UCSF, University of California San Francisco
- cDNA, Complementary DNA
- mAb, Monoclonal antibody
Collapse
Affiliation(s)
- Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Helen Guo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| |
Collapse
|
64
|
Nalbantoglu OU, Gundogdu A. COVID-19 Pandemic: Group Testing. Front Med (Lausanne) 2020; 7:522. [PMID: 32974372 PMCID: PMC7461804 DOI: 10.3389/fmed.2020.00522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/27/2020] [Indexed: 01/12/2023] Open
Affiliation(s)
- Ozkan Ufuk Nalbantoglu
- Department of Computer Engineering, Erciyes University, Kayseri, Turkey
- Genome and Stem Cell Center (GenKok), Erciyes University, Kayseri, Turkey
| | - Aycan Gundogdu
- Genome and Stem Cell Center (GenKok), Erciyes University, Kayseri, Turkey
- Department of Microbiology and Clinical Microbiology, Erciyes University, Kayseri, Turkey
| |
Collapse
|
65
|
Acter T, Uddin N, Das J, Akhter A, Choudhury TR, Kim S. Evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as coronavirus disease 2019 (COVID-19) pandemic: A global health emergency. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 730:138996. [PMID: 32371230 PMCID: PMC7190497 DOI: 10.1016/j.scitotenv.2020.138996] [Citation(s) in RCA: 261] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 05/09/2023]
Abstract
According to data compiled by researchers at Johns Hopkins University in Baltimore, Maryland, more than two and half million cases of coronavirus disease 2019 (COVID-19), caused by a newly discovered virus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have been confirmed on April 20, 2020 (Nature, 2020b). Since the emergence of this infectious disease in Asia (Wuhan, China) late last year, it has been subsequently span to every continent of the world except Antarctica (Rodríguez-Morales et al., 2020). Along with a foothold in every country, the current disease pandemic is disrupting practically every aspect of life all over the world. As the outbreak are continuing to evolve, several research activities have been conducted for better understanding the origin, functions, treatments, and preventions of this novel coronavirus. This review will be a summa of the key features of novel coronavirus (nCoV), the virus causing disease 2019 and the present epidemic situation worldwide up to April 20, 2020. It is expected that this record will play an important role to take more preventive measures for overcoming the challenges faced during this current pandemic.
Collapse
Affiliation(s)
- Thamina Acter
- Department of Mathematical and Physical Sciences, East West University, A/2, Jahurul Islam Avenue, Aftabnagar, Dhaka 1212, Bangladesh
| | - Nizam Uddin
- Department of Nutrition and Food Engineering, Faculty of Allied Health Science, Daffodil International University, 102, Shukrabad, Dhanmondi, Dhaka 1207, Bangladesh.
| | - Jagotamoy Das
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Afroza Akhter
- Institute of Nuclear Medicine and Allied Sciences, Dhaka Medical College Hospital Campus, Bangladesh Atomic Energy Commission (BAEC), Bangladesh
| | - Tasrina Rabia Choudhury
- Analytical Chemistry Laboratory, Chemistry Division, Atomic Energy Centre, Dhaka, Bangladesh Atomic Energy Commission (BAEC), Bangladesh
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu 41566, Republic of Korea; Green-Nano Materials Research Center, Daegu, 41566, Republic of Korea
| |
Collapse
|
66
|
Dhakal S, Karki S. Early Epidemiological Features of COVID-19 in Nepal and Public Health Response. Front Med (Lausanne) 2020; 7:524. [PMID: 32850929 PMCID: PMC7431891 DOI: 10.3389/fmed.2020.00524] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/27/2020] [Indexed: 11/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was first reported in late 2019 from Wuhan, China. Considering COVID-19's alarming levels of spread and severity, the World Health Organization (WHO) declared a global pandemic on March 11, 2020. The first case of COVID-19 in Nepal was reported on January 23, 2020. The Government of Nepal implemented different public health measures to contain COVID-19, including border closures and a countrywide lockdown. We collected the daily data provided by the Ministry of Health and Population (MoHP) of the Government of Nepal and illustrated the early epidemiological characteristics of COVID-19 in Nepal. By May 31, 2020, 1,572 cases and eight deaths were reported in Nepal associated with COVID-19. The estimate of prevalence for COVID-19 among tested populations was 2.25% (95% CI: 2.15–2.37%) and case-fatality rate was 0.5%. The majority of the cases were young males (n = 1,454, 92%), with overall average age being 30.5 years (ranging from 2 months to 81 years) and were mostly asymptomatic. There were only five cases from three districts until the end of March, but cases surged from April and spread to 57 out of 77 districts of Nepal by the end of May 2020 despite the continuous lockdown. Most of these cases are from the southern plains of Nepal, bordering India. As the effect of COVID-19 is expected to persist longer, the Government of Nepal should make appropriate strategies for loosening lockdowns in a phase-wise manner while maintaining social distancing and personal hygiene and increasing its testing, tracking, and medical capacity.
Collapse
Affiliation(s)
- Santosh Dhakal
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Surendra Karki
- Department of Epidemiology and Public Health, Himalayan College of Agricultural Sciences and Technology, Kirtipur, Nepal
| |
Collapse
|
67
|
Gand M, Vanneste K, Thomas I, Van Gucht S, Capron A, Herman P, Roosens NHC, De Keersmaecker SCJ. Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection. Int J Mol Sci 2020; 21:E5585. [PMID: 32759818 PMCID: PMC7432934 DOI: 10.3390/ijms21155585] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January 2020 for initial in silico specificity evaluation and to verify whether the targeted loci are highly conserved. Now that more whole genome data have become available, we used the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time points, to evaluate the specificity of 12 RT-qPCR tests (consisting of a total of 30 primers and probe sets) used for SARS-CoV-2 detection and the impact of the virus' genetic evolution on four of them. The exclusivity of these methods was also assessed using the human reference genome and 2624 closely related other respiratory viral genomes. The specificity of the assays was generally good and stable over time. An exception is the first method developed by the China Center for Disease Control and prevention (CDC), which exhibits three primer mismatches present in 358 SARS-CoV-2 genomes sequenced mainly in Europe from February 2020 onwards. The best results were obtained for the assay of Chan et al. (2020) targeting the gene coding for the spiking protein (S). This demonstrates that our user-friendly strategy can be used for a first in silico specificity evaluation of future RT-qPCR tests, as well as verifying that the former methods are still capable of detecting circulating SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Mathieu Gand
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (M.G.); (K.V.); (N.H.C.R.)
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (M.G.); (K.V.); (N.H.C.R.)
| | - Isabelle Thomas
- Viral Diseases, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (I.T.); (S.V.G.)
| | - Steven Van Gucht
- Viral Diseases, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (I.T.); (S.V.G.)
| | - Arnaud Capron
- Quality of Laboratories, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium;
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium;
| | - Nancy H. C. Roosens
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (M.G.); (K.V.); (N.H.C.R.)
| | - Sigrid C. J. De Keersmaecker
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium; (M.G.); (K.V.); (N.H.C.R.)
| |
Collapse
|
68
|
Almaghlouth I, Islam T, Alamro N, Alsultan A, Alfadda A, Al-Muhsen S, Almasry A, Almadi MA, Hersi A, BaHammam A. Mapping COVID-19 related research from Saudi Arabia, a scoping review. Between reality and dreams. Saudi Med J 2020; 41:791-801. [PMID: 32789418 PMCID: PMC7502955 DOI: 10.15537/smj.2020.8.25163] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To map research production by Saudi-affiliated investigators in order to identify areas of strength and weakness. Method: We followed the Arksey and O'Malley (2005) framework. Medline and Cochrane databases were searched with a focus on identifying articles related to COVID-19 and Saudi Arabia following the PRISMA protocol. The study was conducted at King Saud University, Riyadh, Saudi Arabia between March and May 2020. Results: A total of 53 articles were ultimately included. Most of the research production from Saudi Arabia was opinion and narrative reviews related to the clinicopathological features of COVID-19 as well as control and prevention of virus spread. Conclusion: The results of this scoping review identify a relative deficiency in original research, which requires further investigation.
Collapse
Affiliation(s)
- Ibrahim Almaghlouth
- Department of Medicine, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia. E-mail.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
69
|
Stancioiu F, Papadakis GZ, Kteniadakis S, Izotov BN, Coleman MD, Spandidos DA, Tsatsakis A. A dissection of SARS‑CoV2 with clinical implications (Review). Int J Mol Med 2020; 46:489-508. [PMID: 32626922 PMCID: PMC7307812 DOI: 10.3892/ijmm.2020.4636] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023] Open
Abstract
We are being confronted with the most consequential pandemic since the Spanish flu of 1918‑1920 to the extent that never before have 4 billion people quarantined simultaneously; to address this global challenge we bring to the forefront the options for medical treatment and summarize SARS‑CoV2 structure and functions, immune responses and known treatments. Based on literature and our own experience we propose new interventions, including the use of amiodarone, simvastatin, pioglitazone and curcumin. In mild infections (sore throat, cough) we advocate prompt local treatment for the naso‑pharynx (inhalations; aerosols; nebulizers); for moderate to severe infections we propose a tried‑and‑true treatment: the combination of arginine and ascorbate, administered orally or intravenously. The material is organized in three sections: i) Clinical aspects of COVID‑19; acute respiratory distress syndrome (ARDS); known treatments; ii) Structure and functions of SARS‑CoV2 and proposed antiviral drugs; iii) The combination of arginine‑ascorbate.
Collapse
Affiliation(s)
| | | | | | - Boris Nikovaevich Izotov
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 119991 Moscow, Russia
| | - Michael D. Coleman
- School of Life and Health Sciences, Aston University, B4 7ET Birmingham, UK
| | | | - Aristidis Tsatsakis
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 119991 Moscow, Russia
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, 71003 Heraklion, Greece
| |
Collapse
|
70
|
Kumar R, Verma H, Singhvi N, Sood U, Gupta V, Singh M, Kumari R, Hira P, Nagar S, Talwar C, Nayyar N, Anand S, Rawat CD, Verma M, Negi RK, Singh Y, Lal R. Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution. mSystems 2020; 5:e00505-20. [PMID: 32723797 PMCID: PMC7394360 DOI: 10.1128/msystems.00505-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) that started in Wuhan, China, in December 2019 has spread worldwide, emerging as a global pandemic. The severe respiratory pneumonia caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has so far claimed more than 0.38 million lives and has impacted human lives worldwide. However, as the novel SARS-CoV-2 virus displays high transmission rates, the underlying genomic severity is required to be fully understood. We studied the complete genomes of 95 SARS-CoV-2 strains from different geographical regions worldwide to uncover the pattern of the spread of the virus. We show that there is no direct transmission pattern of the virus among neighboring countries, suggesting that its spread is a result of travel of infected humans to different countries. We revealed unique single nucleotide polymorphisms (SNPs) in nonstructural protein 13 (nsp13), nsp14, nsp15, and nsp16 (ORF1b polyproteins) and in the S-protein within 10 viral isolates from the United States. These viral proteins are involved in RNA replication and binding with the human receptors, indicating that the viral variants that are circulating in the population of the United States are different from those circulating in the populations of other countries. In addition, we found an amino acid addition in nsp16 (mRNA cap-1 methyltransferase) of a U.S. isolate (GenBank accession no. MT188341.1) leading to a shift in the amino acid frame from position 2540 onward. Through comparative structural analysis of the wild-type and mutant proteins, we showed that this addition of a phenylalanine residue renders the protein in the mutant less stable, which might affect mRNA cap-1 methyltransferase function. We further analyzed the SARS-CoV-2-human interactome, which revealed that the interferon signaling pathway is targeted by orf1ab during infection and that it also interacts with NF-κB-repressing factor (NKRF), which is a potential regulator of interleukin-8 (IL-8). We propose that targeting this interaction may subsequently improve the health condition of COVID-19 patients. Our analysis also emphasized that SARS-CoV-2 manipulates spliceosome machinery during infection; hence, targeting splicing might affect viral replication. In conclusion, the replicative machinery of SARS-CoV-2 is targeting interferon and the notch signaling pathway along with spliceosome machinery to evade host challenges.IMPORTANCE The COVID-19 pandemic continues to storm the world, with over 6.5 million cases worldwide. The severity of the disease varies with the territories and is mainly influenced by population density and age factor. In this study, we analyzed the transmission pattern of 95 SARS-CoV-2 genomes isolated from 11 different countries. Our study also revealed several nonsynonymous mutations in ORF1b and S-proteins and the impact on their structural stability. Our analysis showed the manipulation of host system by viral proteins through SARS-CoV-2-human protein interactome, which can be useful to understand the impact of virus on human health.
Collapse
Affiliation(s)
- Roshan Kumar
- P.G. Department of Zoology, Magadh University, Bodh Gaya, Bihar, India
| | - Helianthous Verma
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | | | - Utkarsh Sood
- The Energy and Resources Institute, New Delhi, India
| | - Vipin Gupta
- PhiXGen Private Limited, Gurugram, Haryana, India
| | - Mona Singh
- PhiXGen Private Limited, Gurugram, Haryana, India
| | - Rashmi Kumari
- Department of Zoology, College of Commerce, Arts & Science, Patliputra University, Patna, Bihar, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, New Delhi, India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, India
| | - Namita Nayyar
- Department of Zoology, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Shailly Anand
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Mansi Verma
- Department of Zoology, Sri Venkateswara College, University of Delhi, New Delhi, India
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Rup Lal
- The Energy and Resources Institute, New Delhi, India
| |
Collapse
|
71
|
Dong R, Chu Z, Yu F, Zha Y. Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches. Front Immunol 2020; 11:1784. [PMID: 32849643 PMCID: PMC7399176 DOI: 10.3389/fimmu.2020.01784] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/03/2020] [Indexed: 01/10/2023] Open
Abstract
COVID-19 has recently become the most serious threat to public health, and its prevalence has been increasing at an alarming rate. The incubation period for the virus is ~1-14 days and all age groups may be susceptible to a fatality rate of about 5.9%. COVID-19 is caused by a novel single-stranded, positive (+) sense RNA beta coronavirus. The development of a vaccine for SARS-CoV-2 is an urgent need worldwide. Immunoinformatics approaches are both cost-effective and convenient, as in silico predictions can reduce the number of experiments needed. In this study, with the aid of immunoinformatics tools, we tried to design a multi-epitope vaccine that can be used for the prevention and treatment of COVID-19. The epitopes were computed by using B cells, cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL) base on the proteins of SARS-CoV-2. A vaccine was devised by fusing together the B cell, HTL, and CTL epitopes with linkers. To enhance the immunogenicity, the β-defensin (45 mer) amino acid sequence, and pan-HLA DR binding epitopes (13aa) were adjoined to the N-terminal of the vaccine with the help of the EAAAK linker. To enable the intracellular delivery of the modeled vaccine, a TAT sequence (11aa) was appended to C-terminal. Linkers play vital roles in producing an extended conformation (flexibility), protein folding, and separation of functional domains, and therefore, make the protein structure more stable. The secondary and three-dimensional (3D) structure of the final vaccine was then predicted. Furthermore, the complex between the final vaccine and immune receptors (toll-like receptor-3 (TLR-3), major histocompatibility complex (MHC-I), and MHC-II) were evaluated by molecular docking. Lastly, to confirm the expression of the designed vaccine, the mRNA of the vaccine was enhanced with the aid of the Java Codon Adaptation Tool, and the secondary structure was generated from Mfold. Then we performed in silico cloning. The final vaccine requires experimental validation to determine its safety and efficacy in controlling SARS-CoV-2 infections.
Collapse
Affiliation(s)
- Rong Dong
- Department of Biomedicine, Guizhou University School of Medicine, Guiyang, China
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang, China
- NHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, China
| | - Zhugang Chu
- Department of Urinary Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Fuxun Yu
- NHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, China
| | - Yan Zha
- Department of Biomedicine, Guizhou University School of Medicine, Guiyang, China
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang, China
- NHC Key Laboratory of Pulmonary Immunological Diseases (Guizhou Provincial People's Hospital), Guiyang, China
| |
Collapse
|
72
|
Ahmad M, Dwivedy A, Mariadasse R, Tiwari S, Kar D, Jeyakanthan J, Biswal BK. Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase. ACS OMEGA 2020; 5:18356-18366. [PMID: 32743211 PMCID: PMC7391942 DOI: 10.1021/acsomega.0c02096] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/30/2020] [Indexed: 05/08/2023]
Abstract
The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2.
Collapse
Affiliation(s)
- Mohammed Ahmad
- National
Institute of Immunology, New Delhi 110067, India
| | | | - Richard Mariadasse
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
| | - Satish Tiwari
- National
Institute of Immunology, New Delhi 110067, India
| | - Deepsikha Kar
- National
Institute of Immunology, New Delhi 110067, India
| | - Jeyaraman Jeyakanthan
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
| | | |
Collapse
|
73
|
Kumar D, Batra L, Malik MT. Insights of Novel Coronavirus (SARS-CoV-2) disease outbreak, management and treatment. AIMS Microbiol 2020; 6:183-203. [PMID: 33134740 PMCID: PMC7595841 DOI: 10.3934/microbiol.2020013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
Emerging and re-emerging viral diseases poses a threat to living organisms, and led to serious concern to humankind and public health. The last two decades, viral epidemics such as the severe acute respiratory syndrome (SARS-CoV) reported in the years 2002-2003, and H1N1 influenza (Swine flu) in 2009, middle east respiratory syndrome (MERS-CoV) from Saudi Arabia in 2012, Ebola virus in 2014-2016, and Zika virus in 2015. The recent outbreak of 2019-CoV-2 or severe acute respiratory syndrome-2 (SARS-CoV-2), novel coronavirus (2019-nCoV, or 2019 disease, COVID-19) in Dec 2019, from, Wuhan city of China, has severe implications of health concerns to the whole world, due to global spread and high health risk. More than 423349 deaths had occurred globally and is still increasing every day. The whole world is under a health emergency, and people are advised to stay at their homes to avoid the spread of person-to-person infection, and advised to maintain social distancing. The advancement in clinical diagnosis techniques like Real-Time PCR (RT-PCR), immunological, microscopy, and geographic information system (GIS) mapping technology helped in tacking the rapid diagnosis and tracking viral infection in a short period. In the same way, artificial intelligence (AI), combinatorial chemistry, and deep learning approaches help to find novel therapeutics in less time and wide applicability in biomedical research. National Institute of Allergy and Infectious Diseases (NIAID) has started the clinical trials of investigation COVID-19 vaccine. Therefore, we can expect vaccines to be available for this deadly disease in the coming few months.
Collapse
Affiliation(s)
- Dharmender Kumar
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal-131039, Sonepat, Haryana India
| | - Lalit Batra
- Institute for Cellular Therapeutics,Departments of Microbiology and Immunology, University of Louisville, Louisville, Kentucky-40202, USA
| | - Mohammad Tariq Malik
- Institute for Cellular Therapeutics,Departments of Microbiology and Immunology, University of Louisville, Louisville, Kentucky-40202, USA
- Departments of Microbiology and Immunology, Regenerative Medicine and Stem Cell Biology.and James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky-40202, USA
| |
Collapse
|
74
|
|
75
|
Dharavath B, Yadav N, Desai S, Sunder R, Mishra R, Ketkar M, Bhanshe P, Gupta A, Redhu AK, Patkar N, Dutt S, Gupta S, Dutt A. A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2. Heliyon 2020; 6:e04405. [PMID: 32665985 PMCID: PMC7341355 DOI: 10.1016/j.heliyon.2020.e04405] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 02/08/2023] Open
Abstract
Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts-based on experiments performed by spiking total human RNA with in vitro synthesized viral transcripts. The assay was evaluated by performing 184 validations for the SARS-CoV-2 Nucleocapsid gene and human RNase P as an internal control reference gene with dilutions ranging from 1-100 ng for human RNA on a cohort of 26 clinical samples. 5 of 26 patients were confirmed to be infected with SARS-CoV-2, while 21 tested negative, consistent with the standards. The accuracy of the assay was found to be 100% sensitive and 100% specific based on the 26 clinical samples that need to be further verified using a large number of clinical samples. In summary, we present a rapid, easy to implement real-time PCR based assay with automated analysis using a novel COVID qPCR Analyzer tool with graphical user interface (GUI) to analyze the raw qRT-PCR data in an unbiased manner at a cost of under $3 per reaction and turnaround time of less than 2h, to enable in-house SARS-CoV-2 testing across laboratories.
Collapse
Affiliation(s)
- Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Neelima Yadav
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Roma Sunder
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Madhura Ketkar
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Prasanna Bhanshe
- Haematopathology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Anurodh Gupta
- Haematopathology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Archana Kumari Redhu
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Nikhil Patkar
- Haematopathology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Shilpee Dutt
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Sudeep Gupta
- Department of Medical Oncology, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Adjunct Faculty, Institute of Advanced Virology, Kerala State Council for Science, Technology and Environment, Govt of Kerala, Thonnakkal, Kerala, 695317, India
| |
Collapse
|
76
|
Harenberg J, Favaloro E. COVID-19: progression of disease and intravascular coagulation - present status and future perspectives. Clin Chem Lab Med 2020; 58:1029-1036. [PMID: 32406381 DOI: 10.1515/cclm-2020-0502] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022]
Abstract
The timely and accurate diagnosis of infection with severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), remains the cornerstone of efforts to provide appropriated treatment for patients, to limit further spread of the virus and ultimately to eliminate the virus from the human society. We focus this article on (a) developments for improvement of diagnosis of specific SARS-CoV-2 virus, (b) laboratory changes in the immunologic and coagulation system, (c) therapeutic options for anticoagulant treatment of seriously affected patients and (d) on the perspectives through improvement of diagnostic and therapeutic medical procedures.
Collapse
Affiliation(s)
- Job Harenberg
- University of Heidelberg, DOASENSE GmbH, Waldhofer Str. 102, 69123 Heidelberg, Germany
| | - Emmanuel Favaloro
- Department of Haematology, Sydney Centres for Thrombosis and Haemostasis, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
| |
Collapse
|
77
|
Athar F, Beg MA. Anti-HIV and Anti-HCV drugs are the putative inhibitors of RNA-dependent-RNA polymerase activity of NSP12 of the SARS CoV-2 (COVID-19). ACTA ACUST UNITED AC 2020. [DOI: 10.15406/ppij.2020.08.00292] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
78
|
Zehra Z, Luthra M, Siddiqui SM, Shamsi A, Gaur NA, Islam A. Corona virus versus existence of human on the earth: A computational and biophysical approach. Int J Biol Macromol 2020; 161:271-281. [PMID: 32512089 PMCID: PMC7273167 DOI: 10.1016/j.ijbiomac.2020.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022]
Abstract
SARS-CoV-2 has a positive sense RNA genome of 29.9 kb in size, showing high sequence similarity to the BAT-CoV, SARS-CoV, MERS-CoV. SARS-CoV-2 is composed of 14 open reading frames (ORFs), which encodes for a total of 27 proteins divided into structural and non-structural proteins (NSPs). The fundamental structural protein-encoding genes are a spike protein (S) gene, envelope protein (E) gene, a membrane protein (M) gene, and a nucleocapsid protein (N) gene. They make about 33% of the entire genome and are vital for the viral life cycle. Rest 67% is distributed among different NSPs (such as Mpro, helicase, and RNA-dependent RNA polymerase) encoding genes across the ORFs, which are involved in virus-cell receptor interactions during viral entry. Researchers are trying to formulate vaccines, therapeutic antibodies or protein-targeted antiviral drugs to control the spread. This review proceeds stepwise through the COVID-19 outbreak, structural and genomic organization, entry mechanism, pathogenesis, and finally highlighting the essential proteins involved at each step that might be potential targets for drug discovery. Currently, approved treatment modalities consist of only supportive care and oxygen supplementation. This review is established on the current knowledge that has expanded on structural motifs and topology of proteins and their functions.
Collapse
Affiliation(s)
- Zainy Zehra
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Manav Luthra
- Department of Orthopedics, Medical College, Jalaun, UP, India.
| | - Sobia Manaal Siddiqui
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, UP, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Naseem A Gaur
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| |
Collapse
|
79
|
Fiesco-Sepúlveda KY, Serrano-Bermúdez LM. Contributions of Latin American researchers in the understanding of the novel coronavirus outbreak: a literature review. PeerJ 2020; 8:e9332. [PMID: 32547890 PMCID: PMC7276147 DOI: 10.7717/peerj.9332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
This article aimed to give the visibility of Latin American researchers' contributions to the comprehension of COVID-19; our method was a literature review. Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, in less than 4 months, researchers have published a significant number of articles related to this novel virus. For instance, a search focused on the Scopus database on 10 April 2020, showed 1,224 documents published by authors with 1,797 affiliations from 80 countries. A total of 25.4%, 24.0% and 12.6% of these national affiliations were from China, Europe and the USA, respectively, making these regions leaders in COVID-19 research. In the case of Latin America, on 10 April 2020, we searched different databases, such as Scopus, PubMed and Web of Science, finding that the contribution of this region was 2.7 ± 0.6% of the total publications found. In other words, we found 153 publications related to COVID-19 with at least one Latin American researcher. We summarized and processed the information from these 153 publications, finding active participation in topics like medical, social and environmental considerations, bioinformatics and epidemiology.
Collapse
|
80
|
Alvarez-Moreno CA, Rodríguez-Morales AJ. Testing Dilemmas: Post negative, positive SARS-CoV-2 RT-PCR - is it a reinfection? Travel Med Infect Dis 2020; 35:101743. [PMID: 32416153 PMCID: PMC7228728 DOI: 10.1016/j.tmaid.2020.101743] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 12/02/2022]
Affiliation(s)
- Carlos A Alvarez-Moreno
- Department of Internal Medicine, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia; Clínica Universitaria Colombia, Clinica Colsanitas, Bogotá, Colombia
| | - Alfonso J Rodríguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia; Associate Editor, Travel Medicine and Infectious Diseases, Colombia; Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, 660004, Colombia.
| |
Collapse
|
81
|
Fostering Options for Prevention, Containment, and Care Delivery Service Capabilities on COVID-19 (SARS CoV-2) Pandemic Outbreak Symbiosis. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2020. [DOI: 10.5812/archcid.103878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
82
|
Fulzele S, Sahay B, Yusufu I, Lee TJ, Sharma A, Kolhe R, Isales CM. COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile. Aging Dis 2020; 11:509-522. [PMID: 32489698 PMCID: PMC7220294 DOI: 10.14336/ad.2020.0428] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023] Open
Abstract
The World health organization (WHO) declared Coronavirus disease 2019 (COVID-19) a global pandemic and a severe public health crisis. Drastic measures to combat COVID-19 are warranted due to its contagiousness and higher mortality rates, specifically in the aged patient population. At the current stage, due to the lack of effective treatment strategies for COVID-19 innovative approaches need to be considered. It is well known that host cellular miRNAs can directly target both viral 3'UTR and coding region of the viral genome to induce the antiviral effect. In this study, we did in silico analysis of human miRNAs targeting SARS (4 isolates) and COVID-19 (29 recent isolates from different regions) genome and correlated our findings with aging and underlying conditions. We found 848 common miRNAs targeting the SARS genome and 873 common microRNAs targeting the COVID-19 genome. Out of a total of 848 miRNAs from SARS, only 558 commonly present in all COVID-19 isolates. Interestingly, 315 miRNAs are unique for COVID-19 isolates and 290 miRNAs unique to SARS. We also noted that out of 29 COVID-19 isolates, 19 isolates have identical miRNA targets. The COVID-19 isolates, Netherland (EPI_ISL_422601), Australia (EPI_ISL_413214), and Wuhan (EPI_ISL_403931) showed six, four, and four unique miRNAs targets, respectively. Furthermore, GO, and KEGG pathway analysis showed that COVID-19 targeting human miRNAs involved in various age-related signaling and diseases. Recent studies also suggested that some of the human miRNAs targeting COVID-19 decreased with aging and underlying conditions. GO and KEGG identified impaired signaling pathway may be due to low abundance miRNA which might be one of the contributing factors for the increasing severity and mortality in aged individuals and with other underlying conditions. Further, in vitro and in vivo studies are needed to validate some of these targets and identify potential therapeutic targets.
Collapse
Affiliation(s)
- Sadanand Fulzele
- Department of Medicine, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
| | - Bikash Sahay
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, USA.
| | - Ibrahim Yusufu
- Department of Medicine, Augusta University, Augusta, GA, USA.
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA.
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA.
| | - Ravindra Kolhe
- Departments of Pathology, Augusta University, Augusta, GA 30912, USA
| | - Carlos M Isales
- Department of Medicine, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
| |
Collapse
|
83
|
Sen-Crowe B, McKenney M, Elkbuli A. COVID-19 response and containment strategies in the US, South Korea, and Iceland: Lessons learned and future directions. Am J Emerg Med 2020; 38:1537-1539. [PMID: 32386807 PMCID: PMC7195105 DOI: 10.1016/j.ajem.2020.04.072] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Affiliation(s)
- Brendon Sen-Crowe
- Department of Surgery, Division of Trauma and Surgical Critical Care, Kendall Regional Medical Center, Miami, FL, USA
| | - Mark McKenney
- Department of Surgery, Division of Trauma and Surgical Critical Care, Kendall Regional Medical Center, Miami, FL, USA; University of South Florida, Tampa, FL, USA
| | - Adel Elkbuli
- Department of Surgery, Division of Trauma and Surgical Critical Care, Kendall Regional Medical Center, Miami, FL, USA.
| |
Collapse
|
84
|
Isihak FA, Hamad MA, Mustafa NG. COVID-19: an updated review. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2020. [DOI: 10.15789/2220-7619-cau-1443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
COVID-19 is a zoonotic disease that showed higher levels of transmissibility in humans. Coronavirus has the largest recognized genome (28–33 kb) of a positive-sense single stranded RNA. The genome composed of 5′-end, the translationable mRNA sequences for the key proteins; replicase, spike, envelop membrane, and nucleocapsid and 3′-end (polyA tail). This highly contagious virus may impair the immune system in the early phase of the disease, hence the symptoms of the disease appear very rapidly. Importantly until now, there is no efficient strategy for containing the disease. So, all the world scientists today are in a race against time to find a vaccine or treatment to COVID-19, which requires a deeper understanding.
Collapse
|
85
|
Ollarves-Carrero MF, Rodriguez-Morales AG, Bonilla-Aldana DK, Rodriguez-Morales AJ. Anosmia in a healthcare worker with COVID-19 in Madrid, Spain. Travel Med Infect Dis 2020; 35:101666. [PMID: 32298782 PMCID: PMC7194729 DOI: 10.1016/j.tmaid.2020.101666] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022]
Affiliation(s)
| | - Andrea G Rodriguez-Morales
- Unidad Procedimientos, Policlínico Neurología, Centro de Referencia de Salud Dr. Salvador Allende Gossens, Santiago de Chile, Chile; Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia
| | - D Katterine Bonilla-Aldana
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia; Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia; Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Risaralda, Colombia
| | - Alfonso J Rodriguez-Morales
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia; Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Risaralda, Colombia; Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, Colombia.
| |
Collapse
|
86
|
Akinyemi KO, Fakorede CO, Anjorin AAA, Abegunrin RO, Adunmo O, Ajoseh SO, Akinkunmi FM. Intrigues and Challenges Associated with COVID-19 Pandemic in Nigeria. Health (London) 2020. [DOI: 10.4236/health.2020.128072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|