1
|
Otero-Ruiz A, Rodriguez-Anaya LZ, Lares-Villa F, Lozano Aguirre Beltrán LF, Lares-Jiménez LF, Gonzalez-Galaviz JR, Cruz-Mendívil A. Functional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes. Sci Rep 2023; 13:14318. [PMID: 37653073 PMCID: PMC10471605 DOI: 10.1038/s41598-023-41657-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Balamuthia mandrillaris is a pathogenic protozoan that causes a rare but almost always fatal infection of the central nervous system and, in some cases, cutaneous lesions. Currently, the genomic data for this free-living amoeba include the description of several complete mitochondrial genomes. In contrast, two complete genomes with draft quality are available in GenBank, but none of these have a functional annotation. In the present study, the complete genome of B. mandrillaris isolated from a freshwater artificial lagoon was sequenced and assembled, obtaining an assembled genome with better assembly quality parameter values than the currently available genomes. Afterward, the genome mentioned earlier, along with strains V039 and 2046, were subjected to functional annotation. Finally, comparative genomics analysis was performed, and it was found that homologous genes in the core genome potentially involved in the virulence of Acanthamoeba spp. and Trypanosoma cruzi. Moreover, eleven of fifteen genes were identified in the three strains described as potential target genes to develop new treatment approaches for B. mandrillaris infections. These results describe proteins in this protozoan's complete genome and help prioritize which target genes could be used to develop new treatments.
Collapse
Affiliation(s)
- Alejandro Otero-Ruiz
- Programa de Doctorado en Ciencias Especialidad en Biotecnología, Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | | | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | - Luis Fernando Lozano Aguirre Beltrán
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas de la Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | | | - Abraham Cruz-Mendívil
- CONAHCYT-Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, 81101, Guasave, Sinaloa, Mexico
| |
Collapse
|
2
|
Singhvi N, Talwar C, Mahanta U, Kaur J, Mondal K, Ahmad N, Tyagi I, Sharma G, Gupta V. Comparative genomics and integrated system biology approach unveiled undirected phylogeny patterns, mutational hotspots, functional patterns, and molecule repurposing for monkeypox virus. Funct Integr Genomics 2023; 23:231. [PMID: 37432480 DOI: 10.1007/s10142-023-01168-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023]
Abstract
Monkeypox is a viral zoonosis with symptoms that are reminiscent of those experienced in previous smallpox cases. The GSAID database (Global Initiative on Sharing Avian Influenza Data) was used to assess 630 genomes of MPXV. The phylogenetic study revealed six primary clades, as well as a smaller percentage in radiating clades. Individual clades that make up various nationalities may have formed as a result of a particular SNP hotspot type that mutated in a specific population. The most significant mutation based on a mutational hotspot analysis was found at G3729A and G5143A. The gene ORF138, which encodes the Ankyrin repeat (ANK) protein, was found to have the most mutations. This protein mediates molecular recognition via protein-protein interactions. It was shown that 243 host proteins interacted with 10 monkeypox proteins identified as the hub proteins E3, SPI2, C5, K7, E8, G6, N2, B14, CRMB, and A41 through 262 direct connections. The interaction with chemokine system-related proteins provides further evidence that the monkeypox virus suppresses human proteins to facilitate its survival against innate immunity. Several FDA-approved molecules were evaluated as possible inhibitors of F13, a significant envelope protein on the membrane of extracellular versions of the virus. A total of 2500 putative ligands were individually docked with the F13 protein. The interaction between the F13 protein and these molecules may help prevent the monkeypox virus from spreading. After being confirmed by experiments, these putative inhibitors could have an impact on the activity of these proteins and be used in monkeypox treatments.
Collapse
Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, 248007, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, India, 110007
| | - Utkarsha Mahanta
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, 560100, India
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, 502284, India
| | - Jasvinder Kaur
- Department of Zoology, Gargi College, University of Delhi, New Delhi, 110049, India
| | - Krishnendu Mondal
- Ministry of Environment, Forest and Climate Change, Integrated Regional Office, Dehradun, 248001, India
| | - Nabeel Ahmad
- Department of Biotechnology, School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, 248007, India
| | - Inderjeet Tyagi
- Centre of DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India,, Kolkata, 700053, India
| | - Gaurav Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, 560100, India
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, 502284, India
| | - Vipin Gupta
- Ministry of Environment, Forest and Climate Change, Integrated Regional Office, Dehradun, 248001, India.
| |
Collapse
|
3
|
Nduwimana C, Nzoyikorera N, Ndihokubwayo A, Ihorimbere T, Nibogora C, Ndoreraho A, Hajayandi O, Bizimana JC, Diawara I, Niyonizigiye D, Nyandwi J. Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022. BMC Genomics 2023; 24:312. [PMID: 37301830 DOI: 10.1186/s12864-023-09420-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata. RESULTS In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related. CONCLUSION The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.
Collapse
Affiliation(s)
- Cassien Nduwimana
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi.
| | - Néhémie Nzoyikorera
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
- Mohamed VI University of Health Sciences (UM6SS), Higher Institute of Biosciences and Biotechnology, Casablanca, Morocco
- Mohamed VI Center for Research & Innovation, Laboratory of Microbial Biotechnology and Infectiology Research, Mohamed VI University of Health Sciences (UM6SS), Rabat, Morocco
| | | | - Théogène Ihorimbere
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
| | - Célestin Nibogora
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
| | - Adolphe Ndoreraho
- National Institute of Public Health, Ministry of Public Health and the Fight against AIDS, Bujumbura, Burundi
| | - Oscar Hajayandi
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
| | - Jean Claude Bizimana
- Public Health Emergency Operation Center, Ministry of Public Health and the Fight against AIDS, Bujumbura, Burundi
| | - Idrissa Diawara
- Mohamed VI University of Health Sciences (UM6SS), Higher Institute of Biosciences and Biotechnology, Casablanca, Morocco
- Mohamed VI Center for Research & Innovation, Laboratory of Microbial Biotechnology and Infectiology Research, Mohamed VI University of Health Sciences (UM6SS), Rabat, Morocco
| | - Dionis Niyonizigiye
- National Institute of Public Health, Ministry of Public Health and the Fight against AIDS, Bujumbura, Burundi
| | - Joseph Nyandwi
- National Institute of Public Health, Ministry of Public Health and the Fight against AIDS, Bujumbura, Burundi
- Faculté de Médecine, Université du Burundi, Bujumbura, Burundi
| |
Collapse
|
4
|
Korneeva N, Khalil MI, Ghosh I, Fan R, Arnold T, De Benedetti A. SARS-CoV-2 viral protein Nsp2 stimulates translation under normal and hypoxic conditions. Virol J 2023; 20:55. [PMID: 36998012 PMCID: PMC10060939 DOI: 10.1186/s12985-023-02021-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractWhen viruses like SARS-CoV-2 infect cells, they reprogram the repertoire of cellular and viral transcripts that are being translated to optimize their strategy of replication, often targeting host translation initiation factors, particularly eIF4F complex consisting of eIF4E, eIF4G and eIF4A. A proteomic analysis of SARS-CoV-2/human proteins interaction revealed viral Nsp2 and initiation factor eIF4E2, but a role of Nsp2 in regulating translation is still controversial. HEK293T cells stably expressing Nsp2 were tested for protein synthesis rates of synthetic and endogenous mRNAs known to be translated via cap- or IRES-dependent mechanism under normal and hypoxic conditions. Both cap- and IRES-dependent translation were increased in Nsp2-expressing cells under normal and hypoxic conditions, especially mRNAs that require high levels of eIF4F. This could be exploited by the virus to maintain high translation rates of both viral and cellular proteins, particularly in hypoxic conditions as may arise in SARS-CoV-2 patients with poor lung functioning.
Collapse
|
5
|
Shen JX, Du WW, Xia YL, Zhang ZB, Yu ZF, Fu YX, Liu SQ. Identification of and Mechanistic Insights into SARS-CoV-2 Main Protease Non-Covalent Inhibitors: An In-Silico Study. Int J Mol Sci 2023; 24:ijms24044237. [PMID: 36835648 PMCID: PMC9959744 DOI: 10.3390/ijms24044237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
The indispensable role of the SARS-CoV-2 main protease (Mpro) in the viral replication cycle and its dissimilarity to human proteases make Mpro a promising drug target. In order to identify the non-covalent Mpro inhibitors, we performed a comprehensive study using a combined computational strategy. We first screened the ZINC purchasable compound database using the pharmacophore model generated from the reference crystal structure of Mpro complexed with the inhibitor ML188. The hit compounds were then filtered by molecular docking and predicted parameters of drug-likeness and pharmacokinetics. The final molecular dynamics (MD) simulations identified three effective candidate inhibitors (ECIs) capable of maintaining binding within the substrate-binding cavity of Mpro. We further performed comparative analyses of the reference and effective complexes in terms of dynamics, thermodynamics, binding free energy (BFE), and interaction energies and modes. The results reveal that, when compared to the inter-molecular electrostatic forces/interactions, the inter-molecular van der Waals (vdW) forces/interactions are far more important in maintaining the association and determining the high affinity. Given the un-favorable effects of the inter-molecular electrostatic interactions-association destabilization by the competitive hydrogen bond (HB) interactions and the reduced binding affinity arising from the un-compensable increase in the electrostatic desolvation penalty-we suggest that enhancing the inter-molecular vdW interactions while avoiding introducing the deeply buried HBs may be a promising strategy in future inhibitor optimization.
Collapse
Affiliation(s)
- Jian-Xin Shen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Wen-Wen Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Bi Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China
| | - Ze-Fen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Human Genetics Center and Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA
- Correspondence: (Y.-X.F.); (S.-Q.L.)
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Correspondence: (Y.-X.F.); (S.-Q.L.)
| |
Collapse
|
6
|
González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
Collapse
Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
| |
Collapse
|
7
|
Al Adem K, Ferreira JC, Fadl S, Rabeh WM. pH profiles of 3-chymotrypsin-like protease (3CLpro) from SARS-CoV-2 elucidate its catalytic mechanism and a histidine residue critical for activity. J Biol Chem 2022; 299:102790. [PMID: 36509143 PMCID: PMC9733303 DOI: 10.1016/j.jbc.2022.102790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
3-Chymotrypsin-like protease (3CLpro) is a promising drug target for coronavirus disease 2019 and related coronavirus diseases because of the essential role of this protease in processing viral polyproteins after infection. Understanding the detailed catalytic mechanism of 3CLpro is essential for designing effective inhibitors of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular dynamics studies have suggested pH-dependent conformational changes of 3CLpro, but experimental pH profiles of SARS-CoV-2 3CLpro and analyses of the conserved active-site histidine residues have not been reported. In this work, pH-dependence studies of the kinetic parameters of SARS-CoV-2 3CLpro revealed a bell-shaped pH profile with 2 pKa values (6.9 ± 0.1 and 9.4 ± 0.1) attributable to ionization of the catalytic dyad His41 and Cys145, respectively. Our investigation of the roles of conserved active-site histidines showed that different amino acid substitutions of His163 produced inactive enzymes, indicating a key role of His163 in maintaining catalytically active SARS-CoV-2 3CLpro. By contrast, the H164A and H172A mutants retained 75% and 26% of the activity of WT, respectively. The alternative amino acid substitutions H172K and H172R did not recover the enzymatic activity, whereas H172Y restored activity to a level similar to that of the WT enzyme. The pH profiles of H164A, H172A, and H172Y were similar to those of the WT enzyme, with comparable pKa values for the catalytic dyad. Taken together, the experimental data support a general base mechanism of SARS-CoV-2 3CLpro and indicate that the neutral states of the catalytic dyad and active-site histidine residues are required for maximum enzyme activity.
Collapse
|
8
|
Halma MTJ, Wever MJA, Abeln S, Roche D, Wuite GJL. Therapeutic potential of compounds targeting SARS-CoV-2 helicase. Front Chem 2022; 10:1062352. [PMID: 36561139 PMCID: PMC9763700 DOI: 10.3389/fchem.2022.1062352] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
The economical and societal impact of COVID-19 has made the development of vaccines and drugs to combat SARS-CoV-2 infection a priority. While the SARS-CoV-2 spike protein has been widely explored as a drug target, the SARS-CoV-2 helicase (nsp13) does not have any approved medication. The helicase shares 99.8% similarity with its SARS-CoV-1 homolog and was shown to be essential for viral replication. This review summarizes and builds on existing research on inhibitors of SARS-CoV-1 and SARS-CoV-2 helicases. Our analysis on the toxicity and specificity of these compounds, set the road going forward for the repurposing of existing drugs and the development of new SARS-CoV-2 helicase inhibitors.
Collapse
Affiliation(s)
- Matthew T. J. Halma
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- LUMICKS B. V., Amsterdam, Netherlands
| | - Mark J. A. Wever
- DCM, University of Grenoble Alpes, Grenoble, France
- Edelris, Lyon, France
| | - Sanne Abeln
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Gijs J. L. Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
9
|
Aksenova AY, Likhachev IV, Grishin SY, Galzitskaya OV. The Increased Amyloidogenicity of Spike RBD and pH-Dependent Binding to ACE2 May Contribute to the Transmissibility and Pathogenic Properties of SARS-CoV-2 Omicron as Suggested by In Silico Study. Int J Mol Sci 2022; 23:13502. [PMID: 36362302 PMCID: PMC9655063 DOI: 10.3390/ijms232113502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
SARS-CoV-2 is a rapidly evolving pathogen that has caused a global pandemic characterized by several consecutive waves. Based on epidemiological and NGS data, many different variants of SARS-CoV-2 were described and characterized since the original variant emerged in Wuhan in 2019. Notably, SARS-CoV-2 variants differ in transmissibility and pathogenicity in the human population, although the molecular basis for this difference is still debatable. A significant role is attributed to amino acid changes in the binding surface of the Spike protein to the ACE2 receptor, which may facilitate virus entry into the cell or contribute to immune evasion. We modeled in silico the interaction between Spike RBDs of Wuhan-Hu-1, Delta, and Omicron BA.1 variants and ACE2 at different pHs (pH 5 and pH 7) and showed that the strength of this interaction was higher for the Omicron BA.1 RBD compared to Wuhan-Hu-1 or Delta RBDs and that the effect was more profound at pH 5. This finding is strikingly related to the increased ability of Omicron variants to spread in the population. We also noted that during its spread in the population, SARS-CoV-2 evolved to a more charged, basic composition. We hypothesize that the more basic surface of the Omicron variant may facilitate its spread in the upper respiratory tract but not in the lower respiratory tract, where pH estimates are different. We calculated the amyloidogenic properties of Spike RBDs in different SARS-CoV-2 variants and found eight amyloidogenic regions in the Spike RBDs for each of the variants predicted by the FoldAmyloid program. Although all eight regions were almost identical in the Wuhan to Gamma variants, two of them were significantly longer in both Omicron variants, making the Omicron RBD more amyloidogenic. We discuss how the increased predicted amyloidogenicity of the Omicron variants RBDs may be important for protein stability, influence its interaction with ACE2 and contribute to immune evasion.
Collapse
Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Ilya V. Likhachev
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS, The Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
| |
Collapse
|
10
|
Fang K, Liang G, Zhuang Z, Fang Y, Dong Y, Liang C, Chen X, Guo X. Screening the hub genes and analyzing the mechanisms in discharged COVID-19 patients retesting positive through bioinformatics analysis. J Clin Lab Anal 2022; 36:e24495. [PMID: 35657140 PMCID: PMC9279949 DOI: 10.1002/jcla.24495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND After encountering COVID-19 patients who test positive again after discharge, our study analyzed the pathogenesis to further assess the risk and possibility of virus reactivation. METHODS A separate microarray was acquired from the Gene Expression Omnibus (GEO), and its samples were divided into two groups: a "convalescent-RTP" group consisting of convalescent and "retesting positive" (RTP) patients (group CR) and a "healthy-RTP" group consisting of healthy control and RTP patients (group HR). The enrichment analysis was performed with R software, obtaining the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Subsequently, the protein-protein interaction (PPI) networks of each group were established, and the hub genes were discovered using the cytoHubba plugin. RESULTS In this study, 6622 differentially expressed genes were identified in the group CR, among which RAB11B-AS1, DISP1, MICAL3, PSMG1, and DOCK4 were up-regulated genes, and ANAPC1, IGLV1-40, SORT1, PLPPR2, and ATP1A1-AS1 were down-regulated. 7335 genes were screened in the group HR, including the top 5 up-regulated genes ALKBH6, AMBRA1, MIR1249, TRAV18, and LRRC69, and the top 5 down-regulated genes FAM241B, AC018529.3, AL031963.3, AC006946.1, and FAM149B1. The GO and KEGG analysis of the two groups revealed a significant enrichment in immune response and apoptosis. In the PPI network constructed, group CR and group HR identified 10 genes, respectively, and TP53BP1, SNRPD1, and SNRPD2 were selected as hub genes. CONCLUSIONS Using the messenger ribonucleic acid (mRNA) expression data from GSE166253, we found TP53BP1, SNRPD1, and SNRPD2 as hub genes in RTP patients, which is vital to the management and prognostic prediction of RTP patients.
Collapse
Affiliation(s)
- Ke‐Ying Fang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Gui‐Ning Liang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineNan Shan School of Guangzhou Medical UniversityGuangzhouChina
| | - Zhuo‐Qing Zhuang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Yong‐Xin Fang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Yu‐Qian Dong
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of PeriodonticsThe Stomatologe Medical School of Guangzhou Medical UniversityGuangzhouChina
| | - Chuang‐Jia Liang
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Xin‐Yan Chen
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
| | - Xu‐Guang Guo
- Department of Clinical Laboratory MedicineThe Third Affiliated Hospital of Guangzhou Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Clinical MedicineThe Third Clinical School of Guangzhou Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Major Obstetric DiseasesThe Third Affiliated GuangzhouGuangzhouChina
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education InstitutesThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory MedicineGuangzhou Medical UniversityGuangzhouChina
| |
Collapse
|
11
|
Lal R, Singh BK, Sar P, Phale P. The assessment of microbial ecology: a special emphasis on the Indian scenario. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:325-329. [PMID: 35362197 DOI: 10.1111/1758-2229.13067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Rup Lal
- The Energy & Resources Institute, New Delhi, 110003, India
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Prashant Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| |
Collapse
|
12
|
Abstract
Since November 2019, SARS-CoV-2 has been a matter of global concern due to its rapid spread, the millions of deaths it caused, and repeated waves of infections. One after another, many variants of this novel virus have come into existence due to its constant mutability, specifically in the spike glycoprotein region. The tally for variants of concern (VOCs), which already include Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2), has increased to five with the latest appearance of Omicron (B.1.1.529). In our study, we examine the effect of the transmissibility and infectious potential of the virus due to various mutations of SARS-CoV-2, especially in the receptor-binding domain (RBD). We discuss the role of genome sequencing in tracing all the mutations and the importance of the R value (reproductive number) to understand the virus spread. We also review the effectiveness of the available vaccines on the variants of concern, as the rapid spread of the newly emergent Omicron variant has raised doubts about the usefulness of the current vaccines. The use of a mixed vaccination strategy has proved to be effective, yet the newer variants, such as Omicron, demand booster doses for the population. Multivalent immunogens could be considered as the plausible solution for conferring protection against potential new mutants of the virus in the future.
Collapse
|
13
|
Ferreira JC, Fadl S, Rabeh WM. Key dimer interface residues impact the catalytic activity of 3CLpro, the main protease of SARS-CoV-2. J Biol Chem 2022; 298:102023. [PMID: 35568197 PMCID: PMC9091064 DOI: 10.1016/j.jbc.2022.102023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023] Open
Abstract
3C-like protease (3CLpro) is one of two proteases that process and liberate functional viral proteins essential for the maturation and infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. It has been suggested that 3CLpro is catalytically active as a dimer, making the dimerization interface a target for antiviral development. Guided by structural analysis, here we introduced single amino acid substitutions at nine residues at three key sites of the dimer interface to assess their impact on dimerization and activity. We show that at site 1, alanine substitution of S1 or E166 increased by 2-fold or reduced relative activity, respectively. At site 2, alanine substitution of S10 or E14 eliminated activity, whereas K12A exhibited ∼60% relative activity. At site 3, alanine substitution of R4, E290, or Q299 eliminated activity, whereas S139A exhibited 46% relative activity. We further found the oligomerization states of the dimer interface mutants varied; the inactive mutants R4A, R4Q, S10A/C, E14A/D/Q/S, E290A, and Q299A/E were present as dimers, demonstrating that dimerization is not an indication of catalytically active 3CLpro. In addition, present mostly as monomers, K12A displayed residual activity, which could be attributed to the conspicuous amount of dimer present. Finally, differential scanning calorimetry did not reveal a direct relationship between the thermodynamic stability of mutants with oligomerization or catalytic activity. These results provide insights on two allosteric sites, R4/E290 and S10/E14, that may promote the design of antiviral compounds that target the dimer interface rather than the active site of SARS-CoV-2 3CLpro.
Collapse
Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
14
|
Lal R, Singh B, Sar P, Phale P. Microbiology in India: Status, Challenges, and Scope. Environ Microbiol 2022; 24:2607-2611. [PMID: 35411614 DOI: 10.1111/1462-2920.16005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Rup Lal
- The Energy & Resources Institute, New Delhi, 110003, India
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Pinaki Sar
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Prashant Phale
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| |
Collapse
|
15
|
Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-Kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. iScience 2022; 25:103880. [PMID: 35156006 PMCID: PMC8817759 DOI: 10.1016/j.isci.2022.103880] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/29/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
There is a dearth of information on COVID-19 disease dynamics in Africa. To fill this gap, we investigated the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We investigated the circulating diversity, reconstructed the viral evolutionary divergence and history, and studied the case and death trends in the continent. Almost a fifth (144/782, 18.4%) of Pango lineages found worldwide circulated in Africa, with five different lineages dominating over time. Phylogenetic analysis revealed that African viruses cluster more closely with those from Europe. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the epidemiological and evolutionary dynamics of the circulating viral diversity in Africa. They also emphasize the need to expand surveillance efforts in Africa to help inform and implement better public health measures. SARS-CoV-2 viruses from Africa cluster predominantly with European strains Lower viral diversity observed in Africa is likely due to genomic under-surveillance Number of cases, deaths, and testing show substantial heterogeneity across Africa Two motifs could function as integrin-binding sites and N-glycosylation domains
Collapse
Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria.,Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-Kwashie
- Department of Medical Microbiology, Clinical Virology Unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria.,Helix Biogen Institute, Ogbomoso, Nigeria
| | - Louis Odinakaose Ezediuno
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin,1515 P.M.B, Ilorin, Nigeria
| | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria.,Division of Microbiology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield Pretoria 0028, South Africa
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Medical Microbiology and Parasitology, University of Ilorin 1515, P.M.B, Ilorin, Nigeria
| | - David J Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria.,Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria
| | - Nídia S Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
16
|
Yépez Y, Marcano-Ruiz M, Bezerra RS, Fam B, Ximenez JP, Silva WA, Bortolini MC. Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Genet Mol Biol 2022; 45:e20210309. [PMID: 35266951 PMCID: PMC8908351 DOI: 10.1590/1678-4685-gmb-2021-0309] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022] Open
Abstract
Our goal was to describe in more detail the evolutionary history of Gamma and two
derived lineages (P.1.1 and P.1.2), which are part of the arms race that
SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain
of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive
selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6,
ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic
sites for Gamma lacked a signature of positive selection in our study, but these
were not fixed, apparently escaping the action of purifying selection. Our
network analyses revealed branches leading to expanding haplotypes with sites
under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2
exclusive haplotype H_5 originated from a non-synonymous mutational step
(H3509Y) in H_1 of ORF1a. The selected allele, 3509Y,
represents an adaptive novelty involving ORF1a of P.1. Finally,
we discuss how phenomena such as epistasis and antagonistic pleiotropy could
limit the emergence of new alleles (and combinations thereof) in SARS-COV-2
lineages, maintaining infectivity in humans, while providing rapid response
capabilities to face the arms race triggered by host immuneresponses.
Collapse
Affiliation(s)
- Yuri Yépez
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - Mariana Marcano-Ruiz
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - Rafael S Bezerra
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Bibiana Fam
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - João Pb Ximenez
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Wilson A Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil.,Instituto de Pesquisa do Câncer de Guarapuava, Guarapuava, PR, Brazil
| | - Maria Cátira Bortolini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| |
Collapse
|
17
|
CovDif, a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants. Viruses 2022; 14:v14030561. [PMID: 35336968 PMCID: PMC8955889 DOI: 10.3390/v14030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/17/2022] Open
Abstract
The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification and diagnosis, therapeutics development and epidemiological surveillance to detect the emergence of new viral variants. An intense surveillance of virus variants has led to the identification of Variants of Interest and Variants of Concern. Although these classifications dynamically change as the pandemic evolves, they have been useful to guide public health efforts on containment and mitigation. In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes. CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups. CovDif is able to identify loss in conservation due to point mutations, deletions, inversions and chromosomal rearrangements. In this work, we applied CovDif to SARS-CoV-2 clades (G, GH, GR, GV, L, O, S and G) and variants. We identified all regions for any defining SNPs. We also applied CovDif to a group of population genomes and evaluated the conservation of primer regions for current SARS-CoV-2 detection and diagnostic protocols. We found that some of these protocols should be applied with caution as few of the primer-template regions are no longer conserved in some SARS-CoV-2 variants. We conclude that CovDif is a tool that could be widely applied to study the conservation of any group of viral genomes as long as whole genomes exist.
Collapse
|
18
|
Hassan SS, Basu P, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala MM, Lal A, Chauhan G, Baetas-da-Cruz W, Sherchan SP, Uversky VN. Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution. ENVIRONMENTAL RESEARCH 2022; 204:112092. [PMID: 34562480 PMCID: PMC8457672 DOI: 10.1016/j.envres.2021.112092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 05/20/2023]
Abstract
Various lineages of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have contributed to prolongation of the Coronavirus Disease 2019 (COVID-19) pandemic. Several non-synonymous mutations in SARS-CoV-2 proteins have generated multiple SARS-CoV-2 variants. In our previous report, we have shown that an evenly uneven distribution of unique protein variants of SARS-CoV-2 is geo-location or demography-specific. However, the correlation between the demographic transmutability of the SARS-CoV-2 infection and mutations in various proteins remains unknown due to hidden symmetry/asymmetry in the occurrence of mutations. This study tracked how these mutations are emerging in SARS-CoV-2 proteins in six model countries and globally. In a geo-location, considering the mutations having a frequency of detection of at least 500 in each SARS-CoV-2 protein, we studied the country-wise percentage of invariant residues. Our data revealed that since October 2020, highly frequent mutations in SARS-CoV-2 have been observed mostly in the Open Reading Frame (ORF) 7b and ORF8, worldwide. No such highly frequent mutations in any of the SARS-CoV-2 proteins were found in the UK, India, and Brazil, which does not correlate with the degree of transmissibility of the virus in India and Brazil. However, we have found a signature that SARS-CoV-2 proteins were evolving at a higher rate, and considering global data, mutations are detected in the majority of the available amino acid locations. Fractal analysis of each protein's normalized factor time series showed a periodically aperiodic emergence of dominant variants for SARS-CoV-2 protein mutations across different countries. It was noticed that certain high-frequency variants have emerged in the last couple of months, and thus the emerging SARS-CoV-2 strains are expected to contain prevalent mutations in the ORF3a, membrane, and ORF8 proteins. In contrast to other beta-coronaviruses, SARS-CoV-2 variants have rapidly emerged based on demographically dependent mutations. Characterization of the periodically aperiodic nature of the demographic spread of SARS-CoV-2 variants in various countries can contribute to the identification of the origin of SARS-CoV-2.
Collapse
Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa.
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab, 21934, Alexandria, Egypt.
| | | | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata, 700108, India.
| | - Ángel Serrano-Aroca
- Biomaterials & Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia, San Vicente Mártir, Valencia 46001, Spain.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid, 566, Jordan.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy.
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Departamento de Geńetica, Ecologia e Evolucao, Instituto de Cîencias Bioĺogicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 6068507, Japan.
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, 70112, USA.
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, BT52 1SA, Northern Ireland, UK.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849, Monterrey, Nuevo Léon, Mexico.
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russia.
| |
Collapse
|
19
|
Gusev E, Sarapultsev A, Solomatina L, Chereshnev V. SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19. Int J Mol Sci 2022; 23:1716. [PMID: 35163638 PMCID: PMC8835786 DOI: 10.3390/ijms23031716] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
The review aims to consolidate research findings on the molecular mechanisms and virulence and pathogenicity characteristics of coronavirus disease (COVID-19) causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and their relevance to four typical stages in the development of acute viral infection. These four stages are invasion; primary blockade of antiviral innate immunity; engagement of the virus's protection mechanisms against the factors of adaptive immunity; and acute, long-term complications of COVID-19. The invasion stage entails the recognition of the spike protein (S) of SARS-CoV-2 target cell receptors, namely, the main receptor (angiotensin-converting enzyme 2, ACE2), its coreceptors, and potential alternative receptors. The presence of a diverse repertoire of receptors allows SARS-CoV-2 to infect various types of cells, including those not expressing ACE2. During the second stage, the majority of the polyfunctional structural, non-structural, and extra proteins SARS-CoV-2 synthesizes in infected cells are involved in the primary blockage of antiviral innate immunity. A high degree of redundancy and systemic action characterizing these pathogenic factors allows SARS-CoV-2 to overcome antiviral mechanisms at the initial stages of invasion. The third stage includes passive and active protection of the virus from factors of adaptive immunity, overcoming of the barrier function at the focus of inflammation, and generalization of SARS-CoV-2 in the body. The fourth stage is associated with the deployment of variants of acute and long-term complications of COVID-19. SARS-CoV-2's ability to induce autoimmune and autoinflammatory pathways of tissue invasion and development of both immunosuppressive and hyperergic mechanisms of systemic inflammation is critical at this stage of infection.
Collapse
Affiliation(s)
- Evgenii Gusev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Alexey Sarapultsev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080 Chelyabinsk, Russia
| | - Liliya Solomatina
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Valeriy Chereshnev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| |
Collapse
|
20
|
Cheng XW, Li J, Zhang L, Hu WJ, Zong L, Xu X, Qiao JP, Zheng MJ, Jiang XW, Liang ZK, Zhou YF, Zhang N, Zhu HQ, Xu YH. Identification of SARS-CoV-2 Variants and Their Clinical Significance in Hefei, China. Front Med (Lausanne) 2022; 8:784632. [PMID: 35083244 PMCID: PMC8784789 DOI: 10.3389/fmed.2021.784632] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic represents one of the most exigent threats of our lifetime to global public health and economy. As part of the pandemic, from January 10 to March 10, 2020, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in Hefei (Anhui Province, China) with a total of 174 confirmed cases of COVID-19. During this period, we were able to gather critical information on the transmission and evolution of pathogens through genomic surveillance. Particularly, the objective of our study was to track putative variants of SARS-CoV-2 circulating in Hefei for the first time and contribute to the global effort toward elucidating the molecular epidemic profile of the virus. Patients who showed symptoms of COVID-19 were routinely tested for SARS-CoV-2 infections via RT-PCR at the First Affiliated Hospital of Anhui Medical University. Whole-genome sequencing was performed on 97 clinical samples collected from 29 confirmed COVID-19 patients. As a result, we identified a local novel single-nucleotide polymorphism site (10,380) harboring a G → T mutation (Gly → Val) in Hefei. Further phylogenetic network analysis with all the sequences of SARS-CoV-2 deposited in GenBank collected in East and Southeast Asia revealed a local subtype of S-type SARS-CoV-2 (a1) harboring a C → T synonymous mutation (Leu) at position 18,060 of ORF1b, likely representing a local SARS-CoV-2 mutation site that is obviously concentrated in Hefei and the Yangtze River Delta region. Moreover, clinical investigation on the inflammatory cytokine profile of the patients suggested that mutations at positions 18,060 (the shared variable site of subtype a1) and 28,253(harboring a C → T synonymous mutation, Phe) were associated with milder immune responses in the patients.
Collapse
Affiliation(s)
- Xiao-Wen Cheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Laboratory of Molecular Biology, Department of Biochemistry, Anhui Medical University, Hefei, China
| | - Jie Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lu Zhang
- College of Life Sciences, Anhui Medical University, Hefei, China
| | - Wen-Jun Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lu Zong
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiang Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jin-Ping Qiao
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mei-Juan Zheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xi-Wen Jiang
- Da An Gene Co., Ltd., Sun Yat-sen University, Guangzhou, China.,The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, China
| | - Zhi-Kun Liang
- Clinical Laboratory Center, Guangzhou Darui Biotechnology, Co., Ltd., Guangzhou, China
| | - Yi-Fan Zhou
- Division of Life Sciences and Medicine, Department of Pathology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Ning Zhang
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hua-Qing Zhu
- Laboratory of Molecular Biology, Department of Biochemistry, Anhui Medical University, Hefei, China
| | - Yuan-Hong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| |
Collapse
|
21
|
An overview of human proteins and genes involved in SARS-CoV-2 infection. Gene 2022; 808:145963. [PMID: 34530086 PMCID: PMC8437745 DOI: 10.1016/j.gene.2021.145963] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/14/2021] [Accepted: 09/09/2021] [Indexed: 02/06/2023]
Abstract
As of July 2021, the outbreak of coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has led to more than 200 million infections and more than 4.2 million deaths globally. Complications of severe COVID-19 include acute kidney injury, liver dysfunction, cardiomyopathy, and coagulation dysfunction. Thus, there is an urgent need to identify proteins and genetic factors associated with COVID-19 susceptibility and outcome. We comprehensively reviewed recent findings of host-SARS-CoV-2 interactome analyses. To identify genetic variants associated with COVID-19, we focused on the findings from genome and transcriptome wide association studies (GWAS and TWAS) and bioinformatics analysis. We described established human proteins including ACE2, TMPRSS2, 40S ribosomal subunit, ApoA1, TOM70, HLA-A, and PALS1 interacting with SARS-CoV-2 based on cryo-electron microscopy results. Furthermore, we described approximately 1000 human proteins showing evidence of interaction with SARS-CoV-2 and highlighted host cellular processes such as innate immune pathways affected by infection. We summarized the evidence on more than 20 identified candidate genes in COVID-19 severity. Predicted deleterious and disruptive genetic variants with possible effects on COVID-19 infectivity have been also summarized. These findings provide novel insights into SARS-CoV-2 biology and infection as well as potential strategies for development of novel COVID therapeutic targets and drug repurposing.
Collapse
|
22
|
Farahani M, Niknam Z, Mohammadi Amirabad L, Amiri-Dashatan N, Koushki M, Nemati M, Danesh Pouya F, Rezaei-Tavirani M, Rasmi Y, Tayebi L. Molecular pathways involved in COVID-19 and potential pathway-based therapeutic targets. Biomed Pharmacother 2022; 145:112420. [PMID: 34801852 PMCID: PMC8585639 DOI: 10.1016/j.biopha.2021.112420] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 01/08/2023] Open
Abstract
Deciphering the molecular downstream consequences of severe acute respiratory syndrome coronavirus (SARS-CoV)- 2 infection is important for a greater understanding of the disease and treatment planning. Furthermore, greater understanding of the underlying mechanisms of diagnostic and therapeutic strategies can help in the development of vaccines and drugs against COVID-19. At present, the molecular mechanisms of SARS-CoV-2 in the host cells are not sufficiently comprehended. Some of the mechanisms are proposed considering the existing similarities between SARS-CoV-2 and the other members of the β-CoVs, and others are explained based on studies advanced in the structure and function of SARS-CoV-2. In this review, we endeavored to map the possible mechanisms of the host response following SARS-CoV-2 infection and surveyed current research conducted by in vitro, in vivo and human observations, as well as existing suggestions. We addressed the specific signaling events that can cause cytokine storm and demonstrated three forms of cell death signaling following virus infection, including apoptosis, pyroptosis, and necroptosis. Given the elicited signaling pathways, we introduced possible pathway-based therapeutic targets; ADAM17 was especially highlighted as one of the most important elements of several signaling pathways involved in the immunopathogenesis of COVID-19. We also provided the possible drug candidates against these targets. Moreover, the cytokine-cytokine receptor interaction pathway was found as one of the important cross-talk pathways through a pathway-pathway interaction analysis for SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Masoumeh Farahani
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Niknam
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Nasrin Amiri-Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohadeseh Nemati
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Fahima Danesh Pouya
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Yousef Rasmi
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran; Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran.
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA
| |
Collapse
|
23
|
Cai C, Zhang X, Liu Y, Shen E, Feng Z, Guo C, Han Y, Ouyang Y, Shen H. Gut microbiota imbalance in colorectal cancer patients, the risk factor of COVID-19 mortality. Gut Pathog 2021; 13:70. [PMID: 34863291 PMCID: PMC8643189 DOI: 10.1186/s13099-021-00466-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background COVID-19 pandemic is sweeping across the world. Previous studies have shown that gut microbiota is associated with COVID-19, and operational taxonomic unit (OTU) composed of Blautia genus, Lactobacillus genus, and Ruminococcus genus of Firmicutes is correlated with the severity of COVID-19. Gut microbiota imbalance in colorectal cancer patients may lead to the variation of OTU. Results Based on the GMrepo database, the gut microbiota of 1374 patients with colorectal neoplasms and 27,329 healthy people was analyzed to investigate the differences in the abundance of microbes between colorectal neoplasms patients and healthy people. Furthermore, We collected feces samples from 12 patients with colorectal cancer and 8 healthy people in Xiangya hospital for metabolomic analysis to investigate the potential mechanisms. Our study showed that the abundance of Blautia and Ruminococcus was significantly increased in colorectal neoplasms, which may increase the severity of COVID-19. The gender and age of patients may affect the severity of COVID-19 by shaping the gut microbiota, but the BMI of patients does not. Conclusions Our work draws an initial point that gut microbiota imbalance is a risk factor of COVID-19 mortality and gut microbiota may provide a new therapeutic avenue for colorectal cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00466-w.
Collapse
Affiliation(s)
- Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Xiangyang Zhang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Yihan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Edward Shen
- Department of Life Science, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Ziyang Feng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Cao Guo
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yanhong Ouyang
- Department of Emergency, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, 19 Xiuhua Road, Haikou, 570311, Hainan, China.
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| |
Collapse
|
24
|
Kandimalla R, Chakraborty P, Vallamkondu J, Chaudhary A, Samanta S, Reddy PH, De Feo V, Dewanjee S. Counting on COVID-19 Vaccine: Insights into the Current Strategies, Progress and Future Challenges. Biomedicines 2021; 9:1740. [PMID: 34829969 PMCID: PMC8615473 DOI: 10.3390/biomedicines9111740] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
The emergence of a novel coronavirus viz., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 and its subsequent substantial spread produced the coronavirus disease 2019 (COVID-19) pandemic worldwide. Given its unprecedented infectivity and pathogenicity, the COVID-19 pandemic had a devastating impact on human health, and its clinical management has been a great challenge, which has led to the development and speedy trials of several vaccine candidates against SARS-CoV-2 at an exceptional pace. As a result, several COVID-19 vaccines were made commercially available in the first half of 2021. Although several COVID-19 vaccines showed promising results, crucial insights into their epidemiology, protective mechanisms, and the propensities of reinfection are not largely reviewed. In the present report, we provided insights into the prospects of vaccination against COVID-19 and assessed diverse vaccination strategies including DNA, mRNA, protein subunits, vector-based, live attenuated, and inactivated whole/viral particle-based vaccines. Next, we reviewed major aspects of various available vaccines approved by the World Health Organization and by the local administrations to use against COVID-19. Moreover, we comprehensively assessed the success of these approved vaccines and also their untoward effects, including the possibility of reinfection. We also provided an update on the vaccines that are under development and could be promising candidates in the future. Conclusively, we provided insights into the COVID-19 vaccine epidemiology, their potency, and propensity for SARS-CoV-2 reinfection, while a careful review of their current status, strategies, success, and future challenges was also presented.
Collapse
Affiliation(s)
- Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana, India
- Department of Biochemistry, Kakatiya Medical College, Warangal 506007, Telangana, India
| | - Pratik Chakraborty
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India;
| | | | - Anupama Chaudhary
- Orinin-BioSystems, LE-52, Lotus Road 4, CHD City, Karnal 132001, Haryana, India;
| | - Sonalinandini Samanta
- Department of Dermatology (Skin & Venereology), ESIC Medical College & Hospital, Patna 801103, Bihar, India;
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
- Department of Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Vincenzo De Feo
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India;
| |
Collapse
|
25
|
A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients. Life (Basel) 2021; 11:life11111224. [PMID: 34833100 PMCID: PMC8620851 DOI: 10.3390/life11111224] [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: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Since its first detection in December 2019, more than 232 million cases of COVID-19, including 4.7 million deaths, have been reported by the WHO. The SARS-CoV-2 viral genomes have evolved rapidly worldwide, causing the emergence of new variants. This systematic review and meta-analysis was conducted to provide a global mutational profile of SARS-CoV-2 from December 2019 to October 2020. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA), and a study protocol was lodged with PROSPERO. Data from 62 eligible studies involving 368,316 SARS-CoV-2 genomes were analyzed. The mutational data analyzed showed most studies detected mutations in the Spike protein (n = 50), Nucleocapsid phosphoprotein (n = 34), ORF1ab gene (n = 29), 5′-UTR (n = 28) and ORF3a (n = 25). Under the random-effects model, pooled prevalence of SARS-CoV-2 variants was estimated at 95.1% (95% CI; 93.3–96.4%; I2 = 98.952%; p = 0.000) while subgroup meta-analysis by country showed majority of the studies were conducted ‘Worldwide’ (n = 10), followed by ‘Multiple countries’ (n = 6) and the USA (n = 5). The estimated prevalence indicated a need to continuously monitor the prevalence of new mutations due to their potential influence on disease severity, transmissibility and vaccine effectiveness.
Collapse
|
26
|
Lv J, Tu S, Xu L. Detection of Phenotype-Related Mutations of COVID-19 via the Whole Genomic Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1242-1249. [PMID: 33417561 PMCID: PMC8769011 DOI: 10.1109/tcbb.2021.3049836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 11/30/2020] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
The coronavirus disease 2019 (COVID-19) epidemic continues to spread rapidly around the world and nearly 20 millions people are infected. This paper utilises both single-locus analysis and joint-SNPs analysis for detection of significant single nucleotide polymorphisms (SNPs) in the phenotypes of symptomatic versus asymptomatic, the early collection time versus the late collection time, the old versus the young, and the male versus the female. Also, this paper analyses the relationship between any two SNPs via linkage disequilibrium analysis, and visualises the patterns of cumulative mutations of SNPs over collection time. The results are in three folds. First, the SNP which locates at the nucleotide position 4321 is found to be an independent significant locus associated with all the first three phenotypes. Moreover, 12 significant SNPs are found in the first two studies. Second, gene orf1ab containing SNP-4321 is detected to be significantly associated with the first three phenotypes, and the three genes S, ORF3a, and N, are detected to be significant in the first two phenotypes. Third, some of the detected genes or SNPs are related to the SARS-COV-2 as supported by literature survey, which indicates that the results here may be helpful for further investigation.
Collapse
Affiliation(s)
- Jinxiong Lv
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Shikui Tu
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Lei Xu
- Center for Cognitive Machines and Computational Health (CMaCH)Department of Computer Science and EngineeringShanghai Jiao Tong UniversityShanghai200240China
| |
Collapse
|
27
|
Ferreira JC, Fadl S, Villanueva AJ, Rabeh WM. Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Front Chem 2021; 9:692168. [PMID: 34249864 PMCID: PMC8264439 DOI: 10.3389/fchem.2021.692168] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/14/2021] [Indexed: 01/18/2023] Open
Abstract
Coronaviruses are responsible for multiple pandemics and millions of deaths globally, including the current pandemic of coronavirus disease 2019 (COVID-19). Development of antivirals against coronaviruses, including the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) responsible for COVID-19, is essential for containing the current and future coronavirus outbreaks. SARS-CoV-2 proteases represent important targets for the development of antivirals because of their role in the processing of viral polyproteins. 3-Chymotrypsin-like protease (3CLpro) is one such protease. The cleavage of SARS-CoV-2 polyproteins by 3CLpro is facilitated by a Cys145–His41 catalytic dyad. We here characterized the catalytic roles of the cysteine–histidine pair for improved understanding of the 3CLpro reaction mechanism, to inform the development of more effective antivirals against Sars-CoV-2. The catalytic dyad residues were substituted by site-directed mutagenesis. All substitutions tested (H41A, H41D, H41E, C145A, and C145S) resulted in a complete inactivation of 3CLpro, even when amino acids with a similar catalytic function to that of the original residues were used. The integrity of the structural fold of enzyme variants was investigated by circular dichroism spectroscopy to test if the catalytic inactivation of 3CLpro was caused by gross changes in the enzyme secondary structure. C145A, but not the other substitutions, shifted the oligomeric state of the enzyme from dimeric to a higher oligomeric state. Finally, the thermodynamic stability of 3CLpro H41A, H41D, and C145S variants was reduced relative the wild-type enzyme, with a similar stability of the H41E and C145A variants. Collectively, the above observations confirm the roles of His41 and Cys145 in the catalytic activity and the overall conformational fold of 3CLpro SARS-CoV-2. We conclude that the cysteine–histidine pair should be targeted for inhibition of 3CLpro and development of antiviral against COVID-19 and coronaviruses.
Collapse
Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| |
Collapse
|
28
|
Gorkhali R, Koirala P, Rijal S, Mainali A, Baral A, Bhattarai HK. Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins. Bioinform Biol Insights 2021; 15:11779322211025876. [PMID: 34220199 PMCID: PMC8221690 DOI: 10.1177/11779322211025876] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/25/2021] [Indexed: 01/20/2023] Open
Abstract
SARS-CoV-2 virus, the causative agent of COVID-19 pandemic, has a genomic organization consisting of 16 nonstructural proteins (nsps), 4 structural proteins, and 9 accessory proteins. Relative of SARS-CoV-2, SARS-CoV, has genomic organization, which is very similar. In this article, the function and structure of the proteins of SARS-CoV-2 and SARS-CoV are described in great detail. The nsps are expressed as a single or two polyproteins, which are then cleaved into individual proteins using two proteases of the virus, a chymotrypsin-like protease and a papain-like protease. The released proteins serve as centers of virus replication and transcription. Some of these nsps modulate the host’s translation and immune systems, while others help the virus evade the host immune system. Some of the nsps help form replication-transcription complex at double-membrane vesicles. Others, including one RNA-dependent RNA polymerase and one exonuclease, help in the polymerization of newly synthesized RNA of the virus and help minimize the mutation rate by proofreading. After synthesis of the viral RNA, it gets capped. The capping consists of adding GMP and a methylation mark, called cap 0 and additionally adding a methyl group to the terminal ribose called cap1. Capping is accomplished with the help of a helicase, which also helps remove a phosphate, two methyltransferases, and a scaffolding factor. Among the structural proteins, S protein forms the receptor of the virus, which latches on the angiotensin-converting enzyme 2 receptor of the host and N protein binds and protects the genomic RNA of the virus. The accessory proteins found in these viruses are small proteins with immune modulatory roles. Besides functions of these proteins, solved X-ray and cryogenic electron microscopy structures related to the function of the proteins along with comparisons to other coronavirus homologs have been described in the article. Finally, the rate of mutation of SARS-CoV-2 residues of the proteome during the 2020 pandemic has been described. Some proteins are mutated more often than other proteins, but the significance of these mutation rates is not fully understood.
Collapse
Affiliation(s)
- Ritesh Gorkhali
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | | | - Sadikshya Rijal
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Ashmita Mainali
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Adesh Baral
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | | |
Collapse
|
29
|
Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.17.21257341. [PMID: 34031660 PMCID: PMC8142660 DOI: 10.1101/2021.05.17.21257341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent. To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences. In this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.
Collapse
Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-kwashie
- Department of Medical Microbiology Clinical Virology unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | | | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, University of Ilorin, Nigeria
| | - David J. Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Nídia S. Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
30
|
A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Comput Biol Med 2021; 132:104315. [PMID: 33705994 PMCID: PMC7935700 DOI: 10.1016/j.compbiomed.2021.104315] [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: 02/10/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022]
Abstract
Coronavirus disease (COVID-19) rapidly expands to a global pandemic and its impact on public health varies from country to country. It is caused by a new virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is imperative for relapsing current antiviral therapeutics owing to randomized genetic drift in global SARS-CoV-2 isolates. A molecular mechanism behind the emerging genomic variants is not yet understood for the prioritization of selective antivirals. The present computational study was aimed to repurpose existing antivirals for Indian SARS-CoV-2 isolates by uncovering a hijack mechanism based on structural and functional characteristics of protein variants. Forty-one protein mutations were identified in 12 Indian SARS-CoV-2 isolates by analysis of genome variations across 460 genome sequences obtained from 30 geographic sites in India. Two unique mutations such as W6152R and N5928H found in exonuclease of Surat (GBRC275b) and Gandhinagar (GBRC239) isolates. We report for the first time the impact of folding rate on stabilizing/retaining a sequence-structure-function-virulence link of emerging protein variants leading to accommodate hijack ability from current antivirals. Binding affinity analysis revealed the effect of point mutations on virus infectivity and the drug-escaping efficiency of Indian isolates. Emodin and artinemol suggested herein as repurposable antivirals for the treatment of COVID-19 patients infected with Indian isolates. Our study concludes that a protein folding rate is a key structural and evolutionary determinant to enhance the receptor-binding specificity and ensure hijack ability from the prevalent antiviral therapeutics.
Collapse
|
31
|
Wang R, Hu Q, Wang H, Zhu G, Wang M, Zhang Q, Zhao Y, Li C, Zhang Y, Ge G, Chen H, Chen L. Identification of Vitamin K3 and its analogues as covalent inhibitors of SARS-CoV-2 3CL pro. Int J Biol Macromol 2021; 183:182-192. [PMID: 33901557 PMCID: PMC8064871 DOI: 10.1016/j.ijbiomac.2021.04.129] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022]
Abstract
After the emergence of the pandemic, repurposed drugs have been considered as a quicker way of finding potential antiviral agents. SARS-CoV-2 3CLpro is essential for processing the viral polyproteins into mature non-structural proteins, making it an attractive target for developing antiviral agents. Here we show that Vitamin K3 screened from the FDA-Approved Drug Library containing an array of 1,018 compounds has potent inhibitory activity against SARS-CoV-2 3CLpro with the IC50 value of 4.78 ± 1.03 μM, rather than Vitamin K1, K2 and K4. Next, the time-dependent inhibitory experiment was carried out to confirm that Vitamin K3 could form the covalent bond with SARS-CoV-2 3CLpro. Then we analyzed the structure-activity relationship of Vitamin K3 analogues and identified 5,8-dihydroxy-1,4-naphthoquinone with 9.8 times higher inhibitory activity than Vitamin K3. Further mass spectrometric analysis and molecular docking study verified the covalent binding between Vitamin K3 or 5,8-dihydroxy-1,4-naphthoquinone and SARS-CoV-2 3CLpro. Thus, our findings provide valuable information for further optimization and design of novel inhibitors based on Vitamin K3 and its analogues, which may have the potential to fight against SARS-CoV-2.
Collapse
Affiliation(s)
- Ruyu Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qing Hu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Haonan Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guanghao Zhu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mengge Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yishu Zhao
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chunyu Li
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yani Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guangbo Ge
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Hongzhuan Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Lili Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| |
Collapse
|
32
|
Tsiambas E, Chrysovergis A, Papanikolaou V, Mastronikolis N, Ragos V, Batistatou A, Peschos D, Kavantzas N, Lazaris AC, Kyrodimos E. Impact of Ribosome Activity on SARS-CoV-2 LNP - Based mRNA Vaccines. Front Mol Biosci 2021; 8:654866. [PMID: 33959636 PMCID: PMC8093617 DOI: 10.3389/fmolb.2021.654866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Coronavirus-related Severe Acute Respiratory Syndrome-2 (SARS-CoV-2) initially was detected in Wuhan, Hubei, China. Since early 2021, World Health Organization (WHO) has declared Coronavirus Disease 2019 (COVID-19) a pandemic due to rapidly transformed to a globally massive catastrophic viral infection. In order to confront this emergency situation, many pharmaceutical companies focused on the design and development of efficient vaccines that are considered necessary for providing a level of normalization in totally affected human social-economical activity worldwide. A variety of vaccine types are under development, validation or even some of them have already completed these stages, initially approved as conditional marketing authorisation by Food and Drug Administration (FDA), European Medicines Agency (EMA), and other national health authorities for commercial purposes (in vivo use in general population), accelerating their production and distribution process. Innovative nucleoside-modified viral messenger RNA (v-mRNA)-based vaccines encapsulated within nanoparticles-specifically lipid ones (LNPs)-are now well recognized. Although this is a promising genetic engineering topic in the field of nanopharmacogenomics or targeted nucleic vaccines, there are limited but continuously enriched in vivo data in depth of time regarding their safety, efficacy, and immune response. In the current paper we expand the limited published data in the field of ribosome machinery and SARS-CoV-2 mRNA fragment vaccines interaction by describing their functional specialization and modifications. Additionally, alterations in post-transcriptional/translational molecules and mechanisms that could potentially affect the interaction between target cells and vaccines are also presented. Understanding these mechanisms is a crucial step for the next generation v-mRNA vaccines development.
Collapse
Affiliation(s)
- Evangelos Tsiambas
- Department of Cytology, Molecular Unit, 417 Veterans Army Hospital (NIMTS), Athens, Greece
- Department of Pathology, Medical School, University of Ioannina, Ioannina, Greece
- Department of Maxillofacial, Medical School, University of Ioannina, Ioannina, Greece
| | - Aristeidis Chrysovergis
- 1st ENT Department, Hippocration Hospital, National and Kapodistrian University, Athens, Greece
| | - Vasileios Papanikolaou
- 1st ENT Department, Hippocration Hospital, National and Kapodistrian University, Athens, Greece
| | | | - Vasileios Ragos
- Department of Maxillofacial, Medical School, University of Ioannina, Ioannina, Greece
| | - Anna Batistatou
- Department of Pathology, Medical School, University of Ioannina, Ioannina, Greece
| | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Ioannina, Greece
| | - Nikolaos Kavantzas
- Department of Pathology, Medical School, National and Kapodistrian University, Athens, Greece
| | - Andreas C. Lazaris
- Department of Pathology, Medical School, National and Kapodistrian University, Athens, Greece
| | - Efthimios Kyrodimos
- 1st ENT Department, Hippocration Hospital, National and Kapodistrian University, Athens, Greece
| |
Collapse
|
33
|
Mahalingam S, Peter J, Xu Z, Bordoloi D, Ho M, Kalyanaraman VS, Srinivasan A, Muthumani K. Landscape of humoral immune responses against SARS-CoV-2 in patients with COVID-19 disease and the value of antibody testing. Heliyon 2021; 7:e06836. [PMID: 33898857 PMCID: PMC8052472 DOI: 10.1016/j.heliyon.2021.e06836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/11/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
A new pandemic is ongoing in several parts of the world. The agent responsible is the newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The symptoms associated with this virus are known as the coronavirus disease-2019 (COVID-19). In this review, we summarize the published data on virus specific antibodies in hospitalized patients with COVID-19 disease, patients recovered from the disease and the individuals who are asymptomatic with SARS-CoV-2 infections. The review highlights the following: i) an adjunct role of antibody tests in the diagnosis of COVID-19 in combination with RT-PCR; ii) status of antibodies from COVID-19 convalescent patients to select donors for plasma therapy; iii) the potential confounding effects of other coronaviruses, measles, mumps and rubella in antibody testing due to homology of certain viral genes; and iv) the role of antibody testing for conducting surveillance in populations, incidence estimation, contact tracing and epidemiologic studies.
Collapse
Affiliation(s)
- Sundarasamy Mahalingam
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
| | - John Peter
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Ziyang Xu
- Vaccine & Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Devivasha Bordoloi
- Vaccine & Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Michelle Ho
- Vaccine & Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | | | | | - Kar Muthumani
- Vaccine & Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| |
Collapse
|
34
|
Lee S, Lee MK, Na H, Ahn J, Hong G, Lee Y, Park J, Kim Y, Kim YT, Kim CK, Lim HS, Lee KR. Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. GENE REPORTS 2021; 23:101100. [PMID: 33778182 PMCID: PMC7985685 DOI: 10.1016/j.genrep.2021.101100] [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: 12/12/2020] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 11/27/2022]
Abstract
The spike (S) protein mutations of SARS-CoV-2 are of major concern in terms of viral transmission and pathogenesis. Hence, we developed a PCR-based method to rapidly detect the 6 mutational hotspots (H49Y, G476S, V483A, H519Q, A520S, and D614G) in the S protein and applied this method to analyze the hotspots in the viral isolates from different geographical origins. Here, we identified that there was only the D614G mutation in the viral isolates. As of September 30, 2020, the analysis of 113,381 sequences available from the public repositories revealed that the SARS-CoV-2 variant carrying G614 has become the most prevalent form globally. Our results support recent epidemiological and genomic data demonstrating that the viral infectivity and transmission are enhanced by the S protein D614G mutation.
Collapse
Key Words
- ACE2, angiotensin-converting enzyme-2
- COVID-19, Coronavirus disease
- CT, cycle threshold
- D614G mutation
- Different geographic origins
- E, envelope
- M, membrane
- Mutational hotspots
- N, nucleocapsid
- NGS, next-generation sequencing
- Nsp3, nonstructural protein
- Orf, open reading frame
- RDB, receptor-binding domain
- RT-qPCR, reverse transcriptase-quantitative polymerase chain reaction
- RdRp, RNA-dependent RNA polymerase
- S, Spike
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- Spike gene
- Spike protein
- TMPRSS2, transmembrane serine protease2
Collapse
Affiliation(s)
- Sanghoo Lee
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Mi-Kyeong Lee
- Department of Molecular Diagnostics, Seoul Clinical Laboratories, Republic of Korea
| | - Hyeongkyun Na
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Jinwoo Ahn
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Gayeon Hong
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Youngkee Lee
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Jimyeong Park
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Yejin Kim
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Yun-Tae Kim
- Center for Technology Innovation, Seoul Clinical Laboratories, Republic of Korea
| | - Chang-Ki Kim
- Center for Clinical Trial, Seoul Clinical Laboratories, Republic of Korea
| | - Hwan-Sub Lim
- Department of Molecular Diagnostics, Seoul Clinical Laboratories, Republic of Korea
| | - Kyoung-Ryul Lee
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea.,Department of Molecular Diagnostics, Seoul Clinical Laboratories, Republic of Korea.,Center for Technology Innovation, Seoul Clinical Laboratories, Republic of Korea.,Center for Clinical Trial, Seoul Clinical Laboratories, Republic of Korea
| |
Collapse
|
35
|
Zhang J, Ding N, Song Y, Song R, Pan Y, Wang L, Yan S, Wang Q, Ma S, Wei L, Yu F, Lu L, Zhang F, Chen C, Zeng H. Phylogenomic tracing of asymptomatic transmission in a COVID-19 outbreak. Innovation (N Y) 2021; 2:100099. [PMID: 33778799 PMCID: PMC7982642 DOI: 10.1016/j.xinn.2021.100099] [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: 12/18/2020] [Accepted: 03/17/2021] [Indexed: 01/06/2023] Open
Abstract
SARS-CoV-2 has caused over 100 million deaths and continues to spread rapidly around the world. Asymptomatic transmission of SARS-CoV-2 is the Achilles' heel of COVID-19 public health control measures. Phylogenomic data on SARS-CoV-2 could provide more direct information about asymptomatic transmission. In this study, using a novel MINERVA sequencing technology, we traced asymptomatic transmission of COVID-19 patients in Beijing, China. One hundred and seventy-eight close contacts were quarantined, and 14 COVID-19 patients were laboratory confirmed by RT-PCR. We provide direct phylogenomic evidence of asymptomatic transmission by constructing the median joining network in the cluster. These data could help us to determine whether the current symptom-based screening should cover asymptomatic persons.
Collapse
Affiliation(s)
- Ju Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Nan Ding
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Yangzi Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Yang Pan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing 100013, China
| | - Linghang Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Shuo Yan
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Qi Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Shanfang Ma
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Lirong Wei
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Lianhe Lu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Chen Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Hui Zeng
- Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| |
Collapse
|
36
|
Belizário J. Immunity, virus evolution, and effectiveness of SARS-CoV-2 vaccines. Braz J Med Biol Res 2021; 54:e10725. [PMID: 33729394 PMCID: PMC7959154 DOI: 10.1590/1414-431x202010725] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/29/2020] [Indexed: 12/15/2022] Open
Abstract
Phylogenetic and pathogenesis studies of the severe acute respiratory syndrome-related coronaviruses (SARS-CoVs) strains have highlighted some specific mutations that could confer the RNA genome fitness advantages and immunological resistance for their rapid spread in the human population. The analyses of 30 kb RNA SARS-CoVs genome sequences, protein structures, and functions have provided us a perspective of how host-virus protein-protein complexes act to mediate virus infection. The open reading frame (ORF)1a and ORF1b translation yields 16 non-structural (nsp1-16) and 6 accessory proteins (p6, p7a, p8ab, p9b) with multiple functional domains. Viral proteins recruit over 300 host partners forming hetero-oligomeric complexes enabling the viral RNA synthesis, packing, and virion release. Many cellular host factors and the innate immune cells through pattern-recognition receptors and intracellular RNA sensor molecules act to inhibit virus entry and intracellular replication. However, non-structural ORF proteins hijack them and suppress interferon synthesis and its antiviral effects. Pro-inflammatory chemokines and cytokines storm leads to dysfunctional inflammation, lung injury, and several clinical symptoms in patients. During the global pandemic, COVID-19 patients were identified with non-synonymous substitution of G614D in the spike protein, indicating virus co-evolution in host cells. We review findings that suggest that host RNA editing and DNA repair systems, while carrying on recombination, mutation, and repair of viral RNA intermediates, may facilitate virus evolution. Understanding how the host cell RNA replication process may be driven by SARS-CoV-2 RNA genome fitness will help the testing of vaccines effectiveness to multiple independent mutated coronavirus strains that will emerge.
Collapse
Affiliation(s)
- J.E. Belizário
- Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| |
Collapse
|
37
|
Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. mSystems 2021; 6:6/1/e00030-21. [PMID: 33622851 PMCID: PMC8573956 DOI: 10.1128/msystems.00030-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has resulted in 92 million cases in a span of 1 year. The study focuses on understanding population-specific variations attributing its high rate of infections in specific geographical regions particularly in the United States. Rigorous phylogenomic network analysis of complete SARS-CoV-2 genomes (245) inferred five central clades named a (ancestral), b, c, d, and e (subtypes e1 and e2). Clade d and subclade e2 were found exclusively comprised of U.S. strains. Clades were distinguished by 10 co-mutational combinations in Nsp3, ORF8, Nsp13, S, Nsp12, Nsp2, and Nsp6. Our analysis revealed that only 67.46% of single nucleotide polymorphism (SNP) mutations were at the amino acid level. T1103P mutation in Nsp3 was predicted to increase protein stability in 238 strains except for 6 strains which were marked as ancestral type, whereas co-mutation (P409L and Y446C) in Nsp13 were found in 64 genomes from the United States highlighting its 100% co-occurrence. Docking highlighted mutation (D614G) caused reduction in binding of spike proteins with angiotensin-converting enzyme 2 (ACE2), but it also showed better interaction with the TMPRSS2 receptor contributing to high transmissibility among U.S. strains. We also found host proteins, MYO5A, MYO5B, and MYO5C, that had maximum interaction with viral proteins (nucleocapsid [N], spike [S], and membrane [M] proteins). Thus, blocking the internalization pathway by inhibiting MYO5 proteins which could be an effective target for coronavirus disease 2019 (COVID-19) treatment. The functional annotations of the host-pathogen interaction (HPI) network were found to be closely associated with hypoxia and thrombotic conditions, confirming the vulnerability and severity of infection. We also screened CpG islands in Nsp1 and N conferring the ability of SARS-CoV-2 to enter and trigger zinc antiviral protein (ZAP) activity inside the host cell. IMPORTANCE In the current study, we presented a global view of mutational pattern observed in SARS-CoV-2 virus transmission. This provided a who-infect-whom geographical model since the early pandemic. This is hitherto the most comprehensive comparative genomics analysis of full-length genomes for co-mutations at different geographical regions especially in U.S. strains. Compositional structural biology results suggested that mutations have a balance of opposing forces affecting pathogenicity suggesting that only a few mutations are effective at the translation level. Novel HPI analysis and CpG predictions elucidate the proof of concept of hypoxia and thrombotic conditions in several patients. Thus, the current study focuses the understanding of population-specific variations attributing a high rate of SARS-CoV-2 infections in specific geographical regions which may eventually be vital for the most severely affected countries and regions for sharp development of custom-made vindication strategies.
Collapse
|
38
|
Ferreira JC, Rabeh WM. Biochemical and biophysical characterization of the main protease, 3-chymotrypsin-like protease (3CLpro) from the novel coronavirus SARS-CoV 2. Sci Rep 2020; 10:22200. [PMID: 33335206 PMCID: PMC7747600 DOI: 10.1038/s41598-020-79357-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is responsible for the novel coronavirus disease 2019 (COVID-19). An appealing antiviral drug target is the coronavirus 3C-like protease (3CLpro) that is responsible for the processing of the viral polyproteins and liberation of functional proteins essential for the maturation and infectivity of the virus. In this study, multiple thermal analytical techniques have been implemented to acquire the thermodynamic parameters of 3CLpro at different buffer conditions. 3CLpro exhibited relatively high thermodynamic stabilities over a wide pH range; however, the protease was found to be less stable in the presence of salts. Divalent metal cations reduced the thermodynamic stability of 3CLpro more than monovalent cations; however, altering the ionic strength of the buffer solution did not alter the stability of 3CLpro. Furthermore, the most stable thermal kinetic stability of 3CLpro was recorded at pH 7.5, with the highest enthalpy of activation calculated from the slope of Eyring plot. The biochemical and biophysical properties of 3CLpro explored here may improve the solubility and stability of 3CLpro for optimum conditions for the setup of an enzymatic assay for the screening of inhibitors to be used as lead candidates in the discovery of drugs and design of antiviral therapeutics against COVID-19.
Collapse
Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
39
|
Rishi P, Thakur K, Vij S, Rishi L, Singh A, Kaur IP, Patel SKS, Lee JK, Kalia VC. Diet, Gut Microbiota and COVID-19. Indian J Microbiol 2020; 60:420-429. [PMID: 33012868 PMCID: PMC7521193 DOI: 10.1007/s12088-020-00908-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Worldwide, millions of individuals have been affected by the prevailing SARS-CoV-2. Therefore, a robust immune system remains indispensable, as an immunocompromised host status has proven to be fatal. In the absence of any specific antiviral drug/vaccine, COVID-19 related drug repurposing along with various other non-pharmacological measures coupled with lockdown have been employed to combat this infection. In this context, a plant based rich fiber diet, which happens to be consumed by a majority of the Indian population, appears to be advantageous, as it replenishes the host gut microbiota with beneficial microbes thereby leading to a symbiotic association conferring various health benefits to the host including enhanced immunity. Further, implementation of the lockdown which has proven to be a good non-pharmacological measure, seems to have resulted in consumption of home cooked healthy diet, thereby enriching the beneficial microflora in the gut, which might have resulted in better prognosis of COVID-19 patients in India in comparison to that observed in the western countries.
Collapse
Affiliation(s)
- Praveen Rishi
- Department of Microbiology, Panjab University, BMS Block I, South Campus, Chandigarh, India
| | - Khemraj Thakur
- Department of Microbiology, Panjab University, BMS Block I, South Campus, Chandigarh, India
| | - Shania Vij
- Department of Microbiology, Panjab University, BMS Block I, South Campus, Chandigarh, India
| | | | - Aagamjit Singh
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Indu Pal Kaur
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Vipin C. Kalia
- Department of Chemical Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| |
Collapse
|
40
|
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently caused acute respiratory distress syndrome affecting more than 200 countries with varied mortality rate. Successive genetic variants of SARS-CoV-2 become evident across the globe immediately after its complete genome sequencing. Here, we found a decent association of SARS-CoV-2 ORF3a mutation with higher mortality rate. Extensive in silico studies revealed several amino acid changes in ORF3a protein which ultimately leads to diverse structural modifications like B cell epitope loss, gain/loss of phosphorylation site and loss of leucine zipper motif. We could further relate these changes to the enhanced antigenic diversity of SARS-CoV-2. Through protein−protein network analysis and functional annotation studies, we obtained a close federation of ORF3a protein with host immune response via divergent signal transduction pathways including JAK-STAT, chemokine and cytokine-related pathways. Our data not only unveil the fairly appreciable association of ORF3a mutation with higher mortality rate, but also suggest a potential mechanistic insight towards the immunopathogenic manifestation of SARS-CoV-2 infection.
Collapse
|
41
|
Khodadoost M, Niknam Z, Farahani M, Razzaghi M, Norouzinia M. Investigating the human protein-host protein interactome of SARS-CoV-2 infection in the small intestine. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2020; 13:374-387. [PMID: 33244381 PMCID: PMC7682973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/18/2020] [Indexed: 10/31/2022]
Abstract
AIM The present study aimed to identify human protein-host protein interactions of SARS-CoV-2 infection in the small intestine to discern the potential mechanisms and gain insights into the associated biomarkers and treatment strategies. BACKGROUND Deciphering the tissue and organ interactions of the SARS-CoV-2 infection can be important to discern the potential underlying mechanisms. In the present study, we investigated the human protein-host protein interactions in the small intestine. METHODS Public databases and published works were used to collect data related to small intestine tissue and SARS-CoV-2 infection. We constructed a human protein-protein interaction (PPI) network and showed interactions of host proteins in the small intestine. Associated modules, biological processes, functional pathways, regulatory transcription factors, disease ontology categories, and possible drug candidates for therapeutic targets were identified. RESULTS Thirteen primary protein neighbors were found for the SARS-CoV-2 receptor ACE2. ACE2 and its four partners were observed in a highly clustered module; moreover, 8 host proteins belonged to this module. The protein digestion and absorption as a significant pathway was highlighted with enriched genes of ACE2, MEP1A, MEP1B, DPP4, and XPNPEP2. The HNF4A, HNF1A, and HNF1B transcription factors were found to be regulating the expression of ACE2. A significant association with 12 diseases was deciphered and 116 drug-target interactions were identified. CONCLUSION The protein-host protein interactome revealed the important elements and interactions for SARS-CoV-2 infection in the small intestine, which can be useful in clarifying the mechanisms of gastrointestinal symptoms and inflammation. The results suggest that antiviral targeting of these interactions may improve the condition of COVID-19 patients.
Collapse
Affiliation(s)
- Mahmoud Khodadoost
- Department of Traditional Medicine, School of Traditional Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Niknam
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Farahani
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Norouzinia
- Gastroenterology and Liver Diseases Research Center, Research Institute of Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|