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Ebong U, Büttner SM, Schmidt SA, Flack F, Korf P, Peters L, Grüner B, Stenger S, Stamminger T, Kestler H, Beer M, Kloth C. Quantitative Evaluation of COVID-19 Pneumonia CT Using AI Analysis-Feasibility and Differentiation from Other Common Pneumonia Forms. Diagnostics (Basel) 2023; 13:2129. [PMID: 37371024 DOI: 10.3390/diagnostics13122129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/14/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
PURPOSE: To implement the technical feasibility of an AI-based software prototype optimized for the detection of COVID-19 pneumonia in CT datasets of the lung and the differentiation between other etiologies of pneumonia. METHODS: This single-center retrospective case-control-study consecutively yielded 144 patients (58 female, mean age 57.72 ± 18.25 y) with CT datasets of the lung. Subgroups including confirmed bacterial (n = 24, 16.6%), viral (n = 52, 36.1%), or fungal (n = 25, 16.6%) pneumonia and (n = 43, 30.7%) patients without detected pneumonia (comparison group) were evaluated using the AI-based Pneumonia Analysis prototype. Scoring (extent, etiology) was compared to reader assessment. RESULTS: The software achieved an optimal sensitivity of 80.8% with a specificity of 50% for the detection of COVID-19; however, the human radiologist achieved optimal sensitivity of 80.8% and a specificity of 97.2%. The mean postprocessing time was 7.61 ± 4.22 min. The use of a contrast agent did not influence the results of the software (p = 0.81). The mean evaluated COVID-19 probability is 0.80 ± 0.36 significantly higher in COVID-19 patients than in patients with fungal pneumonia (p < 0.05) and bacterial pneumonia (p < 0.001). The mean percentage of opacity (PO) and percentage of high opacity (PHO ≥ -200 HU) were significantly higher in COVID-19 patients than in healthy patients. However, the total mean HU in COVID-19 patients was -679.57 ± 112.72, which is significantly higher than in the healthy control group (p < 0.001). CONCLUSION: The detection and quantification of pneumonia beyond the primarily trained COVID-19 datasets is possible and shows comparable results for COVID-19 pneumonia to an experienced reader. The advantages are the fast, automated segmentation and quantification of the pneumonia foci.
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Affiliation(s)
- Una Ebong
- Department of Diagnostic and Interventional Radiology, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Susanne Martina Büttner
- Department of Diagnostic and Interventional Radiology, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Stefan A Schmidt
- Department of Diagnostic and Interventional Radiology, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Franziska Flack
- Scientific Collaborations Siemens Healthcare GmbH Erlangen, 91052 Erlangen, Germany
| | - Patrick Korf
- Scientific Collaborations Siemens Healthcare GmbH Erlangen, 91052 Erlangen, Germany
| | - Lynn Peters
- Division of Infectious Diseases, University Hospital and Medical Centre of Ulm, 89081 Ulm, Germany
| | - Beate Grüner
- Division of Infectious Diseases, University Hospital and Medical Centre of Ulm, 89081 Ulm, Germany
| | - Steffen Stenger
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, 89081 Ulm, Germany
| | - Thomas Stamminger
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Hans Kestler
- Institute for Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Meinrad Beer
- Department of Diagnostic and Interventional Radiology, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Christopher Kloth
- Department of Diagnostic and Interventional Radiology, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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2
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Shilts J, Crozier TWM, Teixeira-Silva A, Gabaev I, Gerber PP, Greenwood EJD, Watson SJ, Ortmann BM, Gawden-Bone CM, Pauzaite T, Hoffmann M, Nathan JA, Pöhlmann S, Matheson NJ, Lehner PJ, Wright GJ. LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein. PLoS Biol 2023; 21:e3001959. [PMID: 36735681 PMCID: PMC9897555 DOI: 10.1371/journal.pbio.3001959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/14/2022] [Indexed: 02/04/2023] Open
Abstract
The interactions between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and human host factors enable the virus to propagate infections that lead to Coronavirus Disease 2019 (COVID-19). The spike protein is the largest structural component of the virus and mediates interactions essential for infection, including with the primary angiotensin-converting enzyme 2 (ACE2) receptor. We performed two independent cell-based systematic screens to determine whether there are additional proteins by which the spike protein of SARS-CoV-2 can interact with human cells. We discovered that in addition to ACE2, expression of LRRC15 also causes spike protein binding. This interaction is distinct from other known spike attachment mechanisms such as heparan sulfates or lectin receptors. Measurements of orthologous coronavirus spike proteins implied the interaction was functionally restricted to SARS-CoV-2 by accessibility. We localized the interaction to the C-terminus of the S1 domain and showed that LRRC15 shares recognition of the ACE2 receptor binding domain. From analyzing proteomics and single-cell transcriptomics, we identify LRRC15 expression as being common in human lung vasculature cells and fibroblasts. Levels of LRRC15 were greatly elevated by inflammatory signals in the lungs of COVID-19 patients. Although infection assays demonstrated that LRRC15 alone is not sufficient to permit viral entry, we present evidence that it can modulate infection of human cells. This unexpected interaction merits further investigation to determine how SARS-CoV-2 exploits host LRRC15 and whether it could account for any of the distinctive features of COVID-19.
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Affiliation(s)
- Jarrod Shilts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Thomas W. M. Crozier
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Ana Teixeira-Silva
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Ildar Gabaev
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Pehuén Pereyra Gerber
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Edward J. D. Greenwood
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Samuel James Watson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Brian M. Ortmann
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Christian M. Gawden-Bone
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Tekle Pauzaite
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August University Göttingen, Göttingen, Germany
| | - James A. Nathan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center – Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August University Göttingen, Göttingen, Germany
| | - Nicholas J. Matheson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Paul J. Lehner
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Gavin J. Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
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3
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [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] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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4
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Madilo FK, Letsyo E, Oppong BA, Buachi YB, Klutse CM, Parry-Hanson Kunadu A. Assessing Producers’ Knowledge in Good Manufacturing Practices during the Production of a Traditionally Fermented Food (Ga Kenkey) in the Ho Municipality, Ghana. J FOOD QUALITY 2022; 2022:1-9. [DOI: 10.1155/2022/8462337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
Good manufacturing practice (GMP) is the primary sanitary and processing requirement necessary to ensure the production of safe foods. It ensures that the production facilities and processes have the necessary conditions to prevent potential hazards from contaminating foods. However, little is known about its application in the production of a traditionally fermented and well-patronized food like the Ga kenkey. This study was therefore designed to evaluate the knowledge and practices of Ga kenkey producers in GMPs. A self-administered questionnaire was prepared and used to recruit 42 Ga kenkey producers using convenient sampling techniques. Out of the 42 producers, 83.3% were females, between 18 and 33 years (61.9%) and single (42.9%), and have been in the business for about 0 to 5 years (69.1%). A significant number of producers had neither GMP, food safety nor HACCP training. The producers have inadequate knowledge of GMPs since majority of them do not use gloves and consider wearing them unnecessary. Even though the producers agreed that GMPs improve product qualities, the establishment of reputation, and customer satisfaction and identify problems within the production process, they however did not pay attention to any form of hazards during the production process. Therefore, since education, training, and experience had a significant (
) positive influence on the producers’ knowledge and practices, sufficient training in GMPs coupled with regular supervision should be provided to the producers for the hygienic and safe production of this commonly patronized food.
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Affiliation(s)
- Felix Kwashie Madilo
- Department of Food Science and Technology, Faculty of Applied Sciences and Technology, Ho Technical University, Box HP 217,Volta Region, Ho, Ghana
- Department of Nutrition and Food Science, College of Applied Sciences, University of Ghana, Greater Accra, Ghana
| | - Emmanuel Letsyo
- Department of Food Science and Technology, Faculty of Applied Sciences and Technology, Ho Technical University, Box HP 217,Volta Region, Ho, Ghana
| | - Bless Abrah Oppong
- Department of Food Science and Technology, Faculty of Applied Sciences and Technology, Ho Technical University, Box HP 217,Volta Region, Ho, Ghana
| | - Yayra Benedicta Buachi
- Department of Food Science and Technology, Faculty of Applied Sciences and Technology, Ho Technical University, Box HP 217,Volta Region, Ho, Ghana
| | - Comfort Mawuse Klutse
- Department of Hospitality and Tourism Management, Faculty of Applied Sciences and Technology, Ho Technical University, Box HP 217,Volta Region, Ho, Ghana
| | - Angela Parry-Hanson Kunadu
- Department of Nutrition and Food Science, College of Applied Sciences, University of Ghana, Greater Accra, Ghana
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5
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Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. Sci Rep 2022; 12:4631. [PMID: 35301412 PMCID: PMC8929288 DOI: 10.1038/s41598-022-08780-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
Using next generation sequencing technology, we identified a novel SARS-CoV-2 variant with a truncated ORF8 protein mutation near the end of the viral genome from nucleotides 27,878 to 27,958. This point mutation from C to T at nucleotide 27,956 changed the amino acid codon CAA (glutamine) to a stop codon, TAA, created a novel stop codon in ORF8 gene, resulting in a much smaller ORF8 protein (26 aa) than the wild type ORF8 protein (121 aa). This variant belongs to Pango lineage B.1.1291, which also contains the D614G mutation in the Spike (S) gene. The B.1.1291 lineage is predominantly circulated in the United States of America (97.18%), although it was also found in other counties (Russia, Canada, Latvia, Chile, India, Japan, Colombia, Germany, Greece, Mexico, and UK). A total of 340 closely related variants to this novel variant were identified in GISAID database with collection dates ranged from 3/6/2020 to 10/21/2020. In addition, a search within NCBI Genbank database found that 108,405 of 873,230 (12.4%) SAR-CoV-2 complete genomes contain this truncated ORF8 protein mutation, indicating this mutation may arise spontaneously in other lineages as well. The wide distribution of this mutation indicates that this truncated ORF8 protein mutation may provide the virus a growth advantage and adaptive evolution.
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6
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Takatsuka H, Fahmi M, Hamanishi K, Sakuratani T, Kubota Y, Ito M. In silico Analysis of SARS-CoV-2 ORF8-Binding Proteins Reveals the Involvement of ORF8 in Acquired-Immune and Innate-Immune Systems. Front Med (Lausanne) 2022; 9:824622. [PMID: 35178414 PMCID: PMC8844466 DOI: 10.3389/fmed.2022.824622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 is the causative agent of a new type of coronavirus infection, COVID-19, which has rapidly spread worldwide. The overall genome sequence homology between SARS-CoV-2 and SARS-CoV is 79%. However, the homology of the ORF8 protein between these two coronaviruses is low, at ~26%. Previously, it has been suggested that infection by the ORF8-deleted variant of SARS-CoV-2 results in less severe symptoms than in the case of wild-type SARS-CoV-2. Although we found that ORF8 is involved in the proteasome autoimmunity system, the precise role of ORF8 in infection and pathology has not been fully clarified. In this study, we determined a new network of ORF8-interacting proteins by performing in silico analysis of the binding proteins against the previously described 47 ORF8-binding proteins. We used as a dataset 431 human protein candidates from Uniprot that physically interacted with 47 ORF8-binding proteins, as identified using STRING. Homology and phylogenetic profile analyses of the protein dataset were performed on 446 eukaryotic species whose genome sequences were available in KEGG OC. Based on the phylogenetic profile results, clustering analysis was performed using Ward's method. Our phylogenetic profiling showed that the interactors of the ORF8-interacting proteins were clustered into three classes that were conserved across chordates (Class 1: 152 proteins), metazoans (Class 2: 163 proteins), and eukaryotes (Class 3: 114 proteins). Following the KEGG pathway analysis, classification of cellular localization, tissue-specific expression analysis, and a literature study on each class of the phylogenetic profiling cluster tree, we predicted that the following: protein members in Class 1 could contribute to COVID-19 pathogenesis via complement and coagulation cascades and could promote sarcoidosis; the members of Class 1 and 2, together, may contribute to the downregulation of Interferon-β; and Class 3 proteins are associated with endoplasmic reticulum stress and the degradation of human leukocyte antigen.
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Affiliation(s)
- Hisashi Takatsuka
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Muhamad Fahmi
- Research Department, Research Institute for Humanity and Nature, Kyoto, Japan.,Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Japan
| | - Kotono Hamanishi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Takuya Sakuratani
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Yukihiko Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
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7
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Ndagi U, Abdullahi M, Hamza AN, Magaji MG, Mhlongo NN, Babazhitsu M, Majiya H, Makun HA, Lawal MM. Impact of Drug Repurposing on SARS-Cov-2 Main Protease. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022; 96. [PMCID: PMC10036164 DOI: 10.1134/s0036024423030299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The recent emergence of the severe acute respiratory disease caused by a novel coronavirus remains a concern posing many challenges to public health and the global economy. The resolved crystal structure of the main protease of SARS-CoV-2 or SCV2 (Mpro) has led to its identification as an attractive target for designing potent antiviral drugs. Herein, we provide a comparative molecular impact of hydroxychloroquine (HCQ), remdesivir, and β-D-N4-Hydroxycytidine (NHC) binding on SCV2 Mpro using various computational approaches like molecular docking and molecular dynamics (MD) simulation. Data analyses showed that HCQ, remdesivir, and NHC binding to SARS-CoV-2 Mpro decrease the protease loop capacity to fluctuate. These binding influences the drugs’ optimum orientation in the conformational space of SCV2 Mpro and produce noticeable steric effects on the interactive residues. An increased hydrogen bond formation was observed in SCV2 Mpro–NHC complex with a decreased receptor residence time during NHC binding. The binding mode of remdesivir to SCV2 Mpro differs from other drugs having van der Waals interaction as the force stabilizing protein–remdesivir complex. Electrostatic interaction dominates in the SCV2 Mpro−HCQ and SCV2 Mpro–NHC. Residue Glu166 was highly involved in the stability of remdesivir and NHC binding at the SCV2 Mpro active site, while Asp187 provides stability for HCQ binding.
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Affiliation(s)
- Umar Ndagi
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Maryam Abdullahi
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Asmau N. Hamza
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Mohd G. Magaji
- Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Ndumiso N. Mhlongo
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - Makun Babazhitsu
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, Usman Danfodio University, Sokoto, Nigeria
| | - Hussaini Majiya
- Department of Microbiology, Ibrahim Badamasi Babangida University, Lapai, Niger State, Nigeria
| | - Hussaini Anthony Makun
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Monsurat M. Lawal
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 4001 Durban, South Africa
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8
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Stromberg ZR, Theiler J, Foley BT, Myers Y Gutiérrez A, Hollander A, Courtney SJ, Gans J, Deshpande A, Martinez-Finley EJ, Mitchell J, Mukundan H, Yusim K, Kubicek-Sutherland JZ. Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000207. [PMID: 36962401 PMCID: PMC10021650 DOI: 10.1371/journal.pgph.0000207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 01/23/2022] [Indexed: 12/23/2022]
Abstract
Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire group of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.
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Affiliation(s)
- Zachary R Stromberg
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - James Theiler
- Space Data Science and Systems, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Brian T Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Adán Myers Y Gutiérrez
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Attelia Hollander
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Samantha J Courtney
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jason Gans
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alina Deshpande
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | - Jason Mitchell
- Presbyterian Healthcare Services, Albuquerque, New Mexico, United States of America
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Karina Yusim
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jessica Z Kubicek-Sutherland
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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9
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Khan J, Asoom LIA, Khan M, Chakrabartty I, Dandoti S, Rudrapal M, Zothantluanga JH. Evolution of RNA viruses from SARS to SARS-CoV-2 and diagnostic techniques for COVID-19: a review. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:60. [PMID: 34642633 PMCID: PMC8494164 DOI: 10.1186/s43088-021-00150-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/20/2021] [Indexed: 01/12/2023] Open
Abstract
Background From the start of the twenty-first century up to the year 2021, RNA viruses are the main causative agents of the majority of the disease outbreaks the world has confronted. Recently published reviews on SARS-CoV-2 have mainly focused on its structure, development of the outbreak, relevant precautions, management trials and available therapies. However, in this review, we aim to explore the history, evolution of all coronaviruses and the associated viral outbreaks along with the diagnostics for COVID-19 in the twenty-first century.
Main body We have focused on different RNA viruses’ viz. SARS-CoV, MERS-CoV, and SARS-CoV-2, their classification, and the various disease outbreaks caused by them. In the subsequent section, the comparison of different RNA viruses affecting humans has been made based on the viral genome, structure, time of the outbreak, mode of spread, virulence, causative agents, and transmission. Due to the current mayhem caused by the rapidly emerging virus, special attention is given to SARS-CoV-2, its genome updates, and infectivity. Finally, the current diagnostic techniques such as nucleic acid testing (real time-polymerase chain reaction and loop-mediated isothermal amplification), CRISPR-based diagnostics (CRISPR based DETECTR assay, CRISPR based SHERLOCK test, AIOD-CRISPR, FELUDA, CREST), chest radiographs (computed tomography, X-ray), and serological tests (Lateral flow assay, enzyme-linked immunosorbent assay, chemiluminescent immunoassay, neutralization assay, nano-sensors, blood test, viral sequencing) with their pros and cons, and future diagnostic prospective have been described.
Conclusions The present gloomy scenario mandates clinical manifestations, contact tracing, and laboratory tests as important parameters that need to be taken into consideration to make the final diagnosis.
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Affiliation(s)
- Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952 Saudi Arabia
| | - Lubna Ibrahim Al Asoom
- Physiology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31541 Saudi Arabia
| | - Maryam Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002 India
| | - Ishani Chakrabartty
- Department of Science, P.A. First Grade College (Affiliated To Mangalore University, Mangalore), Nadupadav, Mangalore, Karnataka 574153 India
| | - Sayequa Dandoti
- Department of Biology, Deanship of Preparatory Year, Imam Abdulrahman Bin Faisal University, Dammam, 31541 Saudi Arabia
| | - Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education & Research (Affiliated to Savitribai Phule Pune University, Pune) , Chinchwad, Pune, Maharashtra 411019 India
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam 786004 India
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Abdurrahman L, Fang X, Zhang Y. Molecular Insights of SARS-CoV-2 Infection and Molecular Treatments. Curr Mol Med 2021; 22:621-639. [PMID: 34645374 DOI: 10.2174/1566524021666211013121831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/15/2021] [Accepted: 07/23/2021] [Indexed: 01/18/2023]
Abstract
The coronavirus disease emerged in December 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome-related coronavirus 2 (SARS-CoV-2) and its rapid global spread has brought an international health emergency and urgent responses for seeking efficient prevention and therapeutic treatment. This has led to imperative needs for illustration of the molecular pathogenesis of SARS-CoV-2, identification of molecular targets or receptors, and development of antiviral drugs, antibodies, and vaccines. In this study, we investigated the current research progress in combating SARS-CoV-2 infection. Based on the published research findings, we first elucidated, at the molecular level, SARS-CoV-2 viral structures, potential viral host-cell-invasion and pathogenic mechanisms, main virus-induced immune responses, and emerging SARS-CoV-2 variants. We then focused on the main virus- and host-based potential targets, summarized and categorized effective inhibitory molecules based on drug development strategies for COVID-19, that can guide efforts for the identification of new drugs and treatment for this problematic disease. Current research and development of antibodies and vaccines were also introduced and discussed. We concluded that the main virus entry route- SARS-CoV-2 spike protein interaction with ACE2 receptors has played a key role in guiding the development of therapeutic treatments against COVID-19, four main therapeutic strategies may be considered in developing molecular therapeutics, and drug repurposing is likely to be an easy, fast and low-cost approach in such a short period of time with urgent need of antiviral drugs. Additionally, the quick development of antibody and vaccine candidates has yielded promising results, but the wide-scale deployment of safe and effective COVID-19 vaccines remains paramount in solving the pandemic crisis. As new variants of the virus begun to emerge, the efficacy of these vaccines and treatments must be closely evaluated. Finally, we discussed the possible challenges of developing molecular therapeutics for COVID-19 and suggested some potential future efforts. Despite the limited availability of literatures, our attempt in this work to provide a relatively comprehensive overview of current SARS-CoV-2 studies can be helpful for quickly acquiring the key information of COVID-19 and further promoting this important research to control and diminish the pandemic.
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Affiliation(s)
- Lama Abdurrahman
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| | - Xiaoqian Fang
- Department of Molecular Science, School of Medicine, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
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Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV. Genes Genomics 2021; 43:1351-1359. [PMID: 34228320 PMCID: PMC8258482 DOI: 10.1007/s13258-021-01136-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/29/2021] [Indexed: 01/08/2023]
Abstract
Background COVID-19, as a novel coronavirus disease caused by new coronavirus SARS-CoV-2, spreads all over the world, and brings harm to human in many countries. Humans suffered a lot from both SARS-CoV-2 now and by SARS-CoV in the year 2003. It is important to understand the differences and the relationships between these two types of viruses. Objective To compare relative synonymous codon usage of ORF1ab gene in SARS-CoV-2 and SARS-CoV, relative synonymous codon usage of their genomes are studied in this paper from the bioinformatics perspective. Methods The ORF1ab gene, which is an important non-structural polyprotein coding gene and now used for nucleic acid detection markers in many measurement method, in both SARS-CoV-2 (30 strains) and SARS-CoV (20 strains) are considered to be the research object in the present paper. The relative synonymous codon usage values of the ORF1ab gene are calculated to characterize the differences and the evolutionary characteristics among 50 strains. Results There is a significant difference between SARS-CoV and SARS-CoV-2 when the relative synonymous codon usage value of ORF1ab genes is concerned. The results suggest that codon usage pattern of SARS-CoV is more similar to human than that of the SARS-CoV-2, and that the inner difference in SARS-CoV-2 strains is larger than that of SARS-CoV, which denote the larger diversity exits in the SARS-CoV-2 virus. Conclusion These results show that the relative synonymous codon usage values in the coronavirus could be used for further research on their evolutionary phenomenon.
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Srivastava V, Ahmad A. New perspective towards therapeutic regimen against SARS-CoV-2 infection. J Infect Public Health 2021; 14:852-862. [PMID: 34118735 PMCID: PMC8152204 DOI: 10.1016/j.jiph.2021.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 05/05/2021] [Accepted: 05/16/2021] [Indexed: 12/23/2022] Open
Abstract
The ongoing enormous loss of human life owing to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has led to a global crisis ranging from the collapse of health - care systems to socio-economic instability. As SARS-CoV-2 is a novel virus, very little information is available from researchers and therefore, a rigorous effort is required to decode its pathogenicity. There are no licenced treatment options available for treating SARS-CoV-2 infections and the development of a new antiviral drug targeting coronavirus cannot happen soon. Consequently, drug repurposing is a promising solution for combating the present pandemic. In this review, we have thoroughly discussed all the proteins encoded by the SARS-CoV-2 genome; their importance in pathogenicity and their potential role in drug discovery. Also, the budding threat of co-infections by other pathogenic microbes has been highlighted. Furthermore, the advances made in the medicinal field for the treatment and prevention of this viral infection is explained. Altogether, this review will provide some insightful discussions about this infectious disease and will meet certain of the knowledge gaps which exist by presenting an exhaustive and extensive scientific report on the ongoing mission for COVID-19 drug discovery.
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Affiliation(s)
- Vartika Srivastava
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa; Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, 2193, South Africa.
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Cassaniti I, Percivalle E, Bergami F, Piralla A, Comolli G, Bruno R, Vecchia M, Sambo M, Colaneri M, Zuccaro V, Benazzo M, Robotti C, Calastri A, Maiorano E, Ferrari A, Cambiè G, Baldanti F. SARS-CoV-2 specific T-cell immunity in COVID-19 convalescent patients and unexposed controls measured by ex vivo ELISpot assay. Clin Microbiol Infect 2021; 27:1029-1034. [PMID: 33813122 PMCID: PMC8016542 DOI: 10.1016/j.cmi.2021.03.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVES SARS-CoV-2 T-cell response characterization represents a crucial issue for defining the role of immune protection against COVID-19. The aim of the study was to assess the SARS-CoV-2 T-cell response in a cohort of COVID-19 convalescent patients and in a group of unexposed subjects. METHODS SARS-CoV-2 T-cell response was quantified from peripheral blood mononuclear cells (PBMCs) of 87 COVID-19 convalescent subjects (range 7-239 days after symptom onset) and 33 unexposed donors by ex vivo ELISpot assay. Follow-up of SARS-CoV-2 T-cell response was performed in ten subjects up to 12 months after symptom onset. The role of SARS-CoV-2 specific CD4 and CD8 T cells was characterized in a group of COVID-19 convalescent subjects. Moreover, neutralizing antibodies were determined in serum samples. RESULTS In 14/33 (42.4%) unexposed donors and 85/87 (97.7%) COVID-19 convalescent subjects a positive result for at least one SARS-CoV-2 antigen was observed. A positive response was observed up to 12 months after COVID-19 infection (median 246 days after symptom onset; range 118-362 days). Of note, SARS-CoV-2 T-cell response seems to be mainly mediated by CD4 T cells. A weak positive correlation was observed between Spike-specific T-cell response and neutralizing antibody titre (p 0.0028; r2 = 0.2891) and positive SARS-CoV-2 T-cell response was observed in 8/9 (88.9%) COVID-19 convalescent subjects with undetectable SARS-CoV-2 neutralizing antibodies. DISCUSSION Cross-reactive SARS-CoV-2 T-cell response in uninfected patients may be due to previous infections with other common coronaviruses. Our data suggest that long-term SARS-CoV-2 T-cell response might accompany a waning humoral response.
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Affiliation(s)
- Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy.
| | - Elena Percivalle
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Bergami
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giuditta Comolli
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Experimental Research Laboratories, Biotechnology Area, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Raffaele Bruno
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy; Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marco Vecchia
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Margherita Sambo
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marta Colaneri
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valentina Zuccaro
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marco Benazzo
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy; Department of Otolaryngology Head Neck Surgery, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Carlo Robotti
- Department of Otolaryngology Head Neck Surgery, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Anna Calastri
- Department of Otolaryngology Head Neck Surgery, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Eugenia Maiorano
- Department of Otolaryngology Head Neck Surgery, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alessandro Ferrari
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giuseppe Cambiè
- Immunohematology and Transfusion Medicine Unit, Ospedale Maggiore di Lodi, Lodi, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
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Achour A. Identification of oligopeptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) non structural protein 8 (NSP8) and their similarities with type 1 angiotensin II receptor key sites. Biomed Pharmacother 2021; 141:111722. [PMID: 34144455 PMCID: PMC8179057 DOI: 10.1016/j.biopha.2021.111722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/07/2021] [Indexed: 01/25/2023] Open
Abstract
Coronavirus disease 2019 is associated with clinical symptoms including severe inflammatory syndrome and a higher expression of angiotensin II. As a pro-inflammatory mediator, the physiologic effects of angiotensin II are mediated by a G-protein coupled receptor, termed AT1R. Following binding, AT1R initiates the process of signal desensitization necessary to maintain cellular homeostasis. At the cellular level, this function occurs via the G protein-dependent signaling and the phosphorylation. We describe amino acids similarities between SARS COV-2 nonstructural protein (NSP8) which is associated with intracellular membranes and AT1R key sites. Since abnormal activation of AT1R receptor leads to a number of physiological disorders, we hypothesize that SARS COV-2 might further interfere with the angiotensin II receptor functions.
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Affiliation(s)
- Ammar Achour
- I VS 14 Bis Rue de Mayenne, 94000 Creteil, France.
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Mutations and Epidemiology of SARS-CoV-2 Compared to Selected Corona Viruses during the First Six Months of the COVID-19 Pandemic: A Review. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus (CoV) disease 2019 (COVID-19). This study compared the genome, mutations, and infectivity/transmissibility of SARS-CoV-2 with selected betacoronaviruses (beta-CoVs). This study further examined the origin, risk factors, and outbreaks caused by beta-CoVs. We searched the following databases for relevant studies: PubMed, Google Scholar, and the World Health Organization COVID-19 database. A close relationship between SARS-CoV-2 and SARS bat-like CoV RaTG13 (98.9%) was found at the amino acid level, followed by pangolin CoVs. Non-synonymous mutations occur at high frequencies in the open reading frame (ORF) 1ab, spike (S) protein, and nucleocapsid. Mutations P323L and D614G in the RNA-dependent RNA polymerase (RdRp) and S protein, respectively, occur at a high frequency globally. Mutations at position 3037 in the nonstructural protein (Nsp) 3, 14408 (RdRp), and 23403 (S) confer transmissibility to SARS-CoV-2. SARS-CoV-2 has higher infectivity and transmissibility than SARS-CoV, which shares the same receptor. Although bats are confirmed reservoirs, intermediate hosts are currently unknown. Smoking, old age, diabetes, cardiovascular diseases, and hypertension have all been associated with COVID-19. Within six months of its outbreak, COVID-19 was reported in all countries worldwide, whereas SARS was reported in 28 countries and Middle East respiratory syndrome (MERS) in 5 countries. However, the fatality rate of MERS (65%) was higher than that of COVID-19 (4.9%) and SARS (6.6%). Identifying the SARS-CoV-2 intermediate hosts will help prevent future outbreaks. Attention should be given to the pangolin CoVs. Variations in the S gene may confer transmissibility and infectivity.
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Skariyachan S, Gopal D, Muddebihalkar AG, Uttarkar A, Niranjan V. Structural insights on the interaction potential of natural leads against major protein targets of SARS-CoV-2: Molecular modelling, docking and dynamic simulation studies. Comput Biol Med 2021; 132:104325. [PMID: 33751995 PMCID: PMC7954774 DOI: 10.1016/j.compbiomed.2021.104325] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022]
Abstract
Though significant efforts are in progress for developing drugs and vaccines against COVID-19, limited therapeutic agents are available currently. Thus, it is essential to undertake COVID-19 research and to identify therapeutic interventions in which computational modeling and virtual screening of lead molecules provide significant insights. The present study aimed to predict the interaction potential of natural lead molecules against prospective protein targets of SARS-CoV-2 by molecular modeling, docking, and dynamic simulation. Based on the literature survey and database search, fourteen molecular targets were selected and the three targets which lack the native structures were computationally modeled. The drug-likeliness and pharmacokinetic features of ninety-two natural molecules were predicted. Four lead molecules with ideal drug-likeliness and pharmacokinetic properties were selected and docked against fourteen targets, and their binding energies were compared with the binding energy of the interaction between Chloroquine and Hydroxychloroquine to their usual targets. The stabilities of selected docked complexes were confirmed by MD simulation and energy calculations. Four natural molecules demonstrated profound binding to most of the prioritized targets, especially, Hyoscyamine and Tamaridone to spike glycoprotein and Rotiorinol-C and Scutifoliamide-A to replicase polyprotein-1ab main protease of SARS-CoV-2 showed better binding energy, conformational and dynamic stabilities compared to the binding energy of Chloroquine and its usual target glutathione-S-transferase. The aforementioned lead molecules can be used to develop novel therapeutic agents towards the protein targets of SARS-CoV-2, and the study provides significant insight for structure-based drug development against COVID-19.
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Affiliation(s)
- Sinosh Skariyachan
- Department of Microbiology, St. Pius X College Rajapuram, Kasaragod, Kerala, India,Corresponding author
| | - Dharshini Gopal
- Department of Bioinformatics, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | - Akshay Uttarkar
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
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Keshta AS, Mallah SI, Al Zubaidi K, Ghorab OK, Keshta MS, Alarabi D, Abousaleh MA, Salman MT, Taha OE, Zeidan AA, Elsaid MF, Tang P. COVID-19 versus SARS: A comparative review. J Infect Public Health 2021; 14:967-977. [PMID: 34130121 PMCID: PMC8064890 DOI: 10.1016/j.jiph.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/11/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
The two genetically similar severe acute respiratory syndrome coronaviruses, SARS-CoV-1 and SARS-CoV-2, have each been responsible for global epidemics of vastly different scales. Although both viruses arose from similar origins, they quickly diverged due to differences in their transmission dynamics and spectrum of clinical presentations. The potential involvement of multiple organs systems, including the respiratory, cardiac, gastrointestinal and neurological, during infection necessitates a comprehensive understanding of the clinical pathogenesis of each virus. The management of COVID-19, initially modelled after SARS and other respiratory illnesses, has continued to evolve as we accumulate more knowledge and experience during the pandemic, as well as develop new therapeutics and vaccines. The impact of these two coronaviruses has been profound for our health care and public health systems, and we hope that the lessons learned will not only bring the current pandemic under control, but also prevent and reduce the impact of future pandemics.
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Affiliation(s)
- Ahmed S Keshta
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Saad I Mallah
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Khaled Al Zubaidi
- Division of Paediatric Infectious Diseases, Hamad Medical Corporation, Doha, Qatar
| | - Omar K Ghorab
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Mohamed S Keshta
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Dalal Alarabi
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Mohammad A Abousaleh
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Mustafa Thaer Salman
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Omer E Taha
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Anas A Zeidan
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Mahmoud F Elsaid
- Division of Pediatric Neurology, Hamad Medical Corporation, Doha, Qatar; Division of Neurology, Sidra Medicine, Doha, Qatar; Department of Pediatrics, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar.
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DeRonde S, Deuling H, Parker J, Chen J. Identification of a Novel SARS-CoV-2 Strain with Truncated Protein in ORF8 Gene by Next Generation Sequencing. RESEARCH SQUARE 2021. [PMID: 34013248 PMCID: PMC8132242 DOI: 10.21203/rs.3.rs-413141/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using next generation sequencing technology, we identified a truncated protein mutation located in the ORF8 gene which is near the end of the genome from nucleotides 27,878 to 27,958. The mutation in this novel strain created a stop codon and translates to the novel truncated ORF8 protein, creating a much smaller protein than most other strains of SARS-CoV-2. The novel truncated mutation is most closely related to nine SARS-CoV-2 strains found in Washington state. Our results show a novel strain of SARS-CoV-2 with a truncated ORF8 gene. This shortens the translated ORF8 protein. The effects of ORF8 protein and its functions are still uncertain but a truncated ORF8 could affect antibody response, severity of infection and inflammatory response.
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Zhang J, Zhao C, Zhao W. Virus Caused Imbalance of Type I IFN Responses and Inflammation in COVID-19. Front Immunol 2021; 12:633769. [PMID: 33912161 PMCID: PMC8071932 DOI: 10.3389/fimmu.2021.633769] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/24/2021] [Indexed: 01/18/2023] Open
Abstract
The global expansion of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as one of the greatest public health challenges and imposes a great threat to human health. Innate immunity plays vital roles in eliminating viruses through initiating type I interferons (IFNs)-dependent antiviral responses and inducing inflammation. Therefore, optimal activation of innate immunity and balanced type I IFN responses and inflammation are beneficial for efficient elimination of invading viruses. However, SARS-CoV-2 manipulates the host's innate immune system by multiple mechanisms, leading to aberrant type I IFN responses and excessive inflammation. In this review, we will emphasize the recent advances in the understanding of the crosstalk between host innate immunity and SARS-CoV-2 to explain the imbalance between inflammation and type I IFN responses caused by viral infection, and explore potential therapeutic targets for COVID-19.
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Affiliation(s)
- Jintao Zhang
- Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Chunyuan Zhao
- Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Department of Cell Biology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wei Zhao
- Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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Mohammed MEA. The percentages of SARS-CoV-2 protein similarity and identity with SARS-CoV and BatCoV RaTG13 proteins can be used as indicators of virus origin. ACTA ACUST UNITED AC 2021; 12:81-91. [PMID: 33850392 PMCID: PMC8033097 DOI: 10.1007/s42485-021-00060-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023]
Abstract
There are three types of proteins in coronaviruses: nonstructural, structural, and accessory proteins. Coronavirus proteins are essential for viral replication and for the binding and invasion of hosts and the regulation of host cell metabolism and immunity. This study investigated the amino acid sequence similarity and identity percentages of 10 proteins in SARS-CoV-2, SARS-CoV and the Rhinolophus affinis bat coronavirus (BatCoV RaTG13). The investigated proteins were the 1ab polyprotein, spike protein, orf3a, the envelope protein, the membrane protein, orf6, orf7a, orf7b, orf8, and the nucleocapsid protein. The online sequence alignment service of The European Molecular Biology Open Software Suite (EMBOSS) was used to determine the percentages of protein similarity and identity in the three viruses. The results showed that the similarity and identity percentages of the SARS-CoV-2 and BatCoV RaTG13 proteins were both greater than 95%, while the identity and similarity percentages of SARS-CoV-2 and SARS-CoV were both greater than 38%. The proteins of SARS-CoV-2 and BatCoV RaTG13 have high identity and similarity compared to those of SARS-CoV-2 and SARS-CoV.
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Affiliation(s)
- Mohammed Elimam Ahamed Mohammed
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia.,Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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21
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Fahmi M, Kitagawa H, Yasui G, Kubota Y, Ito M. The Functional Classification of ORF8 in SARS-CoV-2 Replication, Immune Evasion, and Viral Pathogenesis Inferred through Phylogenetic Profiling. Evol Bioinform Online 2021; 17:11769343211003079. [PMID: 33795929 PMCID: PMC7970180 DOI: 10.1177/11769343211003079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/19/2021] [Indexed: 01/02/2023] Open
Abstract
ORF8 is a highly variable genomic region of SARS-CoV-2. Although non-essential and the precise functions are unknown, it has been suggested that this protein assists in SARS-CoV-2 replication in the early secretory pathway and in immune evasion. We utilized the binding partners of SARS-CoV-2 proteins in human HEK293T cells and performed genome-wide phylogenetic profiling and clustering analyses in 446 eukaryotic species to predict and discover ORF8 binding partners that share associated functional mechanisms based on co-evolution. Results classified 47 ORF8 binding partner proteins into 3 clusters (groups 1-3), which were conserved in vertebrates (group 1), metazoan (group 2), and eukaryotes (group 3). Gene ontology analysis indicated that group 1 had no significant associated biological processes, while groups 2 and 3 were associated with glycoprotein biosynthesis process and ubiquitin-dependent endoplasmic reticulum-associated degradation pathways, respectively. Collectively, our results classified potential genes that might be associated with SARS-CoV-2 viral pathogenesis, specifically related to acute respiratory distress syndrome, and the secretory pathway. Here, we discuss the possible role of ORF8 in viral pathogenesis and in assisting viral replication and immune evasion via secretory pathway, as well as the possible factors associated with the rapid evolution of ORF8.
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Affiliation(s)
- Muhamad Fahmi
- Research Organization of Science
and Technology, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Hiromu Kitagawa
- Advanced Life Sciences Program,
Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga,
Japan
| | - Gen Yasui
- Advanced Life Sciences Program,
Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga,
Japan
| | - Yukihiko Kubota
- Department of Bioinformatics,
College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga,
Japan
| | - Masahiro Ito
- Advanced Life Sciences Program,
Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga,
Japan
- Department of Bioinformatics,
College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga,
Japan
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22
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Mohamadian M, Chiti H, Shoghli A, Biglari S, Parsamanesh N, Esmaeilzadeh A. COVID-19: Virology, biology and novel laboratory diagnosis. J Gene Med 2021; 23:e3303. [PMID: 33305456 PMCID: PMC7883242 DOI: 10.1002/jgm.3303] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/15/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND At the end of December 2019, a novel coronavirus tentatively named SARS-CoV-2 in Wuhan, a central city in China, was announced by the World Health Organization. SARS-CoV-2 is an RNA virus that has become a major public health concern after the outbreak of the Middle East Respiratory Syndrome-CoV (MERS-CoV) and Severe Acute Respiratory Syndrome-CoV (SARS-CoV) in 2002 and 2012, respectively. As of 29 October 2020, the total number of COVID-19 cases had reached over 44 million worldwide, with more than 1.17 million confirmed deaths. DISCUSSION SARS-CoV-2 infected patients usually present with severe viral pneumonia. Similar to SARS-CoV, the virus enters respiratory tract cells via the angiotensin-converting enzyme receptor 2. The structural proteins play an essential role in budding the virus particles released from different host cells. To date, an approved vaccine or treatment option of a preventive character to avoid severe courses of COVID-19 is still not available. CONCLUSIONS In the present study, we provide a brief review of the general biological features of CoVs and explain the pathogenesis, clinical symptoms and diagnostic approaches regarding monitoring future infectivity and prevent emerging COVID-19 infections.
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Affiliation(s)
- Malihe Mohamadian
- Department of Molecular MedicineBirjand University of Medical SciencesBirjandIran
- Cellular and Molecular Research CenterBirjand University of Medical SciencesBirjandIran
| | - Hossein Chiti
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Alireza Shoghli
- Social Determinants of Health Research CenterZanjan University of Medical SciencesZanjanIran
| | - Sajjad Biglari
- School of MedicineZanjan University of Medical SciencesZanjanIran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Abdolreza Esmaeilzadeh
- Department of ImmunologyZanjan University of Medical ScienceZanjanIran
- Cancer Gene Therapy Research CenterZanjan University of Medical ScienceZanjanIran
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23
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Muhseen ZT, Hameed AR, Al-Hasani HMH, Ahmad S, Li G. Computational Determination of Potential Multiprotein Targeting Natural Compounds for Rational Drug Design Against SARS-COV-2. Molecules 2021; 26:674. [PMID: 33525411 PMCID: PMC7865386 DOI: 10.3390/molecules26030674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/21/2022] Open
Abstract
SARS-CoV-2 caused the current COVID-19 pandemic and there is an urgent need to explore effective therapeutics that can inhibit enzymes that are imperative in virus reproduction. To this end, we computationally investigated the MPD3 phytochemical database along with the pool of reported natural antiviral compounds with potential to be used as anti-SARS-CoV-2. The docking results demonstrated glycyrrhizin followed by azadirachtanin, mycophenolic acid, kushenol-w and 6-azauridine, as potential candidates. Glycyrrhizin depicted very stable binding mode to the active pocket of the Mpro (binding energy, -8.7 kcal/mol), PLpro (binding energy, -7.9 kcal/mol), and Nucleocapsid (binding energy, -7.9 kcal/mol) enzymes. This compound showed binding with several key residues that are critical to natural substrate binding and functionality to all the receptors. To test docking prediction, the compound with each receptor was subjected to molecular dynamics simulation to characterize the molecule stability and decipher its possible mechanism of binding. Each complex concludes that the receptor dynamics are stable (Mpro (mean RMSD, 0.93 Å), PLpro (mean RMSD, 0.96 Å), and Nucleocapsid (mean RMSD, 3.48 Å)). Moreover, binding free energy analyses such as MMGB/PBSA and WaterSwap were run over selected trajectory snapshots to affirm intermolecular affinity in the complexes. Glycyrrhizin was rescored to form strong affinity complexes with the virus enzymes: Mpro (MMGBSA, -24.42 kcal/mol and MMPBSA, -10.80 kcal/mol), PLpro (MMGBSA, -48.69 kcal/mol and MMPBSA, -38.17 kcal/mol) and Nucleocapsid (MMGBSA, -30.05 kcal/mol and MMPBSA, -25.95 kcal/mol), were dominated mainly by vigorous van der Waals energy. Further affirmation was achieved by WaterSwap absolute binding free energy that concluded all the complexes in good equilibrium and stability (Mpro (mean, -22.44 kcal/mol), PLpro (mean, -25.46 kcal/mol), and Nucleocapsid (mean, -23.30 kcal/mol)). These promising findings substantially advance our understanding of how natural compounds could be shaped to counter SARS-CoV-2 infection.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an 710062, China
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Alaa R Hameed
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad 00964, Iraq
| | - Halah M H Al-Hasani
- Department of Biotechnology, College of Science, University of Diyala, Baqubah 32001, Iraq
| | - Sajjad Ahmad
- Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an 710062, China
- School of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
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24
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Fahmi M, Kharisma VD, Ansori ANM, Ito M. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:839-857. [PMID: 33973215 DOI: 10.1007/978-3-030-63761-3_47] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Sudden emergence and a rapid outbreak of SARS-CoV-2 accompanied by a devastating impact on the economy and public health has driven extensive scientific mobilization to study and elucidate the various associated concerns about SARS-CoV-2. Bioinformatics plays a crucial role in addressing and providing solutions to questions about SARS-CoV-2. It helps shorten the duration for the vaccine development process and the discovery of potential clinical interventions through the simulation and information retrieval, and the development of well-ordered information hubs and resources, which are essential to derive data and meaningful findings from the current massive information about SARS-CoV-2. Advanced algorithms in this field also provide approaches that are essential to elucidate the relationship, origin, and evolutionary process of SARS-CoV-2. Here, we report essential bioinformatics entities, such as database and platform development, molecular evolution and phylogenetic analyses, and vaccine designs, that are useful to solve the SARS-CoV-2 conundrum.
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Affiliation(s)
- Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Kusatsu, Japan
| | - Viol Dhea Kharisma
- Master Program in Biology, Department of Biology, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya, Malang, Indonesia.,Computational Virology and Complexity Science Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia (GENBINESIA) Foundation, Gresik, Indonesia.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Malang, Indonesia
| | - Arif Nur Muhammad Ansori
- Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Kampus C Universitas Airlangga, Surabaya, Indonesia.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Surabaya, Indonesia
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan. .,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Kusatsu, Japan.
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25
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Dimonaco NJ, Salavati M, Shih BB. Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses 2020; 13:E49. [PMID: 33396801 PMCID: PMC7823979 DOI: 10.3390/v13010049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
In 2019, a novel coronavirus, SARS-CoV-2/nCoV-19, emerged in Wuhan, China, and has been responsible for the current COVID-19 pandemic. The evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development. As part of the international "CoronaHack" in April 2020, we employed a collection of contemporary methodologies to compare the genomic sequences of coronaviruses isolated from human (SARS-CoV-2; n = 163), bat (bat-CoV; n = 215) and pangolin (pangolin-CoV; n = 7) available in public repositories. We have also noted the pangolin-CoV isolate MP789 to bare stronger resemblance to SARS-CoV-2 than other pangolin-CoV. Following de novo gene annotation prediction, analyses of gene-gene similarity network, codon usage bias and variant discovery were undertaken. Strong host-associated divergences were noted in ORF3a, ORF6, ORF7a, ORF8 and S, and in codon usage bias profiles. Last, we have characterised several high impact variants (in-frame insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and may be highlighting loci of potential functional relevance.
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Affiliation(s)
- Nicholas J. Dimonaco
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales SY3 3FL, UK
| | - Mazdak Salavati
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Barbara B. Shih
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
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26
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Gupta SP. Progress in Studies on Structural and Remedial Aspects of Newly Born Coronavirus, SARS-CoV-2. Curr Top Med Chem 2020; 20:2362-2378. [PMID: 32962613 DOI: 10.2174/1568026620666200922112300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/10/2020] [Accepted: 09/01/2020] [Indexed: 01/12/2023]
Abstract
The article highlights an up-to-date progress in studies on structural and the remedial aspects of novel coronavirus 2019-nCoV, renamed as SARS-CoV-2, leading to the disease COVID-19, a pandemic. In general, all CoVs including SARS-CoV-2 are spherical positive single-stranded RNA viruses containing spike (S) protein, envelope (E) protein, nucleocapsid (N) protein, and membrane (M) protein, where S protein has a Receptor-binding Domain (RBD) that mediates the binding to host cell receptor, Angiotensin Converting Enzyme 2 (ACE2). The article details the repurposing of some drugs to be tried for COVID-19 and presents the status of vaccine development so far. Besides drugs and vaccines, the role of Convalescent Plasma (CP) therapy to treat COVID-19 is also discussed.
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Affiliation(s)
- Satya P Gupta
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, Meerut-250005, India
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27
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Mayoral EPC, Hernández-Huerta MT, Pérez-Campos Mayoral L, Matias-Cervantes CA, Mayoral-Andrade G, Barrios LÁL, Pérez-Campos E. Factors related to asymptomatic or severe COVID-19 infection. Med Hypotheses 2020; 144:110296. [PMID: 33254487 PMCID: PMC7513914 DOI: 10.1016/j.mehy.2020.110296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/11/2020] [Accepted: 09/18/2020] [Indexed: 01/22/2023]
Abstract
The factors that may contribute to a COVID-19 patient remaining in the asymptomatic stage, or to the infection evolving into the more serious stages are examined. In particular, we refer to the TMPRSS2 expression profile, balance of androgen and estrogen, blood group-A and/or B, nonsynonymous mutations in ORF3, and proteins NS7b and NS8 in SARS-CoV-2. Also, we review other factors related to the susceptibility and pathogenicity of SARS-CoV-2.
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Affiliation(s)
- Eduardo Pérez-Campos Mayoral
- Centro de Investigación Facultad de Medicina UNAM-UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca 68020, Mexico; Laboratorio de Patología Clinica "Eduardo Pérez Ortega", Oaxaca 68000, Mexico
| | - María Teresa Hernández-Huerta
- CONACyT, Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca 68020, Mexico; Laboratorio de Patología Clinica "Eduardo Pérez Ortega", Oaxaca 68000, Mexico
| | - Laura Pérez-Campos Mayoral
- Centro de Investigación Facultad de Medicina UNAM-UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca 68020, Mexico; Laboratorio de Patología Clinica "Eduardo Pérez Ortega", Oaxaca 68000, Mexico.
| | - Carlos Alberto Matias-Cervantes
- CONACyT, Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca 68020, Mexico; Laboratorio de Patología Clinica "Eduardo Pérez Ortega", Oaxaca 68000, Mexico
| | - Gabriel Mayoral-Andrade
- Centro de Investigación Facultad de Medicina UNAM-UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca 68020, Mexico; Laboratorio de Patología Clinica "Eduardo Pérez Ortega", Oaxaca 68000, Mexico
| | - Luis Ángel Laguna Barrios
- Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca 68020, Mexico; Laboratorio de Patología Clinica "Eduardo Pérez Ortega", Oaxaca 68000, Mexico
| | - Eduardo Pérez-Campos
- Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca 68020, Mexico; Tecnológico Nacional de México/IT Oaxaca, Oaxaca 68020, Mexico; Laboratorio de Patología Clinica "Eduardo Pérez Ortega", Oaxaca 68000, Mexico.
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28
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Das SK. The Pathophysiology, Diagnosis and Treatment of Corona Virus Disease 2019 (COVID-19). Indian J Clin Biochem 2020; 35:385-396. [PMID: 32837036 PMCID: PMC7424135 DOI: 10.1007/s12291-020-00919-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022]
Abstract
Since the beginning of this century, beta coronaviruses (CoV) have caused three zoonotic outbreaks. However, little is currently known about the biology of the newly emerged SARS-CoV-2 in late 2019. There is a spectrum of clinical features from mild to severe life threatening disease with major complications like severe pneumonia, acute respiratory distress syndrome, acute cardiac injury and septic shock. The genome of SARS-CoV-2 encodes polyproteins, four structural proteins and six accessory proteins. SARS-CoV-2 tends to utilize Angiotensin-converting enzyme 2 (ACE2) of various mammals. The imbalance between ACE/Ang II/AT1R pathway and ACE2/Ang(1-7)/Mas receptor pathway in the renin-angiotensin system leads to multi-system inflammation. The early symptoms of COVID-19 pneumonia are low to midgrade fever, dry cough and fatigue. Vigilant screening is important. The diagnosis of COVID-19 should be based on imaging findings along with epidemiological history and nucleic acid detection. Isolation and quarantine of suspected cases is recommended. Management is primarily supportive, with newer antiviral drugs/vaccines under investigation.
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Affiliation(s)
- Subir Kumar Das
- Department of Biochemistry, College of Medicine and JNM Hospital, WBUHS, Kalyani, Nadia, West Bengal 741235 India
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29
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da Silva SJR, Germano Mendes RP, Alves da Silva CT, Lorusso A, Kohl A, Pena L. Insights into SARS-CoV-2, the Coronavirus Underlying COVID-19: Recent Genomic Data and the Development of Reverse Genetics Systems. J Gen Virol 2020; 101:1021-1024. [PMID: 32579100 PMCID: PMC7660456 DOI: 10.1099/jgv.0.001458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022] Open
Abstract
The emergence and rapid worldwide spread of a novel pandemic of acute respiratory disease - eventually named coronavirus disease 2019 (COVID-19) by the World Health Organization (WHO) - across the human population has raised great concerns. It prompted a mobilization around the globe to study the underlying pathogen, a close relative of severe acute respiratory syndrome coronavirus (SARS-CoV) called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Numerous genome sequences of SARS-CoV-2 are now available and in-depth analyses are advancing. These will allow detailed characterization of sequence and protein functions, including comparative studies. Care should be taken when inferring function from sequence information alone, and reverse genetics systems can be used to unequivocally identify key features. For example, the molecular markers of virulence, host range and transmissibility of SARS-CoV-2 can be compared to those of related viruses in order to shed light on the biology of this emerging pathogen. Here, we summarize some recent insights from genomic studies and strategies for reverse genetics systems to generate recombinant viruses, which will be useful to investigate viral genome properties and evolution.
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Affiliation(s)
| | - Renata Pessôa Germano Mendes
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife Pernambuco, Brazil
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM), Teramo, Italy
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland G61 1QH, UK
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife Pernambuco, Brazil
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30
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da Silva SJR, Silva CTAD, Guarines KM, Mendes RPG, Pardee K, Kohl A, Pena L. Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19. ACS Infect Dis 2020; 6:2319-2336. [PMID: 32786280 PMCID: PMC7441751 DOI: 10.1021/acsinfecdis.0c00274] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 01/08/2023]
Abstract
In December 2019, a novel beta (β) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis.
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Affiliation(s)
| | - Caroline Targino Alves da Silva
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy,
University of Toronto, Toronto, ON M5S 3M2,
Canada
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus
Research, Glasgow, Scotland G61 1QH, U.K.
| | - Lindomar Pena
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
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31
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Kaniyala Melanthota S, Banik S, Chakraborty I, Pallen S, Gopal D, Chakrabarti S, Mazumder N. Elucidating the microscopic and computational techniques to study the structure and pathology of SARS-CoVs. Microsc Res Tech 2020; 83:1623-1638. [PMID: 32770582 PMCID: PMC7436590 DOI: 10.1002/jemt.23551] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/11/2022]
Abstract
Severe Acute Respiratory Syndrome Coronaviruses (SARS‐CoVs), causative of major outbreaks in the past two decades, has claimed many lives all over the world. The virus effectively spreads through saliva aerosols or nasal discharge from an infected person. Currently, no specific vaccines or treatments exist for coronavirus; however, several attempts are being made to develop possible treatments. Hence, it is important to study the viral structure and life cycle to understand its functionality, activity, and infectious nature. Further, such studies can aid in the development of vaccinations against this virus. Microscopy plays an important role in examining the structure and topology of the virus as well as pathogenesis in infected host cells. This review deals with different microscopy techniques including electron microscopy, atomic force microscopy, fluorescence microscopy as well as computational methods to elucidate various prospects of this life‐threatening virus. Structural analysis of SARS‐CoVs aids in understanding its nature, activity, and pathophysiology Revealing the surface morphology of SARS‐CoVs using scanning electron microscope and atomic force microscopy Computational methods help to understand the structure of SARS‐CoVs and their interactions with various inhibitors
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Affiliation(s)
- Sindhoora Kaniyala Melanthota
- Department of Biophysics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Soumyabrata Banik
- Department of Biophysics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Ishita Chakraborty
- Department of Biophysics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Sparsha Pallen
- Department of Bioinformatics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Dharshini Gopal
- Department of Bioinformatics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Shweta Chakrabarti
- Department of Bioinformatics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life SciencesManipal Academy of Higher EducationManipalKarnataka576104India
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32
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The diagnostic and prognostic role of myocardial injury biomarkers in hospitalized patients with COVID-19. Clin Chim Acta 2020; 510:186-190. [PMID: 32681933 PMCID: PMC7363604 DOI: 10.1016/j.cca.2020.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 02/08/2023]
Abstract
The study comprehensively evaluate predictive value of myocardial injury markers. cTnI-ultra on admission might be the best predictor of in-hospital mortality. Elevated cTnI-ultra was an independent biomarker of the death.
Objective The aim of this study was to systematically and comprehensively evaluate the diagnostic and prognostic value of myocardial injury biomarkers in COVID-19 patients. Methods This is a retrospective cohort study of confirmed COVID-19 patients that were admitted to the Renmin Hospital of Wuhan University from January 30, 2020 to February 15, 2020. Results Receiver operating characteristic (ROC) curve analysis demonstrated that cTnI-ultra had the highest area under the curve (AUC) at 0.855, with a sensitivity of 67.3% and a specificity of 88.7% for the prediction of in-hospital mortality. Patients with higher troponin I-ultra (cTnI-ultra), creatinine kinase-myocardial band (CK-MB), and N-terminal pro-B-type natriuretic peptide (NT-proBNP) were associated with higher mortality, compared to those who lower levels. The multivariable cox regression indicated that age (hazard ratio (HR) 3.450, 95% confidence interval (CI) 1.627–7.314, P = 0.001), coronary heart disease (HR 1.855, 95% CI 1.006–3.421; P = 0.048), elevated cTnI-ultra (HR 3.083, 95% CI 1.616–5.883, P = 0.001), elevated CK-MB (HR 2.907, 95% CI 1.233–6.854; P = 0.015), and elevated NT-proBNP (HR 5.776, 95% CI 2.272–14.682; P < 0.001) were associated with in-hospital mortality. Conclusions cTnI-ultra might be the best predictor of in-hospital mortality among myocardial injury biomarkers. Elevated cTnI-ultra, CK-MB, and NT-proBNP were independent biomarkers of the mortality in COVID-19 patients.
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Zeouk I, Bekhti K, Lorenzo-Morales J. From Wuhan to COVID-19 Pandemic: An Up-to-Date Review of Its Pathogenesis, Potential Therapeutics, and Recent Advances. Microorganisms 2020; 8:E850. [PMID: 32512950 PMCID: PMC7355460 DOI: 10.3390/microorganisms8060850] [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: 04/27/2020] [Revised: 05/20/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel human coronavirus (SARS-CoV-2) causing severe contagious respiratory tract infections presents a serious threat to public health worldwide. To date, there are no specific antiviral agents available for this disease, currently known as COVID-19. Therefore, genomic sequencing and therapeutic clinical trials are being conducted to develop effective antiviral agents. Several reports have investigated FDA-approved drugs as well as in silico virtual screening approaches such as molecular docking and modeling to find novel antiviral agents. Until now, antiparasitic drugs such as chloroquine have shown the most relevant results. Furthermore, there is an urgent need to understand the pathogenesis of this novel coronavirus, its transmission routes, surface survival and evolution in the environment. So far, the scientific community has indicated a possible transmission of COVID-19 via blood transfusion which is challenging in the case of asymptomatic individuals. Protocols for pathogen inactivation are also needed. In this paper, we reviewed recent findings about this life-threatening pandemic.
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Affiliation(s)
- Ikrame Zeouk
- Instituto Universitario De Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, S/N, La Laguna, Tenerife, 38203 Islas Canarias, Spain
- Faculty of Sciences and Techniques, Sidi Mohamed Ben Abdellah University, PB 2202, Fez 30000, Morocco;
| | - Khadija Bekhti
- Faculty of Sciences and Techniques, Sidi Mohamed Ben Abdellah University, PB 2202, Fez 30000, Morocco;
| | - Jacob Lorenzo-Morales
- Instituto Universitario De Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, S/N, La Laguna, Tenerife, 38203 Islas Canarias, Spain
- Departamento de Obstetricia, Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad De La Laguna, La Laguna, Tenerife, 38203 Islas Canarias, Spain
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Absalan A, Doroud D, Salehi-Vaziri M, Kaghazian H, Ahmadi N, Zali F, Pouriavali's MH, Mousavi-Nasab SD. Computation screening and molecular docking of FDA approved viral protease inhibitors as a potential drug against COVID-19. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2020; 13:355-360. [PMID: 33244378 PMCID: PMC7682959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/29/2020] [Indexed: 11/08/2022]
Abstract
AIM This study demonstrated potent inhibitors against COVID-19 using the molecular docking approach of FDA approved viral antiprotease drugs. BACKGROUND COVID-19 has now spread throughout world. There is a serious need to find potential therapeutic agents. The 3C-like protease (Mpro/6LU7) is an attractive molecular target for rational anti-CoV drugs. METHODS The tertiary structure of COVID-19 Mpro was obtained from a protein data bank repository, and molecular docking screening was performed by Molegro Virtual Docker, ver. 6, with a grid resolution of 0.30 Å. Docking scores (DOS) are representative of calculated ligand-receptor (protein) interaction energy; therefore, more negative scores mean better binding tendency. Another docking study was then applied on each of the selected drugs with the best ligands separately and using a more accurate RMSD algorithm. RESULTS The docking of COVID-19 major protease (6LU7) with 17 selected drugs resulted in four FDA approved viral antiprotease drugs (Temoporfin, Simeprevir, Cobicistat, Ritonavir) showing the best docking scores. Among these 4 compounds, Temoporfin exhibited the best DOS (-202.88) and the best screened ligand with COVID-19 Mpro, followed by Simeprevir (-201.66), Cobicistat (-187.75), and Ritonavir (-186.66). As the best screened ligand, Temoporfin could target the Mpro with 20 different conformations, while Simeprevir, Cobicistat, and Ritonavir make 14, 10, and 10 potential conformations at the binding site, respectively. CONCLUSION The findings showed that the four selected FDA approved drugs can be potent inhibitors against COVID-19; among them, Temoporfin may be more potent for the treatment of the disease. Based on the findings, it is recommended that in-vitro and in-vivo evaluations be conducted to determine the effectiveness of these drugs against COVID-19.
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Affiliation(s)
- Abdorrahim Absalan
- Department of Medical Laboratory Sciences, Khomein University of Medical Sciences, Markazi Province, Iran
| | - Delaram Doroud
- Department of Research and Development, Production and Research Complex, Pasteur Institute, Tehran, Iran
- Viral vaccine research center, Pasteur institute of Iran
| | | | - Hooman Kaghazian
- Department of Research and Development, Production and Research Complex, Pasteur Institute, Tehran, Iran
- Viral vaccine research center, Pasteur institute of Iran
| | - Nayebali Ahmadi
- Proteomics Research Center, Department of Medical Lab Technology, Faculty of Paramedical Sciences,Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Zali
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Science, Tehran, Iran
| | | | - Seyed Dawood Mousavi-Nasab
- Department of Research and Development, Production and Research Complex, Pasteur Institute, Tehran, Iran
- Viral vaccine research center, Pasteur institute of Iran
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Chellapandi P, Saranya S. Genomics insights of SARS-CoV-2 (COVID-19) into target-based drug discovery. Med Chem Res 2020; 29:1777-1791. [PMID: 32837137 PMCID: PMC7394272 DOI: 10.1007/s00044-020-02610-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/24/2020] [Indexed: 01/07/2023]
Abstract
Coronavirus disease (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is a global health emergency and no clinically approved vaccines or antiviral drugs available to date. Intensive research on SARS-CoV-2 is urgently warranted to understand its pathogenesis and virulence mechanisms and to discover target-based antiviral therapeutics. Among various research logics, current bioinformatics highlights novel testable hypotheses for systematic drug repositioning and designing against COVID-19. A total of 121 articles related to bioinformatics facets of this virus were collected from the PubMed Central. The content of each investigation was comprehensively reviewed, manually curated, and included herein. Interestingly, 109 COVID-19-related literature published in 2020 (January-June) were included in this review. The present article emphasizes novel resource development on its genome structure, evolution, therapeutic targets, drug designing, and drug repurposing strategies. Genome organization, the function of coding genes, origin, and evolution of SARS-CoV-2 is described in detail. Genomic insights into understanding the structure-function relationships of drug targets including spike, main protease, and RNA-dependent RNA polymerase of SARS-CoV-2 are discussed intensively. Several molecular docking and systems pharmacology approaches have been investigated some promising antiviral drugs against SARS-CoV-2 based on its genomic characteristics, pathogenesis mechanism, and host specificity. Perhaps, the present genomic insights of this virus will provide a lead to the researchers to design or repurpose of antiviral drugs soon and future directions to control the spread of COVID-19.
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Affiliation(s)
- P. Chellapandi
- grid.411678.d0000 0001 0941 7660Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
| | - S. Saranya
- grid.411678.d0000 0001 0941 7660Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
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