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Gerashchenko GV, Hryshchenko NV, Melnichuk NS, Marchyshak TV, Chernushyn SY, Demchyshina IV, Chernenko LM, Kuzin IV, Tkachuk ZY, Kashuba VI, Tukalo MA. Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022. Heliyon 2024; 10:e25618. [PMID: 38380034 PMCID: PMC10877268 DOI: 10.1016/j.heliyon.2024.e25618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
The aim of our study was to identify and characterize the SARS-CoV-2 variants in COVID-19 patients' samples collected from different regions of Ukraine to determine the relationship between SARS-CoV-2 phylogenetics and COVID-19 epidemiology. Patients and methods Samples were collected from COVID-19 patients during 2021 and the beginning of 2022 (401 patients). The SARS-CoV-2 genotyping was performed by parallel whole genome sequencing. Results The obtained SARS-CoV-2 genotypes showed that three waves of the COVID-19 pandemic in Ukraine were represented by three main variants of concern (VOC), named Alpha, Delta and Omicron; each VOC successfully replaced the earlier variant. The VOC Alpha strain was presented by one B.1.1.7 lineage, while VOC Delta showed a spectrum of 25 lineages that had different prevalence in 19 investigated regions of Ukraine. The VOC Omicron in the first half of the pandemic was represented by 13 lines that belonged to two different clades representing B.1 and B.2 Omicron strains. Each of the three epidemic waves (VOC Alpha, Delta, and Omicron) demonstrated their own course of disease, associated with genetic changes in the SARS-CoV-2 genome. The observed epidemiological features are associated with the genetic characteristics of the different VOCs, such as point mutations, deletions and insertions in the viral genome. A phylogenetic and transmission analysis showed the different mutation rates; there were multiple virus sources with a limited distribution between regions. Conclusions The evolution of SARS-CoV-2 virus and high levels of morbidity due to COVID-19 are still registered in the world. Observed multiple virus sourses with the limited distribution between regions indicates the high efficiency of the anti-epidemic policy pursued by the Ministry of Health of Ukraine to prevent the spread of the epidemic, despite the low level of vaccination of the Ukrainian population.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zenovii Yu Tkachuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Mykhailo A. Tukalo
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
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2
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Philip AM, Ahmed WS, Biswas KH. Reversal of the unique Q493R mutation increases the affinity of Omicron S1-RBD for ACE2. Comput Struct Biotechnol J 2023; 21:1966-1977. [PMID: 36936816 PMCID: PMC10006685 DOI: 10.1016/j.csbj.2023.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/28/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The SARS-CoV-2 Omicron variant containing 15 mutations, including the unique Q493R, in the spike protein receptor binding domain (S1-RBD) is highly infectious. While comparison with previously reported mutations provide some insights, the mechanism underlying the increased infections and the impact of the reversal of the unique Q493R mutation seen in BA.4, BA.5, BA.2.75, BQ.1 and XBB lineages is not yet completely understood. Here, using structural modelling and molecular dynamics (MD) simulations, we show that the Omicron mutations increases the affinity of S1-RBD for ACE2, and a reversal of the unique Q493R mutation further increases the ACE2-S1-RBD affinity. Specifically, we performed all atom, explicit solvent MD simulations using a modelled structure of the Omicron S1-RBD-ACE2 and compared the trajectories with the WT complex revealing a substantial reduction in the Cα-atom fluctuation in the Omicron S1-RBD and increased hydrogen bond and other interactions. Residue level analysis revealed an alteration in the interaction between several residues including a switch in the interaction of ACE2 D38 from S1-RBD Y449 in the WT complex to the mutated R residue (Q493R) in Omicron complex. Importantly, simulations with Revertant (Omicron without the Q493R mutation) complex revealed further enhancement of the interaction between S1-RBD and ACE2. Thus, results presented here not only provide insights into the increased infectious potential of the Omicron variant but also a mechanistic basis for the reversal of the Q493R mutation seen in some Omicron lineages and will aid in understanding the impact of mutations in SARS-CoV-2 evolution.
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Affiliation(s)
- Angelin M. Philip
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Wesam S. Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
- Corresponding author.
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3
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Periwal N, Rathod SB, Sarma S, Johar GS, Jain A, Barnwal RP, Srivastava KR, Kaur B, Arora P, Sood V. Time Series Analysis of SARS-CoV-2 Genomes and Correlations among Highly Prevalent Mutations. Microbiol Spectr 2022; 10:e0121922. [PMID: 36069583 PMCID: PMC9603882 DOI: 10.1128/spectrum.01219-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/03/2022] [Indexed: 12/30/2022] Open
Abstract
The efforts of the scientific community to tame the recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seem to have been diluted by the emergence of new viral strains. Therefore, it is imperative to understand the effect of mutations on viral evolution. We performed a time series analysis on 59,541 SARS-CoV-2 genomic sequences from around the world to gain insights into the kinetics of the mutations arising in the viral genomes. These 59,541 genomes were grouped according to month (January 2020 to March 2021) based on the collection date. Meta-analysis of these data led us to identify significant mutations in viral genomes. Pearson correlation of these mutations led us to the identification of 16 comutations. Among these comutations, some of the individual mutations have been shown to contribute to viral replication and fitness, suggesting a possible role of other unexplored mutations in viral evolution. We observed that the mutations 241C>T in the 5' untranslated region (UTR), 3037C>T in nsp3, 14408C>T in the RNA-dependent RNA polymerase (RdRp), and 23403A>G in spike are correlated with each other and were grouped in a single cluster by hierarchical clustering. These mutations have replaced the wild-type nucleotides in SARS-CoV-2 sequences. Additionally, we employed a suite of computational tools to investigate the effects of T85I (1059C>T), P323L (14408C>T), and Q57H (25563G>T) mutations in nsp2, RdRp, and the ORF3a protein of SARS-CoV-2, respectively. We observed that the mutations T85I and Q57H tend to be deleterious and destabilize the respective wild-type protein, whereas P323L in RdRp tends to be neutral and has a stabilizing effect. IMPORTANCE We performed a meta-analysis on SARS-CoV-2 genomes categorized by collection month and identified several significant mutations. Pearson correlation analysis of these significant mutations identified 16 comutations having absolute correlation coefficients of >0.4 and a frequency of >30% in the genomes used in this study. The correlation results were further validated by another statistical tool called hierarchical clustering, where mutations were grouped in clusters on the basis of their similarity. We identified several positive and negative correlations among comutations in SARS-CoV-2 isolates from around the world which might contribute to viral pathogenesis. The negative correlations among some of the mutations in SARS-CoV-2 identified in this study warrant further investigations. Further analysis of mutations such as T85I in nsp2 and Q57H in ORF3a protein revealed that these mutations tend to destabilize the protein relative to the wild type, whereas P323L in RdRp is neutral and has a stabilizing effect. Thus, we have identified several comutations which can be further characterized to gain insights into SARS-CoV-2 evolution.
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Affiliation(s)
- Neha Periwal
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
| | - Shravan B. Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat, India
| | - Sankritya Sarma
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | | | - Avantika Jain
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
- Delhi Institute of Pharmaceutical Sciences and Research, New Delhi, Delhi, India
| | - Ravi P. Barnwal
- Department of Biophysics, Panjab University, Chandigarh, India
| | | | - Baljeet Kaur
- Department of Computer Science, Hansraj College, University of Delhi, New Delhi, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | - Vikas Sood
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
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4
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Pascarella S, Bianchi M, Giovanetti M, Benvenuto D, Borsetti A, Cauda R, Cassone A, Ciccozzi M. The Biological Properties of the SARS-CoV-2 Cameroon Variant Spike: An Intermediate between the Alpha and Delta Variants. Pathogens 2022; 11:pathogens11070814. [PMID: 35890058 PMCID: PMC9315702 DOI: 10.3390/pathogens11070814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/08/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
An analysis of the structural effect of the mutations of the B.1.640.2 (IHU) Spike Receptor Binding Domain (RBD) and N-terminal Domain (NTD) is reported along with a comparison with the sister lineage B.1.640.1. and a selection of variants of concern. The effect of the mutations on the RBD–ACE2 interaction was also assessed. The structural analysis applied computational methods that are able to carry out in silico mutagenesis to calculate energy minimization and the folding energy variation consequent to residue mutations. Tools for electrostatic calculation were applied to quantify and display the protein surface electrostatic potential. Interactions at the RBD–ACE2 interface were scrutinized using computational tools that identify the interactions and predict the contribution of each interface residue to the stability of the complex. The comparison among the RBDs shows that the most evident differences between the variants is in the distribution of the surface electrostatic potential: that of B.1.640.1 is as that of the Alpha RBD, while B.1.640.2 appears to have an intermediate surface potential pattern with characteristics between those of the Alpha and Delta variants. Moreover, the B.1.640.2 Spike includes the mutation E484K that in other variants has been suggested to be involved in immune evasion. These properties may hint at the possibility that B.1.640.2 emerged with a potentially increased infectivity with respect to the sister B.1.640.1 variant, but significantly lower than that of the Delta and Omicron variants. However, the analysis of their NTD domains highlights deletions, destabilizing mutations and charge alterations that can limit the ability of the B.1.640.1 and B.1.640.2 variants to interact with cellular components, such as cell surface receptors.
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Affiliation(s)
- Stefano Pascarella
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma La Sapienza, 00185 Roma, Italy; (S.P.); (M.B.)
| | - Martina Bianchi
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma La Sapienza, 00185 Roma, Italy; (S.P.); (M.B.)
| | - Marta Giovanetti
- Laboratory of Flavivirus, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil;
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00185 Rome, Italy
| | - Domenico Benvenuto
- Faculty of Medicine, University of Campus Bio-Medico di Roma, 00185 Rome, Italy;
| | | | - Roberto Cauda
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Roma, Italy;
| | - Antonio Cassone
- Universita degli Studi di Siena—Sede di Arezzo, 52100 Arezzo, Italy;
| | - Massimo Ciccozzi
- Faculty of Medicine, University of Campus Bio-Medico di Roma, 00185 Rome, Italy;
- Correspondence: ; Tel.: +39-06-225411
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5
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Bazargan M, Elahi R, Esmaeilzadeh A. OMICRON: Virology, immunopathogenesis, and laboratory diagnosis. J Gene Med 2022; 24:e3435. [PMID: 35726542 PMCID: PMC9350010 DOI: 10.1002/jgm.3435] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 12/19/2022] Open
Abstract
Since its emersion, coronavirus disease 2019 (COVID-19) has been a significant global dilemma. Several mutations in the severe acute respiratory virus (SARS-Co-2) genome has given rise to different variants with various levels of transmissibility, severity and mortality. Up until November 2021, the variants of concern declared by the World Health Organization were Alpha, Beta, Delta and Gamma. Since then, a novel variant named Omicron (B.1.1.529) has been developed. BA.1, BA.1.1, BA.2 and BA.3 are four known subvariants of Omicron. The Omicron variant involves new mutations in its spike protein, most of which are in its receptor binding site, and increase its transmissibility and decrease its antibody and vaccine response. Understanding the virology and mutations of Omicron is necessary for developing diagnostic and therapeutic methods. Moreover, important issues, such as the risk of re-infection, the response to different kinds of vaccines, the need for a booster vaccine dose and the increased risk of Omicron infection in pediatrics, need to be addressed. In this article, we provide an overview of the biological and immunopathological properties of Omicron and its subvariants, its clinical signs and symptoms, Omicron and pediatrics, vaccines against Omicron, re-infection with Omicron, diagnostic approaches and specific challenges of Omicron in the successful control and management of the rapid global spread of this variant.
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Affiliation(s)
- Mahsa Bazargan
- Department of Immunology, School of MedicineSahid Beheshti University of Medical SciencesTehranIran
- Virology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Masih Daneshvari HospitalSahid Beheshti University of Medical SciencesTehranIran
| | - Reza Elahi
- School of MedicineZanjan University of Medical SciencesZanjanIran
| | - Abdolreza Esmaeilzadeh
- Department of ImmunologyZanjan University of Medical SciencesZanjanIran
- Cancer Gene Therapy Research CenterZanjan University of Medical SciencesZanjanIran
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6
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Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience 2022; 25:104685. [PMID: 35789750 PMCID: PMC9242679 DOI: 10.1016/j.isci.2022.104685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 06/23/2022] [Indexed: 01/20/2023] Open
Abstract
Noncoding RNAs are important regulators of mucoinflammatory response, but little is known about the contribution of airway long noncoding RNAs (lncRNAs) in COVID-19. RNA-seq analysis showed a more than 4-fold increased expression of IL-6, ICAM-1, CXCL-8, and SCGB1A1 inflammatory factors; MUC5AC and MUC5B mucins; and SPDEF, FOXA3, and FOXJ1 transcription factors in COVID-19 patient nasal samples compared with uninfected controls. A lncRNA on antisense strand to ICAM-1 or LASI was induced 2-fold in COVID-19 patients, and its expression was directly correlated with viral loads. A SARS-CoV-2-infected 3D-airway model largely recapitulated these clinical findings. RNA microscopy and molecular modeling indicated a possible interaction between viral RNA and LASI lncRNA. Notably, blocking LASI lncRNA reduced the SARS-CoV-2 replication and suppressed MUC5AC mucin levels and associated inflammation, and select LASI-dependent miRNAs (e.g., let-7b-5p and miR-200a-5p) were implicated. Thus, LASI lncRNA represents an essential facilitator of SARS-CoV-2 infection and associated airway mucoinflammatory response.
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Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Michael D. Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA,Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Mehdi Mirsaeidi
- Miller School of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Miami, Miami, FL 33136, USA
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA,Corresponding author
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA,Corresponding author
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7
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Ji M, Chai Z, Chen J, Li G, Li Q, Li M, Ding Y, Lu S, Ju G, Hou J. Insights into the Allosteric Effect of SENP1 Q597A Mutation on the Hydrolytic Reaction of SUMO1 via an Integrated Computational Study. Molecules 2022; 27:molecules27134149. [PMID: 35807394 PMCID: PMC9268427 DOI: 10.3390/molecules27134149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 11/26/2022] Open
Abstract
Small ubiquitin-related modifier (SUMO)-specific protease 1 (SENP1) is a cysteine protease that catalyzes the cleavage of the C-terminus of SUMO1 for the processing of SUMO precursors and deSUMOylation of target proteins. SENP1 is considered to be a promising target for the treatment of hepatocellular carcinoma (HCC) and prostate cancer. SENP1 Gln597 is located at the unstructured loop connecting the helices α4 to α5. The Q597A mutation of SENP1 allosterically disrupts the hydrolytic reaction of SUMO1 through an unknown mechanism. Here, extensive multiple replicates of microsecond molecular dynamics (MD) simulations, coupled with principal component analysis, dynamic cross-correlation analysis, community network analysis, and binding free energy calculations, were performed to elucidate the detailed mechanism. Our MD simulations showed that the Q597A mutation induced marked dynamic conformational changes in SENP1, especially in the unstructured loop connecting the helices α4 to α5 which the mutation site occupies. Moreover, the Q597A mutation caused conformational changes to catalytic Cys603 and His533 at the active site, which might impair the catalytic activity of SENP1 in processing SUMO1. Moreover, binding free energy calculations revealed that the Q597A mutation had a minor effect on the binding affinity of SUMO1 to SENP1. Together, these results may broaden our understanding of the allosteric modulation of the SENP1−SUMO1 complex.
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Affiliation(s)
- Mingfei Ji
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
- Department of Urology, Second Affiliated Hospital of Navy Medical University, Shanghai 200433, China; (J.C.); (Y.D.)
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200433, China;
| | - Jie Chen
- Department of Urology, Second Affiliated Hospital of Navy Medical University, Shanghai 200433, China; (J.C.); (Y.D.)
| | - Gang Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
| | - Qiang Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
| | - Miao Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
| | - Yelei Ding
- Department of Urology, Second Affiliated Hospital of Navy Medical University, Shanghai 200433, China; (J.C.); (Y.D.)
| | - Shaoyong Lu
- Department of Bioinformatics and Medicinal Chemistry Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
- Correspondence: (S.L.); (G.J.); (J.H.)
| | - Guanqun Ju
- Department of Urology, Second Affiliated Hospital of Navy Medical University, Shanghai 200433, China; (J.C.); (Y.D.)
- Correspondence: (S.L.); (G.J.); (J.H.)
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
- Department of Urology, Dushuhu Public Hospital Affiliated to Soochow University, Suzhou 215000, China
- Correspondence: (S.L.); (G.J.); (J.H.)
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8
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Acharya A, Kutateladze TG, Byrareddy SN. Combining antiviral drugs with BET inhibitors is beneficial in combatting SARS-CoV-2 infection. Clin Transl Discov 2022; 2:e66. [PMID: 35633739 PMCID: PMC9137278 DOI: 10.1002/ctd2.66] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has resulted in more than 500 million cases and 6 million deaths. Several antiviral therapies and vaccines have been developed to mitigate the spread of this infection. However, new approaches are required to battle emerging SARS-CoV-2 variants containing mutations that can reduce the vaccines' efficacy. The use of a combination of viral drugs with inhibitors of the mTOR signaling pathways has emerged as one of the promising novel approaches. We recently showed that SF2523, a dual activity small molecule that inhibits PI3K and BRD4, acts synergistically with the antiviral drugs remdesivir and MU-UNMC-2. Our findings suggest that the mTOR pathways are necessary for SARS-CoV-2 pathogenesis in human cells and targeting PI3K/BET (bromodomain and extra-terminal domain proteins) alone or combined with antiviral therapies is beneficial in mitigating SARS-CoV-2 and its variants of concern (VOCs).
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Affiliation(s)
- Arpan Acharya
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | | | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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9
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Malik P, Jain S, Jain P, Kumawat J, Dwivedi J, Kishore D. A comprehensive update on the structure and synthesis of potential drug targets for combating the coronavirus pandemic caused by SARS-CoV-2. Arch Pharm (Weinheim) 2022; 355:e2100382. [PMID: 35040187 PMCID: PMC9011541 DOI: 10.1002/ardp.202100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 01/18/2023]
Abstract
The outbreak of the coronavirus pandemic COVID-19 created by its severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) variant, known for producing a very severe acute respiratory syndrome, has created an unprecedented situation by its continual assault around the world. The crisis caused by the SARS-CoV-2 variant has been a global challenge, calling to mitigate this unprecedented pandemic that has engulfed the whole world. Since the outbreak and spread of COVID-19, many researchers globally have been grappling to find new clinically trialed active drugs with anti-COVID-19 activity, from antimalarial drugs to JAK inhibitors, antiviral drugs, immune suppressants, and so forth. This article presents a brief discussion on the activity and synthesis of some active molecules such as favipiravir, hydroxychloroquine, pirfenidone, remdesivir, lopinavir, camostat, chloroquine, baricitinib, molnupiravir, and so forth, which are under trial.
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Affiliation(s)
- Prerna Malik
- Department of ChemistryBanasthali VidyapithJaipurIndia
| | - Sonika Jain
- Department of ChemistryBanasthali VidyapithJaipurIndia
| | - Pankaj Jain
- Department of PharmacyBanasthali VidyapithJaipurIndia
| | - Jyoti Kumawat
- Department of ChemistryBanasthali VidyapithJaipurIndia
| | - Jaya Dwivedi
- Department of ChemistryBanasthali VidyapithJaipurIndia
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10
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Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J, Edbali O, Madhusoodanan N, Kolesnikov A, Lopez R. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 2022; 50:W276-W279. [PMID: 35412617 PMCID: PMC9252731 DOI: 10.1093/nar/gkac240] [Citation(s) in RCA: 821] [Impact Index Per Article: 410.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/28/2022] [Indexed: 12/11/2022] Open
Abstract
The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI’s data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.
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Affiliation(s)
- Fábio Madeira
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matt Pearce
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adrian R N Tivey
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Prasad Basutkar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joon Lee
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ossama Edbali
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nandana Madhusoodanan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anton Kolesnikov
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rodrigo Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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11
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Wertenauer C, Brenner Michael G, Dressel A, Pfeifer C, Hauser U, Wieland E, Mayer C, Mutschmann C, Roskos M, Wertenauer HJ, Moissl AP, Lorkowski S, März W. Diagnostic Performance of Rapid Antigen Testing for SARS-CoV-2: The COVid-19 AntiGen (COVAG) study. Front Med (Lausanne) 2022; 9:774550. [PMID: 35386920 PMCID: PMC8979030 DOI: 10.3389/fmed.2022.774550] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/17/2022] [Indexed: 12/19/2022] Open
Abstract
Background Rapid diagnostic testing for SARS-Cov-2 antigens is used to combat the ongoing pandemic. In this study we aimed to compare two RDTs, the SD Biosensor Q SARS-CoV-2 Rapid Antigen Test (Roche) and the Panbio COVID-19 Ag Rapid Test (Abbott), against rRT-PCR. Methods We included 2,215 all-comers at a diagnostic center between February 1 and March 31, 2021. rRT-PCR-positive samples were examined for SARS-CoV-2 variants. Findings Three hundred and thirty eight participants (15%) were rRT-PCR-positive for SARS-CoV-2. The sensitivities of Roche-RDT and Abbott-RDT were 60.4 and 56.8% (P < 0.0001) and specificities 99.7% and 99.8% (P = 0.076). Sensitivity inversely correlated with rRT-PCR-Ct values. The RDTs had higher sensitivities in individuals referred by treating physicians (79.5%, 78.7%) than in those referred by health departments (49.5%, 44.3%) or tested for other reasons (50%, 45.8%), in persons without any comorbidities (74.4%, 71%) compared to those with comorbidities (38.2%, 34.4%), in individuals with COVID-19 symptoms (75.2%, 74.3%) compared to those without (31.9%, 23.3%), and in the absence of SARS-CoV-2 variants (87.7%, 84%) compared to Alpha variant carriers (77.1%, 72.3%). If 10,000 symptomatic individuals are tested of which 500 are truly positive, the RDTs would generate 38 false-positive and 124 false-negative results. If 10,000 asymptomatic individuals are tested, including 50 true positives, 18 false-positives and 34 false-negatives would be generated. Interpretation The sensitivities of the two RDTs for asymptomatic SARS-CoV-2 carriers are unsatisfactory. Their widespread use may not be effective in the ongoing SARS-CoV-2 pandemic. The virus genotype influences the sensitivity of the two RDTs. RDTs should be evaluated for different SARS-CoV-2 variants.
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Affiliation(s)
- Christoph Wertenauer
- Hausärzte am Schillerplatz, Stuttgart, Germany.,Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Faculty of Medicine, Riga Stradins University, Riga, Latvia.,SYNLAB Holding Deutschland GmbH, Augsburg, Germany
| | | | | | | | - Ulrike Hauser
- SYNLAB Medical Care Center Augsburg GmbH, Augsburg, Germany
| | - Eberhard Wieland
- SYNLAB Medical Care Center Leinfelden-Echterdingen GmbH, Leinfelden-Echterdingen, Germany
| | | | | | | | | | - Angela P Moissl
- Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany.,Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany.,Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
| | - Winfried März
- Medical Clinic V, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany.,Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
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12
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Aghamirza Moghim Aliabadi H, Eivazzadeh‐Keihan R, Beig Parikhani A, Fattahi Mehraban S, Maleki A, Fereshteh S, Bazaz M, Zolriasatein A, Bozorgnia B, Rahmati S, Saberi F, Yousefi Najafabadi Z, Damough S, Mohseni S, Salehzadeh H, Khakyzadeh V, Madanchi H, Kardar GA, Zarrintaj P, Saeb MR, Mozafari M. COVID-19: A systematic review and update on prevention, diagnosis, and treatment. MedComm (Beijing) 2022; 3:e115. [PMID: 35281790 PMCID: PMC8906461 DOI: 10.1002/mco2.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 01/09/2023] Open
Abstract
Since the rapid onset of the COVID-19 or SARS-CoV-2 pandemic in the world in 2019, extensive studies have been conducted to unveil the behavior and emission pattern of the virus in order to determine the best ways to diagnosis of virus and thereof formulate effective drugs or vaccines to combat the disease. The emergence of novel diagnostic and therapeutic techniques considering the multiplicity of reports from one side and contradictions in assessments from the other side necessitates instantaneous updates on the progress of clinical investigations. There is also growing public anxiety from time to time mutation of COVID-19, as reflected in considerable mortality and transmission, respectively, from delta and Omicron variants. We comprehensively review and summarize different aspects of prevention, diagnosis, and treatment of COVID-19. First, biological characteristics of COVID-19 were explained from diagnosis standpoint. Thereafter, the preclinical animal models of COVID-19 were discussed to frame the symptoms and clinical effects of COVID-19 from patient to patient with treatment strategies and in-silico/computational biology. Finally, the opportunities and challenges of nanoscience/nanotechnology in identification, diagnosis, and treatment of COVID-19 were discussed. This review covers almost all SARS-CoV-2-related topics extensively to deepen the understanding of the latest achievements (last updated on January 11, 2022).
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Affiliation(s)
- Hooman Aghamirza Moghim Aliabadi
- Protein Chemistry LaboratoryDepartment of Medical BiotechnologyBiotechnology Research CenterPasteur Institute of IranTehranIran
- Advance Chemical Studies LaboratoryFaculty of ChemistryK. N. Toosi UniversityTehranIran
| | | | - Arezoo Beig Parikhani
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | | | - Ali Maleki
- Department of ChemistryIran University of Science and TechnologyTehranIran
| | | | - Masoume Bazaz
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | | | | | - Saman Rahmati
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | - Fatemeh Saberi
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Zeinab Yousefi Najafabadi
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
- ImmunologyAsthma & Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Shadi Damough
- Department of Medical BiotechnologyBiotechnology Research CenterPasteur InstituteTehranIran
| | - Sara Mohseni
- Non‐metallic Materials Research GroupNiroo Research InstituteTehranIran
| | | | - Vahid Khakyzadeh
- Department of ChemistryK. N. Toosi University of TechnologyTehranIran
| | - Hamid Madanchi
- School of MedicineSemnan University of Medical SciencesSemnanIran
- Drug Design and Bioinformatics UnitDepartment of Medical BiotechnologyBiotechnology Research CenterPasteur Institute of IranTehranIran
| | - Gholam Ali Kardar
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
- ImmunologyAsthma & Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Payam Zarrintaj
- School of Chemical EngineeringOklahoma State UniversityStillwaterOklahomaUSA
| | - Mohammad Reza Saeb
- Department of Polymer TechnologyFaculty of ChemistryGdańsk University of TechnologyGdańskPoland
| | - Masoud Mozafari
- Department of Tissue Engineering & Regenerative MedicineIran University of Medical SciencesTehranIran
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13
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Hok L, Rimac H, Mavri J, Vianello R. COVID-19 infection and neurodegeneration: Computational evidence for interactions between the SARS-CoV-2 spike protein and monoamine oxidase enzymes. Comput Struct Biotechnol J 2022. [PMID: 35228857 PMCID: PMC8868002 DOI: 10.1016/j.csbj.2022.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
WT and the South African SARS‐CoV‐2 variant show comparable ACE2 and MAO affinities. Identified MAO/spike protein complexes modify MAO affinity for its neurotransmitters. Such changes impact metabolic clearance of brain amines and misbalance their level. This links MAO interference with neurological illnesses following COVID‐19 infection. More contagious SA variant gives larger MAO disturbances, which should not be ignored.
Although COVID-19 has been primarily associated with pneumonia, recent data show that its causative agent, the SARS-CoV-2 coronavirus, can infect many vital organs beyond the lungs, including the heart, kidneys and the brain. The literature agrees that COVID-19 is likely to have long-term mental health effects on infected individuals, which signifies a need to understand the role of the virus in the pathophysiology of brain disorders that is currently unknown and widely debated. Our docking and molecular dynamics simulations show that the affinity of the spike protein from the wild type (WT) and the South African B.1.351 (SA) variant towards MAO enzymes is comparable to that for its ACE2 receptor. This allows for the WT/SA⋅⋅⋅MAO complex formation, which changes MAO affinities for their neurotransmitter substrates, thereby impacting their metabolic conversion and misbalancing their levels. Knowing that this fine regulation is strongly linked with the etiology of various brain pathologies, these results are the first to highlight the possibility that the interference with the brain MAO catalytic activity is responsible for the increased neurodegenerative illnesses following a COVID-19 infection, thus placing a neurobiological link between these two conditions in the spotlight. Since the obtained insight suggests that a more contagious SA variant causes even larger disturbances, and with new and more problematic strains likely emerging in the near future, we firmly advise that the presented prospect of the SARS-CoV-2 induced neurological complications should not be ignored, but rather requires further clinical investigations to achieve an early diagnosis and timely therapeutic interventions.
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14
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Kannan SR, Spratt AN, Sharma K, Chand HS, Byrareddy SN, Singh K. Omicron SARS-CoV-2 variant: Unique features and their impact on pre-existing antibodies. J Autoimmun 2021; 126:102779. [PMID: 34915422 PMCID: PMC8666303 DOI: 10.1016/j.jaut.2021.102779] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/26/2022]
Abstract
Severe Acute Respiratory Coronavirus (SARS-CoV-2) has been emerging in the form of different variants since its first emergence in early December 2019. A new Variant of Concern (VOC) named the Omicron variant (B.1.1.529) was reported recently. This variant has a large number of mutations in the S protein. To date, there exists a limited information on the Omicron variant. Here we present the analyses of mutation distribution, the evolutionary relationship of Omicron with previous variants, and probable structural impact of mutations on antibody binding. Our analyses show the presence of 46 high prevalence mutations specific to Omicron. Twenty-three of these are localized within the spike (S) protein and the rest localized to the other 3 structural proteins of the virus, the envelope (E), membrane (M), and nucleocapsid (N). Phylogenetic analysis showed that the Omicron is closely related to the Gamma (P.1) variant. The structural analyses showed that several mutations are localized to the region of the S protein that is the major target of antibodies, suggesting that the mutations in the Omicron variant may affect the binding affinities of antibodies to the S protein.
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Affiliation(s)
- Saathvik R Kannan
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Austin N Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Kalicharan Sharma
- Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Hitendra S Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA; Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Delhi Pharmaceutical Sciences and Research University, New Delhi, India; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden; Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.
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15
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Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D’Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Gitter A, Greene CS. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. mSystems 2021; 6:e0009521. [PMID: 34698547 PMCID: PMC8547481 DOI: 10.1128/msystems.00095-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. IMPORTANCE COVID-19 involves a number of organ systems and can present with a wide range of symptoms. From how the virus infects cells to how it spreads between people, the available research suggests that these patterns are very similar to those seen in the closely related viruses SARS-CoV-1 and possibly Middle East respiratory syndrome-related CoV (MERS-CoV). Understanding the pathogenesis of the SARS-CoV-2 virus also contextualizes how the different biological systems affected by COVID-19 connect. Exploring the structure, phylogeny, and pathogenesis of the virus therefore helps to guide interpretation of the broader impacts of the virus on the human body and on human populations. For this reason, an in-depth exploration of viral mechanisms is critical to a robust understanding of SARS-CoV-2 and, potentially, future emergent human CoVs (HCoVs).
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Affiliation(s)
- Halie M. Rando
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Alexandra J. Lee
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sandipan Ray
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Ashwin N. Skelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth Sell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John J. Dziak
- Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Lucy D’Agostino McGowan
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Marouen Ben Guebila
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Nils Wellhausen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Simina M. Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Stephen Capone
- St. George’s University School of Medicine, St. George’s, Grenada
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
| | - YoSon Park
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Mai
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yuchen Sun
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
| | - Joel D. Boerckel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - James Brian Byrd
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Jinhui Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - John P. Barton
- Department of Physics and Astronomy, University of California-Riverside, Riverside, California, USA
| | - Rishi Raj Goel
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Tiago Lubiana
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - COVID-19 Review Consortium
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen, Germany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Mercer University, Macon, Georgia, USA
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, North Carolina, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
- Georgia State University, Atlanta, Georgia, USA
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
- St. George’s University School of Medicine, St. George’s, Grenada
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Clinical Sciences, Lund University, Lund, Sweden
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
- Azimuth1, McLean, Virginia, USA
- Allen Institute for Immunology, Seattle, Washington, USA
- Department of Physics and Astronomy, University of California-Riverside, Riverside, California, USA
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Casey S. Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
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16
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Acharya A, Pandey K, Thurman M, Klug E, Trivedi J, Sharma K, Lorson CL, Singh K, Byrareddy SN. Discovery and evaluation of entry inhibitors for SARS-CoV-2 and its emerging variants. J Virol 2021;:JVI0143721. [PMID: 34550770 DOI: 10.1128/JVI.01437-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 19 (COVID-19) pandemic. Despite unprecedented research and developmental efforts, SARS-CoV-2-specific antivirals are still unavailable for the treatment of COVID-19. In most instances, SARS-CoV-2 infection initiates with the binding of Spike glycoprotein to the host cell ACE2 receptor. Utilizing the crystal structure of the ACE2/Spike receptor-binding domain (S-RBD) complex (PDB file 6M0J) in a computer-aided drug design approach, we identified and validated five potential inhibitors of S-RBD and ACE-2 interaction. Two of the five compounds, MU-UNMC-1 and MU-UNMC-2, blocked the entry of pseudovirus particles expressing SARS-CoV-2 Spike glycoprotein. In live SARS-CoV-2 infection assays, both compounds showed antiviral activity with IC50 values in the micromolar range (MU-UNMC-1: IC50 = 0.67 μM and MU-UNMC-2: IC50 = 1.72 μM) in human bronchial epithelial cells. Furthermore, MU-UNMC-1 and MU-UNMC-2 effectively blocked the replication of rapidly transmitting variants of concern: South African variant B.1.351 (IC50 = 9.27 and 3.00 μM) and Scotland variant B.1.222 (IC50 = 2.64 and 1.39 μM), respectively. Following these assays, we conducted “induced-fit (flexible) docking” to understand the binding mode of MU-UNMC-1/MU-UNMC-2 at the S-RBD/ACE2 interface. Our data showed that mutation N501Y (present in B.1.351 variant) alters the binding mode of MU-UNMC-2 such that it is partially exposed to the solvent and has reduced polar contacts. Finally, MU-UNMC-2 displayed high synergy with remdesivir, the only approved drug for treating hospitalized COVID-19 patients. IMPORTANCE The ongoing coronavirus infectious disease 2019 (COVID-19) pandemic is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 207 million people have been infected globally, and 4.3 million have died due to this viral outbreak. While a few vaccines have been deployed, a SARS-CoV-2-specific antiviral for the treatment of COVID-19 is yet to be approved. As the interaction of SARS-CoV-2 Spike protein with ACE2 is critical for cellular entry, using a combination of a computer-aided drug design (CADD) approach and cell-based in vitro assays, we report the identification of five potential SARS-CoV-2 entry inhibitors. Out of the five, two compounds (MU-UNMC-1 and MU-UNMC-2) have antiviral activity against ancestral SARS-CoV-2 and emerging variants from South Africa and Scotland. Furthermore, MU-UNMC-2 acts synergistically with remdesivir (RDV), suggesting that RDV and MU-UNMC-2 can be developed as a combination therapy to treat COVID-19 patients.
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17
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Paniri A, Hosseini MM, Akhavan-Niaki H. Impact of new UK (B.1.1.7) SARS-Cov-2 variant on interacting with ACE2 and host immune response. Gene Rep 2021; 25:101342. [PMID: 34493993 PMCID: PMC8414842 DOI: 10.1016/j.genrep.2021.101342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/28/2021] [Accepted: 08/31/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Alireza Paniri
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | | | - Haleh Akhavan-Niaki
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.,Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran
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18
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Yang J, Yan Y, Zhong W. Application of omics technology to combat the COVID-19 pandemic. MedComm (Beijing) 2021; 2:381-401. [PMID: 34766152 PMCID: PMC8554664 DOI: 10.1002/mco2.90] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
As of August 27, 2021, the ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to over 220 countries, areas, and territories. Thus far, 214,468,601 confirmed cases, including 4,470,969 deaths, have been reported to the World Health Organization. To combat the COVID-19 pandemic, multiomics-based strategies, including genomics, transcriptomics, proteomics, and metabolomics, have been used to study the diagnosis methods, pathogenesis, prognosis, and potential drug targets of COVID-19. In order to help researchers and clinicians to keep up with the knowledge of COVID-19, we summarized the most recent progresses reported in omics-based research papers. This review discusses omics-based approaches for studying COVID-19, summarizing newly emerged SARS-CoV-2 variants as well as potential diagnostic methods, risk factors, and pathological features of COVID-19. This review can help researchers and clinicians gain insight into COVID-19 features, providing direction for future drug development and guidance for clinical treatment, so that patients can receive appropriate treatment as soon as possible to reduce the risk of disease progression.
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Affiliation(s)
- Jingjing Yang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
- School of Pharmaceutical SciencesHainan UniversityHaikouHainanChina
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Wu Zhong
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
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Kannan SR, Spratt AN, Cohen AR, Naqvi SH, Chand HS, Quinn TP, Lorson CL, Byrareddy SN, Singh K. Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. J Autoimmun 2021; 124:102715. [PMID: 34399188 DOI: 10.1016/j.jaut.2021.102715] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/31/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been rapidly evolving in the form of new variants. At least eleven known variants have been reported. The objective of this study was to delineate the differences in the mutational profile of Delta and Delta Plus variants. High-quality sequences (n = 1756) of Delta (B.1.617.2) and Delta Plus (AY.1 or B.1.617.2.1) variants were used to determine the prevalence of mutations (≥20 %) in the entire SARS-CoV-2 genome, their co-existence, and change in prevalence over a period of time. Structural analysis was conducted to get insights into the impact of mutations on antibody binding. A Sankey diagram was generated using phylogenetic analysis coupled with sequence-acquisition dates to infer the migration of the Delta Plus variant and its presence in the United States. The Delta Plus variant had a significant number of high-prevalence mutations (≥20 %) than in the Delta variant. Signature mutations in Spike (G142D, A222V, and T95I) existed at a more significant percentage in the Delta Plus variant than the Delta variant. Three mutations in Spike (K417N, V70F, and W258L) were exclusively present in the Delta Plus variant. A new mutation was identified in ORF1a (A1146T), which was only present in the Delta Plus variant with ~58 % prevalence. Furthermore, five key mutations (T95I, A222V, G142D, R158G, and K417N) were significantly more prevalent in the Delta Plus than in the Delta variant. Structural analyses revealed that mutations alter the sidechain conformation to weaken the interactions with antibodies. Delta Plus, which first emerged in India, reached the United States through England and Japan, followed by its spread to more than 20 the United States. Based on the results presented here, it is clear that the Delta and Delta Plus variants have unique mutation profiles, and the Delta Plus variant is not just a simple addition of K417N to the Delta variant. Highly correlated mutations may have emerged to keep the structural integrity of the virus.
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