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Meng Z, Wang S, Yu L, Zhao K, Wu T, Zhu X, Yang N, Qiao Q, Ma J, Wu B, Ge Y, Cui L. A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition. mSystems 2024; 9:e0122223. [PMID: 38564711 PMCID: PMC11097644 DOI: 10.1128/msystems.01222-23] [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: 12/05/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Rapid and accurate sequencing of the entire viral genome, coupled with continuous monitoring of genetic changes, is crucial for understanding the epidemiology of coronaviruses. We designed a novel method called micro target hybrid capture system (MT-Capture) to enable whole-genome sequencing in a timely manner. The novel design of probes used in target binding exhibits a unique and synergistic "hand-in-hand" conjugation effect. The entire hybrid capture process is within 2.5 hours, overcoming the time-consuming and complex operation characteristics of the traditional liquid-phase hybrid capture (T-Capture) system. By designing specific probes for these coronaviruses, MT-Capture effectively enriched isolated strains and 112 clinical samples of coronaviruses with cycle threshold values below 37. Compared to multiplex PCR sequencing, it does not require frequent primer updates and has higher compatibility. MT-Capture is highly sensitive and capable of tracking variants.IMPORTANCEMT-Capture is meticulously designed to enable the efficient acquisition of the target genome of the common human coronavirus. Coronavirus is a kind of virus that people are generally susceptible to and is epidemic and infectious, and it is the virus with the longest genome among known RNA viruses. Therefore, common human coronavirus samples are selected to evaluate the accuracy and sensitivity of MT-Capture. This method utilizes innovative probe designs optimized through probe conjugation techniques, greatly shortening the time and simplifying the handwork compared with traditional hybridization capture processes. Our results demonstrate that MT-Capture surpasses multiplex PCR in terms of sensitivity, exhibiting a thousandfold increase. Moreover, MT-Capture excels in the identification of mutation sites. This method not only is used to target the coronaviruses but also may be used to diagnose other diseases, including various infectious diseases, genetic diseases, or tumors.
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Affiliation(s)
- Zixinrong Meng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuo Wang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Liping Yu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Kangchen Zhao
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Tao Wu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiaojuan Zhu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Ning Yang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiao Qiao
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Junyan Ma
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bin Wu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yiyue Ge
- School of Public Health, Nanjing Medical University, Nanjing, China
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Lunbiao Cui
- School of Public Health, Nanjing Medical University, Nanjing, China
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
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Kumar S, Granados J, Aceves M, Peralta J, Leandro AC, Thomas J, Williams-Blangero S, Curran JE, Blangero J. Pre-Infection Innate Immunity Attenuates SARS-CoV-2 Infection and Viral Load in iPSC-Derived Alveolar Epithelial Type 2 Cells. Cells 2024; 13:369. [PMID: 38474333 PMCID: PMC10931100 DOI: 10.3390/cells13050369] [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: 12/17/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
A large portion of the heterogeneity in coronavirus disease 2019 (COVID-19) susceptibility and severity of illness (SOI) remains poorly understood. Recent evidence suggests that SARS-CoV-2 infection-associated damage to alveolar epithelial type 2 cells (AT2s) in the distal lung may directly contribute to disease severity and poor prognosis in COVID-19 patients. Our in vitro modeling of SARS-CoV-2 infection in induced pluripotent stem cell (iPSC)-derived AT2s from 10 different individuals showed interindividual variability in infection susceptibility and the postinfection cellular viral load. To understand the underlying mechanism of the AT2's capacity to regulate SARS-CoV-2 infection and cellular viral load, a genome-wide differential gene expression analysis between the mock and SARS-CoV-2 infection-challenged AT2s was performed. The 1393 genes, which were significantly (one-way ANOVA FDR-corrected p ≤ 0.05; FC abs ≥ 2.0) differentially expressed (DE), suggest significant upregulation of viral infection-related cellular innate immune response pathways (p-value ≤ 0.05; activation z-score ≥ 3.5), and significant downregulation of the cholesterol- and xenobiotic-related metabolic pathways (p-value ≤ 0.05; activation z-score ≤ -3.5). Whilst the effect of post-SARS-CoV-2 infection response on the infection susceptibility and postinfection viral load in AT2s is not clear, interestingly, pre-infection (mock-challenged) expression of 238 DE genes showed a high correlation with the postinfection SARS-CoV-2 viral load (FDR-corrected p-value ≤ 0.05 and r2-absolute ≥ 0.57). The 85 genes whose expression was negatively correlated with the viral load showed significant enrichment in viral recognition and cytokine-mediated innate immune GO biological processes (p-value range: 4.65 × 10-10 to 2.24 × 10-6). The 153 genes whose expression was positively correlated with the viral load showed significant enrichment in cholesterol homeostasis, extracellular matrix, and MAPK/ERK pathway-related GO biological processes (p-value range: 5.06 × 10-5 to 6.53 × 10-4). Overall, our results strongly suggest that AT2s' pre-infection innate immunity and metabolic state affect their susceptibility to SARS-CoV-2 infection and viral load.
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Affiliation(s)
- Satish Kumar
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Jose Granados
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Miriam Aceves
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Juan Peralta
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - Ana C. Leandro
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - John Thomas
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Sarah Williams-Blangero
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - Joanne E. Curran
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - John Blangero
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
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3
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Zhao L, Lythgoe KA. The social role of defective viral genomes in chronic viral infections: a commentary on Leeks et al. 2023. J Evol Biol 2023; 36:1577-1581. [PMID: 37975505 PMCID: PMC10880559 DOI: 10.1111/jeb.14244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of MedicineUniversity of OxfordOxfordUK
- Pandemic Sciences Institute, Nuffield Department for MedicineUniversity of OxfordOxfordUK
| | - Katrina A. Lythgoe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of MedicineUniversity of OxfordOxfordUK
- Pandemic Sciences Institute, Nuffield Department for MedicineUniversity of OxfordOxfordUK
- Department of BiologyUniversity of OxfordOxfordUK
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Grosche VR, Souza LPF, Ferreira GM, Guevara-Vega M, Carvalho T, Silva RRDS, Batista KLR, Abuna RPF, Silva JS, Calmon MDF, Rahal P, da Silva LCN, Andrade BS, Teixeira CS, Sabino-Silva R, Jardim ACG. Mannose-Binding Lectins as Potent Antivirals against SARS-CoV-2. Viruses 2023; 15:1886. [PMID: 37766292 PMCID: PMC10536204 DOI: 10.3390/v15091886] [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: 05/23/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The SARS-CoV-2 entry into host cells is mainly mediated by the interactions between the viral spike protein (S) and the ACE-2 cell receptor, which are highly glycosylated. Therefore, carbohydrate binding agents may represent potential candidates to abrogate virus infection. Here, we evaluated the in vitro anti-SARS-CoV-2 activity of two mannose-binding lectins isolated from the Brazilian plants Canavalia brasiliensis and Dioclea violacea (ConBR and DVL). These lectins inhibited SARS-CoV-2 Wuhan-Hu-1 strain and variants Gamma and Omicron infections, with selectivity indexes (SI) of 7, 1.7, and 6.5, respectively for ConBR; and 25, 16.8, and 22.3, for DVL. ConBR and DVL inhibited over 95% of the early stages of the viral infection, with strong virucidal effect, and also protected cells from infection and presented post-entry inhibition. The presence of mannose resulted in the complete lack of anti-SARS-CoV-2 activity by ConBR and DVL, recovering virus titers. ATR-FTIR, molecular docking, and dynamic simulation between SARS-CoV-2 S and either lectins indicated molecular interactions with predicted binding energies of -85.4 and -72.0 Kcal/Mol, respectively. Our findings show that ConBR and DVL lectins possess strong activities against SARS-CoV-2, potentially by interacting with glycans and blocking virus entry into cells, representing potential candidates for the development of novel antiviral drugs.
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Affiliation(s)
- Victória Riquena Grosche
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | - Leandro Peixoto Ferreira Souza
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Giulia Magalhães Ferreira
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
| | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Tamara Carvalho
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | | | | | - Rodrigo Paolo Flores Abuna
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (R.P.F.A.); (J.S.S.)
- Oswaldo Cruz Foundation (Fiocruz), Bi-Institutional Platform for Translational Medicine, Ribeirão Preto 14049-900, Brazil
| | - João Santana Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (R.P.F.A.); (J.S.S.)
- Oswaldo Cruz Foundation (Fiocruz), Bi-Institutional Platform for Translational Medicine, Ribeirão Preto 14049-900, Brazil
| | - Marília de Freitas Calmon
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | - Paula Rahal
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | | | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, State University of Southwest of Bahia, Jequié 45205-490, Brazil;
| | - Claudener Souza Teixeira
- Center of Agrarian Science and Biodiversity, Federal University of Cariri (UFCA), Crato 63130-025, Brazil; (R.R.d.S.S.); (C.S.T.)
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
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5
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Soto J, Linsley C, Song Y, Chen B, Fang J, Neyyan J, Davila R, Lee B, Wu B, Li S. Engineering Materials and Devices for the Prevention, Diagnosis, and Treatment of COVID-19 and Infectious Diseases. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2455. [PMID: 37686965 PMCID: PMC10490511 DOI: 10.3390/nano13172455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023]
Abstract
Following the global spread of COVID-19, scientists and engineers have adapted technologies and developed new tools to aid in the fight against COVID-19. This review discusses various approaches to engineering biomaterials, devices, and therapeutics, especially at micro and nano levels, for the prevention, diagnosis, and treatment of infectious diseases, such as COVID-19, serving as a resource for scientists to identify specific tools that can be applicable for infectious-disease-related research, technology development, and treatment. From the design and production of equipment critical to first responders and patients using three-dimensional (3D) printing technology to point-of-care devices for rapid diagnosis, these technologies and tools have been essential to address current global needs for the prevention and detection of diseases. Moreover, advancements in organ-on-a-chip platforms provide a valuable platform to not only study infections and disease development in humans but also allow for the screening of more effective therapeutics. In addition, vaccines, the repurposing of approved drugs, biomaterials, drug delivery, and cell therapy are promising approaches for the prevention and treatment of infectious diseases. Following a comprehensive review of all these topics, we discuss unsolved problems and future directions.
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Affiliation(s)
- Jennifer Soto
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chase Linsley
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yang Song
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Binru Chen
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jun Fang
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
- School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Josephine Neyyan
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Raul Davila
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon Lee
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Benjamin Wu
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Dentistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Song Li
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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Rosli SNZ, Dimeng SR, Shamsuddin F, Mohd Ali MR, Muhamad Hendri NA, Suppiah J, Mohd Zain R, Thayan R, Ahmad N. Vero CCL-81 and Calu-3 Cell Lines as Alternative Hosts for Isolation and Propagation of SARS-CoV-2 Isolated in Malaysia. Biomedicines 2023; 11:1658. [PMID: 37371753 DOI: 10.3390/biomedicines11061658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as the etiologic agent for the pneumonia outbreak that started in early December 2019 in Wuhan City, Hubei Province, China. To date, coronavirus disease (COVID-19) has caused almost 6 million deaths worldwide. The ability to propagate the virus into a customizable volume will enable better research on COVID-19 therapy, vaccine development, and many others. In the search for the most efficient replication host, we inoculated three (3) local SARS-CoV-2 isolates of different lineages (Clade L/Lineage B Wuhan, Clade GR/Lineage B.1.1.354, and Clade O/Lineage B.6.2) into various clinically important mammalian cell lines. The replication profile of these isolates was evaluated based on the formation of cytopathic effects (CPE), viral load (Ct value and plaque-forming unit (pfu)), as well as observation by electron microscopy (EM). Next-generation sequencing (NGS) was performed to examine the genomic stability of the propagated SARS-CoV-2 in these cell lines. Our study found that Vero E6 and Vero CCL-81 cell lines posed similar capacities in propagating the local isolates, with Vero CCL-81 demonstrating exceptional potency in conserving the genomic stability of the Lineage B Wuhan isolate. In addition, our study demonstrated the utility of Calu-3 cells as a replication host for SARS-CoV-2 without causing substantial cellular senescence. In conclusion, this study provides crucial information on the growth profile of Malaysian SARS-CoV-2 in various mammalian cell lines and thus will be a great source of reference for better isolation and propagation of the SARS-CoV-2 virus isolated in Malaysia.
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Affiliation(s)
- Siti Nur Zawani Rosli
- Bacteriology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Sitti Rahmawati Dimeng
- Bacteriology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Farah Shamsuddin
- Bacteriology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Mohammad Ridhuan Mohd Ali
- Bacteriology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Nur Afrina Muhamad Hendri
- Electron Microscopy Unit, Special Resource Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Jeyanthi Suppiah
- Virology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Rozainanee Mohd Zain
- Virology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Ravindran Thayan
- Virology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Norazah Ahmad
- Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
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7
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Shrock EL, Timms RT, Kula T, Mena EL, West AP, Guo R, Lee IH, Cohen AA, McKay LGA, Bi C, Keerti, Leng Y, Fujimura E, Horns F, Li M, Wesemann DR, Griffiths A, Gewurz BE, Bjorkman PJ, Elledge SJ. Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses. Science 2023; 380:eadc9498. [PMID: 37023193 PMCID: PMC10273302 DOI: 10.1126/science.adc9498] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023]
Abstract
Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant "public epitopes" at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition. Systematic analysis of antibody-antigen structures uncovered 18 human and 21 partially overlapping mouse germline-encoded amino acid-binding (GRAB) motifs within heavy and light V gene segments that in case studies proved critical for public epitope recognition. GRAB motifs represent a fundamental component of the immune system's architecture that promotes recognition of pathogens and leads to species-specific public antibody responses that can exert selective pressure on pathogens.
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Affiliation(s)
- Ellen L. Shrock
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
| | - Richard T. Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
- Present address: Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Elijah L. Mena
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rui Guo
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - I-Hsiu Lee
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lindsay G. A. McKay
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Caihong Bi
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Keerti
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric Fujimura
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Felix Horns
- Department of Bioengineering, Department of Applied Physics, Chan Zuckerberg Biohub and Stanford University, Stanford, CA 94305, USA
| | - Mamie Li
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Duane R. Wesemann
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139 USA
| | - Anthony Griffiths
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Benjamin E. Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
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8
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Castillo G, Nelli RK, Phadke KS, Bravo-Parra M, Mora-Díaz JC, Bellaire BH, Giménez-Lirola LG. SARS-CoV-2 Is More Efficient than HCoV-NL63 in Infecting a Small Subpopulation of ACE2+ Human Respiratory Epithelial Cells. Viruses 2023; 15:v15030736. [PMID: 36992445 PMCID: PMC10059808 DOI: 10.3390/v15030736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
Human coronavirus (HCoV)-NL63 is an important contributor to upper and lower respiratory tract infections, mainly in children, while severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, can cause lower respiratory tract infections, and more severe, respiratory and systemic disease, which leads to fatal consequences in many cases. Using microscopy, immunohistochemistry (IHC), virus-binding assay, reverse transcriptase qPCR (RT-qPCR) assay, and flow cytometry, we compared the characteristics of the susceptibility, replication dynamics, and morphogenesis of HCoV-NL63 and SARS-CoV-2 in monolayer cultures of primary human respiratory epithelial cells (HRECs). Less than 10% HRECs expressed ACE2, and SARS-CoV-2 seemed much more efficient than HCoV-NL63 at infecting the very small proportion of HRECs expressing the ACE2 receptors. Furthermore, SARS-CoV-2 replicated more efficiently than HCoV-NL63 in HREC, which correlates with the cumulative evidence of the differences in their transmissibility.
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Affiliation(s)
- Gino Castillo
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Rahul K. Nelli
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Kruttika S. Phadke
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Marlene Bravo-Parra
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Juan Carlos Mora-Díaz
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Bryan H. Bellaire
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
- Correspondence:
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9
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The Prognostic Value of Pentraxin-3 in COVID-19 Patients: A Systematic Review and Meta-Analysis of Mortality Incidence. Int J Mol Sci 2023; 24:ijms24043537. [PMID: 36834949 PMCID: PMC9958638 DOI: 10.3390/ijms24043537] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Over the last three years, humanity has been facing one of the most serious health emergencies due to the global spread of Coronavirus disease (COVID-19). In this scenario, the research of reliable biomarkers of mortality from COVID-19 represents a primary objective. Pentraxin 3 (PTX3), a highly conserved protein of innate immunity, seems to be associated with a worse outcome of the disease. Based on the above, this systematic review and meta-analysis evaluated the prognostic potential of PTX3 in COVID-19 disease. We included 12 clinical studies evaluating PTX3 in COVID-19 patients. From our research, we found increased PTX3 levels compared to healthy subjects, and notably, PTX3 was even more augmented in severe COVID-19 rather than non-severe cases. Moreover, we performed a meta-analysis to establish if there were differences between ICU and non-ICU COVID-19 patients in PTX3-related death. We combined 5 studies for a total of 543 ICU vs. 515 non-ICU patients. We found high significative PTX3-related death in ICU COVID-19 hospitalized individuals (184 out of 543) compared to non-ICU (37 out of 515), with an overall effect OR: 11.30 [2.00, 63.73]; p = 0.006. In conclusion, we probed PTX3 as a reliable marker of poor outcomes after COVID-19 infection as well as a predictor of hospitalized patients' stratification.
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10
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Barnwal A, Basu B, Tripathi A, Soni N, Mishra D, Banerjee A, Kumar R, Vrati S, Bhattacharyya J. SARS-CoV-2 Spike Protein-Activated Dendritic Cell-Derived Extracellular Vesicles Induce Antiviral Immunity in Mice. ACS Biomater Sci Eng 2022; 8:5338-5348. [PMID: 36445062 PMCID: PMC9717688 DOI: 10.1021/acsbiomaterials.2c01094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022]
Abstract
The onset and spread of the SARS-CoV-2 virus have created an unprecedented universal crisis. Although vaccines have been developed against the parental SARS-CoV-2, outbreaks of the disease still occur through the appearance of different variants, suggesting a continuous need for improved and effective therapeutic strategies. Therefore, we developed a novel nanovesicle presenting Spike protein on the surface of the dendritic cell-derived extracellular vesicles (DEVs) for use as a potential vaccine platform against SARS-CoV-2. DEVs express peptide/MHC-I (pMHC-I) complexes, CCR-7, on their surface. The immunogenicity and efficacy of the Spike-activated DEVs were tested in mice and compared with free Spike protein. A 1/10 Spike equivalent dose of DEVs showed a superior potency in inducing anti-Spike IgG titers in blood of mice when compared to dendritic cells or free Spike protein treatment. Moreover, DEV-induced sera effectively reduced viral infection by 55-60% within 15 days of booster dose administration. Furthermore, a 1/10 Spike equivalent dose of DEV-treated mice was found to be equally effective in inducing CD19+CD38+ T-cells in the spleen and lymph node; CD8 cells in the bone marrow, spleen, and lymph node; and CD4+CD25+ T-cells in the spleen and lymph node after 90 days of treatment. Thus, our results support the immunogenic nature of DEVs, demonstrating that a low dose of DEVs induces antibodies to inhibit SARS-CoV-2 infection in vitro, therefore warranting further investigations.
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Affiliation(s)
- Anjali Barnwal
- Centre for Biomedical
Engineering, Indian Institute of Technology
Delhi, New Delhi 110016, India
- Department
of Biomedical Engineering, All India Institute
of Medical Science, New Delhi 110029, India
| | - Brohmomoy Basu
- Laboratory
of Virology, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Aarti Tripathi
- Laboratory
of Virology, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Naina Soni
- Laboratory
of Virology, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Debasish Mishra
- Laboratory
of Virology, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Arup Banerjee
- Laboratory
of Virology, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Rajesh Kumar
- Translational
Health Science & Technology Institute, Faridabad 121001, Haryana, India
| | - Sudhanshu Vrati
- Laboratory
of Virology, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Jayanta Bhattacharyya
- Centre for Biomedical
Engineering, Indian Institute of Technology
Delhi, New Delhi 110016, India
- Department
of Biomedical Engineering, All India Institute
of Medical Science, New Delhi 110029, India
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11
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Tinker SC, Prince-Guerra JL, Vermandere K, Gettings J, Drenzik C, Voccio G, Parrott T, Drobeniuc J, Hayden T, Briggs S, Heida D, Thornburg N, Barrios LC, Neatherlin JC, Madni S, Rasberry CN, Swanson KD, Tamin A, Harcourt JL, Lester S, Atherton L, Honein MA. Evaluation of self-administered antigen testing in a college setting. Virol J 2022; 19:202. [PMID: 36457114 PMCID: PMC9713151 DOI: 10.1186/s12985-022-01927-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The objective of our investigation was to better understand barriers to implementation of self-administered antigen screening testing for SARS-CoV-2 at institutions of higher education (IHE). METHODS Using the Quidel QuickVue At-Home COVID-19 Test, 1347 IHE students and staff were asked to test twice weekly for seven weeks. We assessed seroconversion using baseline and endline serum specimens. Online surveys assessed acceptability. RESULTS Participants reported 9971 self-administered antigen test results. Among participants who were not antibody positive at baseline, the median number of tests reported was eight. Among 324 participants seronegative at baseline, with endline antibody results and ≥ 1 self-administered antigen test results, there were five COVID-19 infections; only one was detected by self-administered antigen test (sensitivity = 20%). Acceptability of self-administered antigen tests was high. CONCLUSIONS Twice-weekly serial self-administered antigen testing in a low prevalence period had low utility in this investigation. Issues of testing fatigue will be important to address in future testing strategies.
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Affiliation(s)
- Sarah C. Tinker
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Jessica L. Prince-Guerra
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA ,grid.416738.f0000 0001 2163 0069Laboratory Leadership Service, CDC, Atlanta, GA USA
| | - Kelly Vermandere
- grid.420388.50000 0004 4692 4364Georgia Department of Public Health, Atlanta, GA USA
| | - Jenna Gettings
- grid.420388.50000 0004 4692 4364Georgia Department of Public Health, Atlanta, GA USA ,grid.416738.f0000 0001 2163 0069Epidemic Intelligence Service, CDC, Atlanta, GA USA
| | - Cherie Drenzik
- grid.420388.50000 0004 4692 4364Georgia Department of Public Health, Atlanta, GA USA
| | - Gary Voccio
- grid.420388.50000 0004 4692 4364Georgia Department of Public Health, Atlanta, GA USA
| | | | - Jan Drobeniuc
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Tonya Hayden
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Stephen Briggs
- grid.423400.10000 0000 9002 0195Berry College, Rome, GA USA
| | - Debbie Heida
- grid.423400.10000 0000 9002 0195Berry College, Rome, GA USA
| | - Natalie Thornburg
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Lisa C. Barrios
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - John C. Neatherlin
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Sabrina Madni
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Catherine N. Rasberry
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Kenneth D. Swanson
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Azaibi Tamin
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Jennifer L. Harcourt
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Sandra Lester
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Lydia Atherton
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
| | - Margaret A. Honein
- grid.416738.f0000 0001 2163 0069COVID-19 Response Team, Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd NE, Atlanta, GA 30333 USA
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12
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Mustajab T, Kwamboka MS, Choi DA, Kang DW, Kim J, Han KR, Han Y, Lee S, Song D, Chwae YJ. Update on Extracellular Vesicle-Based Vaccines and Therapeutics to Combat COVID-19. Int J Mol Sci 2022; 23:ijms231911247. [PMID: 36232549 PMCID: PMC9569487 DOI: 10.3390/ijms231911247] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/23/2022] Open
Abstract
The COVID-19 pandemic has had a deep impact on people worldwide since late 2019 when SARS-CoV-2 was first identified in Wuhan, China. In addition to its effect on public health, it has affected humans in various aspects of life, including social, economic, cultural, and political. It is also true that researchers have made vigorous efforts to overcome COVID-19 throughout the world, but they still have a long way to go. Accordingly, innumerable therapeutics and vaccine candidates have been studied for their efficacies and have been tried clinically in a very short span of time. For example, the versatility of extracellular vesicles, which are membrane-bound particles released from all types of cells, have recently been highlighted in terms of their effectiveness, biocompatibility, and safety in the fight against COVID-19. Thus, here, we tried to explain the use of extracellular vesicles as therapeutics and for the development of vaccines against COVID-19. Along with the mechanisms and a comprehensive background of their application in trapping the coronavirus or controlling the cytokine storm, we also discuss the obstacles to the clinical use of extracellular vesicles and how these could be resolved in the future.
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Affiliation(s)
- Tamanna Mustajab
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Moriasi Sheba Kwamboka
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Da Ae Choi
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Dae Wook Kang
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Junho Kim
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Kyu Ri Han
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Yujin Han
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Sorim Lee
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Dajung Song
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
| | - Yong-Joon Chwae
- Department of Microbiology, School of Medicine, Ajou University, Suwon 16499, Korea
- Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Korea
- Correspondence: ; Tel.: +82-031-219-5073
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13
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Wei X, Rong N, Liu J. Prospects of animal models and their application in studies on adaptive immunity to SARS-CoV-2. Front Immunol 2022; 13:993754. [PMID: 36189203 PMCID: PMC9523127 DOI: 10.3389/fimmu.2022.993754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/05/2022] [Indexed: 01/08/2023] Open
Abstract
The adaptive immune response induced by SARS-CoV-2 plays a key role in the antiviral process and can protect the body from the threat of infection for a certain period of time. However, owing to the limitations of clinical studies, the antiviral mechanisms, protective thresholds, and persistence of the immune memory of adaptive immune responses remain unclear. This review summarizes existing research models for SARS-CoV-2 and elaborates on the advantages of animal models in simulating the clinical symptoms of COVID-19 in humans. In addition, we systematically summarize the research progress on the SARS-CoV-2 adaptive immune response and the remaining key issues, as well as the application and prospects of animal models in this field. This paper provides direction for in-depth analysis of the anti-SARS-CoV-2 mechanism of the adaptive immune response and lays the foundation for the development and application of vaccines and drugs.
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Affiliation(s)
- Xiaohui Wei
- National Health Commission Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | | | - Jiangning Liu
- National Health Commission Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
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14
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Sbarigia C, Vardanyan D, Buccini L, Tacconi S, Dini L. SARS-CoV-2 and extracellular vesicles: An intricate interplay in pathogenesis, diagnosis and treatment. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.987034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Extracellular vesicles (EVs) are widely recognized as intercellular communication mediators. Among the different biological processes, EVs play a role in viral infections, supporting virus entrance and spread into host cells and immune response evasion. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection became an urgent public health issue with significant morbidity and mortality worldwide, being responsible for the current COVID-19 pandemic. Since EVs are implicated in SARS-CoV-2 infection in a morphological and functional level, they have gained growing interest for a better understanding of SARS-CoV-2 pathogenesis and represent possible diagnostic tools to track the disease progression. Furthermore, thanks to their biocompatibility and efficient immune activation, the use of EVs may also represent a promising strategy for the development of new therapeutic strategies against COVID-19. In this review, we explore the role of EVs in viral infections with a focus on SARS-CoV-2 biology and pathogenesis, considering recent morphometric studies. The common biogenesis aspects and structural similarities between EVs and SARS-CoV-2 will be examined, offering a panoramic of their multifaceted interplay and presenting EVs as a machinery supporting the viral cycle. On the other hand, EVs may be exploited as early diagnostic biomarkers and efficient carriers for drug delivery and vaccination, and ongoing studies will be reviewed to highlight EVs as potential alternative therapeutic strategies against SARS-CoV-2 infection.
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15
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Mercado-Gómez M, Prieto-Fernández E, Goikoetxea-Usandizaga N, Vila-Vecilla L, Azkargorta M, Bravo M, Serrano-Maciá M, Egia-Mendikute L, Rodríguez-Agudo R, Lachiondo-Ortega S, Lee SY, Eguileor Giné A, Gil-Pitarch C, González-Recio I, Simón J, Petrov P, Jover R, Martínez-Cruz LA, Ereño-Orbea J, Delgado TC, Elortza F, Jiménez-Barbero J, Nogueiras R, Prevot V, Palazon A, Martínez-Chantar ML. The spike of SARS-CoV-2 promotes metabolic rewiring in hepatocytes. Commun Biol 2022; 5:827. [PMID: 35978143 PMCID: PMC9383691 DOI: 10.1038/s42003-022-03789-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 08/02/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a multi-organ damage that includes hepatic dysfunction, which has been observed in over 50% of COVID-19 patients. Liver injury in COVID-19 could be attributed to the cytopathic effects, exacerbated immune responses or treatment-associated drug toxicity. Herein we demonstrate that hepatocytes are susceptible to infection in different models: primary hepatocytes derived from humanized angiotensin-converting enzyme-2 mice (hACE2) and primary human hepatocytes. Pseudotyped viral particles expressing the full-length spike of SARS-CoV-2 and recombinant receptor binding domain (RBD) bind to ACE2 expressed by hepatocytes, promoting metabolic reprogramming towards glycolysis but also impaired mitochondrial activity. Human and hACE2 primary hepatocytes, where steatosis and inflammation were induced by methionine and choline deprivation, are more vulnerable to infection. Inhibition of the renin-angiotensin system increases the susceptibility of primary hepatocytes to infection with pseudotyped viral particles. Metformin, a common therapeutic option for hyperglycemia in type 2 diabetes patients known to partially attenuate fatty liver, reduces the infection of human and hACE2 hepatocytes. In summary, we provide evidence that hepatocytes are amenable to infection with SARS-CoV-2 pseudovirus, and we propose that metformin could be a therapeutic option to attenuate infection by SARS-CoV-2 in patients with fatty liver. SARS-CoV-2 pseudovirus infects human hepatocytes leading to metabolic reprogramming towards glycolysis and impaired mitochondrial activity, and metformin can reduce infection under steatotic conditions.
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Affiliation(s)
- Maria Mercado-Gómez
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Endika Prieto-Fernández
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Laura Vila-Vecilla
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRedISCIII, 48160, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Miren Bravo
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Rubén Rodríguez-Agudo
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Sofia Lachiondo-Ortega
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - So Young Lee
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Alvaro Eguileor Giné
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Clàudia Gil-Pitarch
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Irene González-Recio
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Jorge Simón
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Petar Petrov
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Experimental Hepatology Joint Research Unit, IIS Hospital La Fe, Valencia, Spain
| | - Ramiro Jover
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Experimental Hepatology Joint Research Unit, IIS Hospital La Fe, Valencia, Spain.,Dep. Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - June Ereño-Orbea
- Chemical Glycobiology Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry, University of the Basque Country, UPV/EHU, 48940, Leioa, Spain
| | - Teresa Cardoso Delgado
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRedISCIII, 48160, Derio, Bizkaia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Jesús Jiménez-Barbero
- Chemical Glycobiology Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry, University of the Basque Country, UPV/EHU, 48940, Leioa, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Respiratorias (CIBERES), 28029, Madrid, Spain
| | - Ruben Nogueiras
- Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela-Instituto de Investigación Sanitaria, CIBER Fisiopatología de a Obesidad y Nutrición (CIBERobn), Galician Agency of Innovation (GAIN), Xunta de Galicia, 15782, Santiago de Compostela, Spain
| | - Vincent Prevot
- Univ. Lille, Inserm, CHU Lille, Development and Plasticity of the Neuroendocrine Brain Lab, UMR-S1172 INSERM, DISTALZ, EGID, Lille, France
| | - Asis Palazon
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - María L Martínez-Chantar
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160, Derio, Bizkaia, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029, Madrid, Spain.
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16
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Ait Mahiout L, Bessonov N, Kazmierczak B, Volpert V. Mathematical modeling of respiratory viral infection and applications to SARS-CoV-2 progression. MATHEMATICAL METHODS IN THE APPLIED SCIENCES 2022; 46:MMA8606. [PMID: 36247228 PMCID: PMC9538414 DOI: 10.1002/mma.8606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 06/16/2023]
Abstract
Viral infection in cell culture and tissue is modeled with delay reaction-diffusion equations. It is shown that progression of viral infection can be characterized by the viral replication number, time-dependent viral load, and the speed of infection spreading. These three characteristics are determined through the original model parameters including the rates of cell infection and of virus production in the infected cells. The clinical manifestations of viral infection, depending on tissue damage, correlate with the speed of infection spreading, while the infectivity of a respiratory infection depends on the viral load in the upper respiratory tract. Parameter determination from the experiments on Delta and Omicron variants allows the estimation of the infection spreading speed and viral load. Different variants of the SARS-CoV-2 infection are compared confirming that Omicron is more infectious and has less severe symptoms than Delta variant. Within the same variant, spreading speed (symptoms) correlates with viral load allowing prognosis of disease progression.
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Affiliation(s)
- Latifa Ait Mahiout
- Laboratoire d'équations aux dérivées partielles non linéaires et histoire des mathématiquesEcole Normale SupérieureAlgiersAlgeria
| | - Nikolai Bessonov
- Institute of Problems of Mechanical EngineeringRussian Academy of SciencesSaint PetersburgRussia
| | - Bogdan Kazmierczak
- Institute of Fundamental Technological ResearchPolish Academy of SciencesWarsawPoland
| | - Vitaly Volpert
- Institut Camille Jordan, UMR 5208 CNRSUniversity Lyon 1VilleurbanneFrance
- Peoples' Friendship University of Russia6 Miklukho‐Maklaya StMoscowRussia
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17
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Abstract
The U.S. Food and Drug Administration-authorized mRNA- and adenovirus-based SARS-CoV-2 vaccines are intramuscularly injected in two doses and effective in preventing COVID-19, but they do not induce efficient mucosal immunity or prevent viral transmission. Here, we report the first noninfectious, bacteriophage T4-based, multicomponent, needle- and adjuvant-free, mucosal vaccine harboring engineered Spike trimers on capsid exterior and nucleocapsid protein in the interior. Intranasal administration of two doses of this T4 SARS-CoV-2 vaccine 21 days apart induced robust mucosal immunity, in addition to strong systemic humoral and cellular immune responses. The intranasal vaccine induced broad virus neutralization antibody titers against multiple variants, Th1-biased cytokine responses, strong CD4+ and CD8+ T cell immunity, and high secretory IgA titers in sera and bronchoalveolar lavage specimens from vaccinated mice. All of these responses were much stronger in intranasally vaccinated mice than those induced by the injected vaccine. Furthermore, the nasal vaccine provided complete protection and sterilizing immunity against the mouse-adapted SARS-CoV-2 MA10 strain, the ancestral WA-1/2020 strain, and the most lethal Delta variant in both BALB/c and human angiotensin converting enzyme (hACE2) knock-in transgenic mouse models. In addition, the vaccine elicited virus-neutralizing antibodies against SARS-CoV-2 variants in bronchoalveolar lavage specimens, did not affect the gut microbiota, exhibited minimal lung lesions in vaccinated and challenged mice, and is completely stable at ambient temperature. This modular, needle-free, phage T4 mucosal vaccine delivery platform is therefore an excellent candidate for designing efficacious mucosal vaccines against other respiratory infections and for emergency preparedness against emerging epidemic and pandemic pathogens.
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18
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Bestion E, Halfon P, Mezouar S, Mège JL. Cell and Animal Models for SARS-CoV-2 Research. Viruses 2022; 14:1507. [PMID: 35891487 PMCID: PMC9319816 DOI: 10.3390/v14071507] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
During the last two years following the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, development of potent antiviral drugs and vaccines has been a global health priority. In this context, the understanding of virus pathophysiology, the identification of associated therapeutic targets, and the screening of potential effective compounds have been indispensable advancements. It was therefore of primary importance to develop experimental models that recapitulate the aspects of the human disease in the best way possible. This article reviews the information concerning available SARS-CoV-2 preclinical models during that time, including cell-based approaches and animal models. We discuss their evolution, their advantages, and drawbacks, as well as their relevance to drug effectiveness evaluation.
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Affiliation(s)
- Eloïne Bestion
- Microbe Evolution Phylogeny Infection, Institut pour la Recherche et le Developpement, Assistance Publique Hopitaux de Marseille, Aix-Marseille University, 13005 Marseille, France; (E.B.); (P.H.)
- Institue Hospitalo, Universitaire Mediterranée Infection, 13005 Marseille, France
- Genoscience Pharma, 13005 Marseille, France
| | - Philippe Halfon
- Microbe Evolution Phylogeny Infection, Institut pour la Recherche et le Developpement, Assistance Publique Hopitaux de Marseille, Aix-Marseille University, 13005 Marseille, France; (E.B.); (P.H.)
- Institue Hospitalo, Universitaire Mediterranée Infection, 13005 Marseille, France
- Genoscience Pharma, 13005 Marseille, France
| | - Soraya Mezouar
- Microbe Evolution Phylogeny Infection, Institut pour la Recherche et le Developpement, Assistance Publique Hopitaux de Marseille, Aix-Marseille University, 13005 Marseille, France; (E.B.); (P.H.)
- Institue Hospitalo, Universitaire Mediterranée Infection, 13005 Marseille, France
- Genoscience Pharma, 13005 Marseille, France
| | - Jean-Louis Mège
- Microbe Evolution Phylogeny Infection, Institut pour la Recherche et le Developpement, Assistance Publique Hopitaux de Marseille, Aix-Marseille University, 13005 Marseille, France; (E.B.); (P.H.)
- Institue Hospitalo, Universitaire Mediterranée Infection, 13005 Marseille, France
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19
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Singh B, Avula K, Chatterjee S, Datey A, Ghosh A, De S, Keshry SS, Ghosh S, Suryawanshi AR, Dash R, Senapati S, Beuria TK, Prasad P, Raghav S, Swain R, Parida A, Hussain Syed G, Chattopadhyay S. Isolation and Characterization of Five Severe Acute Respiratory Syndrome Coronavirus 2 Strains of Different Clades and Lineages Circulating in Eastern India. Front Microbiol 2022; 13:856913. [PMID: 35847066 PMCID: PMC9279865 DOI: 10.3389/fmicb.2022.856913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a serious pandemic has altered the global socioeconomic dynamics. The wide prevalence, high death counts, and rapid emergence of new variants urge for the establishment of research infrastructure to facilitate the rapid development of efficient therapeutic modalities and preventive measures. In agreement with this, SARS-CoV-2 strains were isolated from patient swab samples collected during the first COVID-19 wave in Odisha, India. The viral isolates were adapted to in vitro cultures and further characterized to identify strain-specific variations in viral growth characteristics. The neutralization susceptibility of viral isolates to vaccine-induced antibodies was determined using sera from individuals vaccinated in the Government-run vaccine drive in India. The major goal was to isolate and adapt SARS-CoV-2 viruses in cell culture with minimum modifications to facilitate research activities involved in the understanding of the molecular virology, host-virus interactions, drug discovery, and animal challenge models that eventually contribute toward the development of reliable therapeutics.
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Affiliation(s)
- Bharati Singh
- Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Kiran Avula
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sanchari Chatterjee
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ankita Datey
- Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Arup Ghosh
- Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Saikat De
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Supriya Suman Keshry
- Institute of Life Sciences, Bhubaneswar, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Soumyajit Ghosh
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | | | - Rupesh Dash
- Institute of Life Sciences, Bhubaneswar, India
| | | | | | | | | | | | - Ajay Parida
- Institute of Life Sciences, Bhubaneswar, India
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20
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Prince T, Dong X, Penrice-Randal R, Randle N, Hartley C, Goldswain H, Jones B, Semple MG, Baillie JK, Openshaw PJM, Turtle L, Hughes GL, Anderson ER, Patterson EI, Druce J, Screaton G, Carroll MW, Stewart JP, Hiscox JA. Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages. mSphere 2022; 7:e0091321. [PMID: 35491827 PMCID: PMC9241508 DOI: 10.1128/msphere.00913-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/18/2022] [Indexed: 01/02/2023] Open
Abstract
New variants of SARS-CoV-2 are continuing to emerge and dominate the global sequence landscapes. Several variants have been labeled variants of concern (VOCs) because they may have a transmission advantage, increased risk of morbidity and/or mortality, or immune evasion upon a background of prior infection or vaccination. Placing the VOCs in context with the underlying variability of SARS-CoV-2 is essential in understanding virus evolution and selection pressures. Dominant genome sequences and the population genetics of SARS-CoV-2 in nasopharyngeal swabs from hospitalized patients were characterized. Nonsynonymous changes at a minor variant level were identified. These populations were generally preserved when isolates were amplified in cell culture. To place the Alpha, Beta, Delta, and Omicron VOCs in context, their growth was compared to clinical isolates of different lineages from earlier in the pandemic. The data indicated that the growth in cell culture of the Beta variant was more than that of the other variants in Vero E6 cells but not in hACE2-A549 cells. Looking at each time point, Beta grew more than the other VOCs in hACE2-A549 cells at 24 to 48 h postinfection. At 72 h postinfection there was no difference in the growth of any of the variants in either cell line. Overall, this work suggested that exploring the biology of SARS-CoV-2 is complicated by population dynamics and that these need to be considered with new variants. In the context of variation seen in other coronaviruses, the variants currently observed for SARS-CoV-2 are very similar in terms of their clinical spectrum of disease. IMPORTANCE SARS-CoV-2 is the causative agent of COVID-19. The virus has spread across the planet, causing a global pandemic. In common with other coronaviruses, SARS-CoV-2 genomes can become quite diverse as a consequence of replicating inside cells. This has given rise to multiple variants from the original virus that infected humans. These variants may have different properties and in the context of a widespread vaccination program may render vaccines less effective. Our research confirms the degree of genetic diversity of SARS-CoV-2 in patients. By comparing the growth of previous variants to the pattern seen with four variants of concern (VOCs) (Alpha, Beta, Delta, and Omicron), we show that, at least in cells, Beta variant growth exceeds that of Alpha, Delta, and Omicron VOCs at 24 to 48 h in both Vero E6 and hACE2-A549 cells, but by 72 h postinfection, the amount of virus is not different from that of the other VOCs.
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Affiliation(s)
- Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nadine Randle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Benjamin Jones
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Malcolm G. Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Department of Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - J. Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Enyia R. Anderson
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Edward I. Patterson
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Julian Druce
- Virus Identification Laboratory, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Gavin Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Miles W. Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Public Health England, Salisbury, United Kingdom
| | - James P. Stewart
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Infectious Disease, University of Georgia, Georgia, USA
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
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21
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The Cellular Characterization of SARS-CoV-2 Spike Protein in Virus-Infected Cells Using the Receptor Binding Domain Binding Specific Human Monoclonal Antibodies. J Virol 2022; 96:e0045522. [PMID: 35727030 PMCID: PMC9278116 DOI: 10.1128/jvi.00455-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A human monoclonal antibody panel (PD4, PD5, PD7, SC23, and SC29) was isolated from the B cells of convalescent patients and used to examine the S protein in SARS-CoV-2-infected cells. While all five antibodies bound conformational-specific epitopes within SARS-CoV-2 spike (S) protein, only PD5, PD7, and SC23 were able to bind to the receptor binding domain (RBD). Immunofluorescence microscopy was used to examine the S protein RBD in cells infected with the Singapore isolates SARS-CoV-2/0334 and SARS-CoV-2/1302. The RBD-binders exhibited a distinct cytoplasmic staining pattern that was primarily localized within the Golgi complex and was distinct from the diffuse cytoplasmic staining pattern exhibited by the non-RBD-binders (PD4 and SC29). These data indicated that the S protein adopted a conformation in the Golgi complex that enabled the RBD recognition by the RBD-binders. The RBD-binders also recognized the uncleaved S protein, indicating that S protein cleavage was not required for RBD recognition. Electron microscopy indicated high levels of cell-associated virus particles, and multiple cycle virus infection using RBD-binder staining provided evidence for direct cell-to-cell transmission for both isolates. Although similar levels of RBD-binder staining were demonstrated for each isolate, SARS-CoV-2/1302 exhibited slower rates of cell-to-cell transmission. These data suggest that a conformational change in the S protein occurs during its transit through the Golgi complex that enables RBD recognition by the RBD-binders and suggests that these antibodies can be used to monitor S protein RBD formation during the early stages of infection. IMPORTANCE The SARS-CoV-2 spike (S) protein receptor binding domain (RBD) mediates the attachment of SARS-CoV-2 to the host cell. This interaction plays an essential role in initiating virus infection, and the S protein RBD is therefore a focus of therapeutic and vaccine interventions. However, new virus variants have emerged with altered biological properties in the RBD that can potentially negate these interventions. Therefore, an improved understanding of the biological properties of the RBD in virus-infected cells may offer future therapeutic strategies to mitigate SARS- CoV-2 infection. We used physiologically relevant antibodies that were isolated from the B cells of convalescent COVID-19 patients to monitor the RBD in cells infected with SARS-CoV-2 clinical isolates. These immunological reagents specifically recognize the correctly folded RBD and were used to monitor the appearance of the RBD in SARS-CoV-2-infected cells and identified the site where the RBD first appears.
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22
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Dolskiy AA, Grishchenko IV, Bodnev SA, Nazarenko AA, Smirnova AM, Matveeva AK, Bulychev LE, Ovchinnikova AS, Tregubchak TV, Zaykovskaya AV, Imatdinov IR, Pyankov OV, Gavrilova EV, Maksyutov RA, Yudkin DV. Increased LAMP1 Expression Enhances SARS-CoV-1 and SARS-CoV-2 Production in Vero-Derived Transgenic Cell Lines. Mol Biol 2022; 56:463-468. [PMID: 35693978 PMCID: PMC9165926 DOI: 10.1134/s0026893322030050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/22/2022]
Abstract
Coronaviridae is a family of single-stranded RNA (ssRNA) viruses that can cause diseases with high mortality rates. SARS-CoV-1 and MERS-CoV appeared in 2002‒2003 and 2012, respectively. A novel coronavirus, SARS-CoV-2, emerged in 2019 in Wuhan (China) and has caused more than 5 million deaths in worldwide. The entry of SARS-CoV-1 into the cell is due to the interaction of the viral spike (S) protein and the cell protein, angiotensin-converting enzyme 2 (ACE2). After infection, virus assembly occurs in Golgi apparatus-derived vesicles during exocytosis. One of the possible participants in this process is LAMP1 protein. We established transgenic Vero cell lines with increased expression of human LAMP1 gene and evaluated SARS-CoV-1 and SARS-CoV-2 production. An increase in the production of both viruses in LAMP1-expressing cells when compared with Vero cells was observed, especially in the presence of trypsin during infection. From these results it can be assumed that LAMP1 promotes SARS-CoV-1 and SARS-CoV-2 production due to enhanced exocytosis.
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Affiliation(s)
- A. A. Dolskiy
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - I. V. Grishchenko
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - S. A. Bodnev
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - A. A. Nazarenko
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - A. M. Smirnova
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - A. K. Matveeva
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - L. E. Bulychev
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - A. S. Ovchinnikova
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - T. V. Tregubchak
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - A. V. Zaykovskaya
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - I. R. Imatdinov
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - O. V. Pyankov
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - E. V. Gavrilova
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - R. A. Maksyutov
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
| | - D. V. Yudkin
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk Region Russia
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23
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Chang JJY, Gleeson J, Rawlinson D, De Paoli-Iseppi R, Zhou C, Mordant FL, Londrigan SL, Clark MB, Subbarao K, Stinear TP, Coin LJM, Pitt ME. Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection. Front Immunol 2022; 13:832223. [PMID: 35464437 PMCID: PMC9019466 DOI: 10.3389/fimmu.2022.832223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative to help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) using Oxford Nanopore Technologies (ONT) long-reads to measure differential host gene expression, transcript polyadenylation and isoform usage within various epithelial cell lines permissive and non-permissive for SARS-CoV-2 infection. SARS-CoV-2-infected and mock-infected Vero (African green monkey kidney epithelial cells), Calu-3 (human lung adenocarcinoma epithelial cells), Caco-2 (human colorectal adenocarcinoma epithelial cells) and A549 (human lung carcinoma epithelial cells) were analyzed over time (0, 2, 24, 48 hours). Differential polyadenylation was found to occur in both infected Calu-3 and Vero cells during a late time point (48 hpi), with Gene Ontology (GO) terms such as viral transcription and translation shown to be significantly enriched in Calu-3 data. Poly(A) tails showed increased lengths in the majority of the differentially polyadenylated transcripts in Calu-3 and Vero cell lines (up to ~101 nt in mean poly(A) length, padj = 0.029). Of these genes, ribosomal protein genes such as RPS4X and RPS6 also showed downregulation in expression levels, suggesting the importance of ribosomal protein genes during infection. Furthermore, differential transcript usage was identified in Caco-2, Calu-3 and Vero cells, including transcripts of genes such as GSDMB and KPNA2, which have previously been implicated in SARS-CoV-2 infections. Overall, these results highlight the potential role of differential polyadenylation and transcript usage in host immune response or viral manipulation of host mechanisms during infection, and therefore, showcase the value of long-read sequencing in identifying less-explored host responses to disease.
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Affiliation(s)
- Jessie J-Y Chang
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Josie Gleeson
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Daniel Rawlinson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Ricardo De Paoli-Iseppi
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Chenxi Zhou
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Francesca L Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Sarah L Londrigan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Michael B Clark
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Disease, Imperial College London, London, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Miranda E Pitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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24
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Strobelt R, Adler J, Paran N, Yahalom-Ronen Y, Melamed S, Politi B, Shulman Z, Schmiedel D, Shaul Y. Imatinib inhibits SARS-CoV-2 infection by an off-target-mechanism. Sci Rep 2022; 12:5758. [PMID: 35388061 PMCID: PMC8984672 DOI: 10.1038/s41598-022-09664-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. More than 274 million individuals have suffered from COVID-19 and over five million people have died from this disease so far. Therefore, there is an urgent need for therapeutic drugs. Repurposing FDA approved drugs should be favored since evaluation of safety and efficacy of de-novo drug design are both costly and time consuming. We report that imatinib, an Abl tyrosine kinase inhibitor, robustly decreases SARS-CoV-2 infection and uncover a mechanism of action. We show that imatinib inhibits the infection of SARS-CoV-2 and its surrogate lentivector pseudotype. In latter, imatinib inhibited both routes of viral entry, endocytosis and membrane-fusion. We utilized a system to quantify in real-time cell-cell membrane fusion mediated by the SARS-CoV-2 surface protein, Spike, and its receptor, hACE2, to demonstrate that imatinib inhibits this process in an Abl1 and Abl2 independent manner. Furthermore, cellular thermal shift assay revealed a direct imatinib-Spike interaction that affects Spike susceptibility to trypsin digest. Collectively, our data suggest that imatinib inhibits Spike mediated viral entry by an off-target mechanism. These findings mark imatinib as a promising therapeutic drug in inhibiting the early steps of SARS-CoV-2 infection.
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Affiliation(s)
- Romano Strobelt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ziv Shulman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Dominik Schmiedel
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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25
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Fisher T, Gluck A, Narayanan K, Kuroda M, Nachshon A, Hsu JC, Halfmann PJ, Yahalom-Ronen Y, Finkel Y, Schwartz M, Weiss S, Tseng CTK, Israely T, Paran N, Kawaoka Y, Makino S, Stern-Ginossar N. Parsing the role of NSP1 in SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.14.484208. [PMID: 35313595 PMCID: PMC8936099 DOI: 10.1101/2022.03.14.484208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 19 (COVID-19) pandemic. Despite its urgency, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis and its ability to antagonize innate immune responses. SARS-CoV-2 leads to shutoff of cellular protein synthesis and over-expression of nsp1, a central shutoff factor in coronaviruses, inhibits cellular gene translation. However, the diverse molecular mechanisms nsp1 employs as well as its functional importance in infection are still unresolved. By overexpressing various nsp1 mutants and generating a SARS-CoV-2 mutant in which nsp1 does not bind ribosomes, we untangle the effects of nsp1. We uncover that nsp1, through inhibition of translation and induction of mRNA degradation, is the main driver of host shutoff during SARS-CoV-2 infection. Furthermore, we find the propagation of nsp1 mutant virus is inhibited specifically in cells with intact interferon (IFN) response as well as in-vivo , in infected hamsters, and this attenuation is associated with stronger induction of type I IFN response. This illustrates that nsp1 shutoff activity has an essential role mainly in counteracting the IFN response. Overall, our results reveal the multifaceted approach nsp1 uses to shut off cellular protein synthesis and uncover the central role it plays in SARS-CoV-2 pathogenesis, explicitly through blockage of the IFN response.
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Affiliation(s)
- Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
- T. Fisher, A. Gluck, K. Narayanan, and K. Makoto contributed equally to the studies
| | - Avi Gluck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
- T. Fisher, A. Gluck, K. Narayanan, and K. Makoto contributed equally to the studies
| | - Krishna Narayanan
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- T. Fisher, A. Gluck, K. Narayanan, and K. Makoto contributed equally to the studies
| | - Makoto Kuroda
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
- T. Fisher, A. Gluck, K. Narayanan, and K. Makoto contributed equally to the studies
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jason C. Hsu
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Peter J. Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
- Department of Virology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 162-8655 Tokyo, Japan
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Department of Virology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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26
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Dogan K, Erol E, Didem Orhan M, Degirmenci Z, Kan T, Gungor A, Yasa B, Avsar T, Cetin Y, Durdagi S, Guzel M. Instant determination of the artemisinin from various Artemisia annua L. extracts by LC-ESI-MS/MS and their in-silico modelling and in vitro antiviral activity studies against SARS-CoV-2. PHYTOCHEMICAL ANALYSIS : PCA 2022; 33:303-319. [PMID: 34585460 PMCID: PMC8662158 DOI: 10.1002/pca.3088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Numerous efforts in natural product drug development are reported for the treatment of Coronavirus. Based on the literature, among these natural plants Artemisia annua L. shows some promise for the treatment of SARS-CoV-2. OBJECTIVE The main objective of our study was to determine artemisinin content by liquid chromatography electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS), to investigate the in vitro biological activity of artemisinin from the A. annua plants grown in Turkey with various extracted methods, to elaborate in silico activity against SARS-CoV-2 using molecular modelling. METHODOLOGY Twenty-one different extractions were applied. Direct and sequential extractions studies were compared with ultrasonic assisted maceration, Soxhlet, and ultra-rapid determined artemisinin active molecules by LC-ESI-MS/MS methods. The inhibition of spike protein and main protease (3CL) enzyme activity of SARS-CoV-2 virus was assessed by time resolved fluorescence energy transfer (TR-FRET) assay. RESULTS Artemisinin content in the range 0.062-0.066%. Artemisinin showed significant inhibition of 3CL protease activity but not Spike/ACE-2 binding. The 50% effective concentration (EC50 ) of artemisinin against SARS-CoV-2 Spike pseudovirus was found greater than 50 μM (EC45 ) in HEK293T cell line whereas the cell viability was 94% of the control (P < 0.01). The immunosuppressive effects of artemisinin on TNF-α production on both pseudovirus and lipopolysaccharide (LPS)-induced THP-1 cells were found significant in a dose dependent manner. CONCLUSION Further studies of these extracts for COVID-19 treatment will shed light to seek alternative treatment options. Moreover, these natural extracts can be used as an additional treatment option with medicines, as well as prophylactic use can be very beneficial for patients.
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Affiliation(s)
- Kubra Dogan
- Chemical and Metallurgical Engineering Institute, Food EngineeringYildiz Technical UniversityIstanbulTurkey
- Research Institute for Health Sciences and Technologies (SABITA), Centre of Drug Discovery and DevelopmentIstanbul Medipol UniversityIstanbulTurkey
| | - Ebru Erol
- Research Institute for Health Sciences and Technologies (SABITA), Centre of Drug Discovery and DevelopmentIstanbul Medipol UniversityIstanbulTurkey
- Faculty of Pharmacy, Department of Analytical ChemistryBezmialem Vakif UniversityIstanbulTurkey
| | - Muge Didem Orhan
- Health Sciences Institute, Neuroscience LaboratoryBahcesehir UniversityIstanbulTurkey
| | - Zehra Degirmenci
- Health Sciences Institute, Neuroscience LaboratoryBahcesehir UniversityIstanbulTurkey
| | - Tugce Kan
- TUBITAK MAM Research CentreGenetic Engineering and Biotechnology InstituteGebze‐KocaeliTurkey
| | - Aysen Gungor
- TUBITAK MAM Research CentreGenetic Engineering and Biotechnology InstituteGebze‐KocaeliTurkey
| | - Belkis Yasa
- Faculty of Forestry, Department of Forest Industry EngineeringBursa Technical UniversityBursaTurkey
| | - Timucin Avsar
- Health Sciences Institute, Neuroscience LaboratoryBahcesehir UniversityIstanbulTurkey
- School of Medicine, Department of Medical BiologyBahcesehir UniversityIstanbulTurkey
| | - Yuksel Cetin
- TUBITAK MAM Research CentreGenetic Engineering and Biotechnology InstituteGebze‐KocaeliTurkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of MedicineBahcesehir UniversityIstanbulTurkey
| | - Mustafa Guzel
- Research Institute for Health Sciences and Technologies (SABITA), Centre of Drug Discovery and DevelopmentIstanbul Medipol UniversityIstanbulTurkey
- International School of Medicine, Department of Medical PharmacologyIstanbul Medipol UniversityIstanbulTurkey
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27
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Pathak AK, Mishra GP, Uppili B, Walia S, Fatihi S, Abbas T, Banu S, Ghosh A, Kanampalliwar A, Jha A, Fatma S, Aggarwal S, Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Kabra S, Rakshit P, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK, Mukerji M. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acids Res 2022; 50:1551-1561. [PMID: 35048970 PMCID: PMC8860616 DOI: 10.1093/nar/gkab1297] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.
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Affiliation(s)
- Ankit K Pathak
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Bharathram Uppili
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Safal Walia
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Saman Fatihi
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tahseen Abbas
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sofia Banu
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Arup Ghosh
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | | | - Atimukta Jha
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Sana Fatma
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Shifu Aggarwal
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mahesh Shanker Dhar
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | | | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Sandhya Kabra
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Partha Rakshit
- Biotechnology Division, National Centre for Disease Control (NCDC), New Delhi, India
| | - Rahul C Bhoyar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Abhinav Jain
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohit Kumar Divakar
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohamed Imran
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohammed Faruq
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Divya Tej Sowpati
- CSIR - Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Lipi Thukral
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Sunil K Raghav
- Institute of Life Sciences (ILS), Bhubaneswar, Odisha, India
| | - Mitali Mukerji
- CSIR - Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Indian Institute of Technology (IIT), Jodhpur, India
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28
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Rizvi ZA, Dalal R, Sadhu S, Binayke A, Dandotiya J, Kumar Y, Shrivastava T, Gupta SK, Aggarwal S, Tripathy MR, Rathore DK, Yadav AK, Medigeshi GR, Pandey AK, Samal S, Asthana S, Awasthi A. Golden Syrian hamster as a model to study cardiovascular complications associated with SARS-CoV-2 infection. eLife 2022; 11:73522. [PMID: 35014610 PMCID: PMC8794466 DOI: 10.7554/elife.73522] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection in the Golden Syrian hamster causes lung pathology that resembles human coronavirus disease (COVID-19). However, extra-pulmonary pathologies associated with SARS-CoV-2 infection and post COVID sequelae remain to be understood. Here we show, using a hamster model, that the early phase of SARS-CoV-2 infection leads to an acute inflammatory response and lung pathologies, while the late phase of infection causes cardiovascular complications (CVC) characterized by ventricular wall thickening associated with increased ventricular mass/ body mass ratio and interstitial coronary fibrosis. Molecular profiling further substantiated our findings of CVC, as SARS-CoV-2-infected hamsters showed elevated levels of serum cardiac Troponin-I (cTnI), cholesterol, low-density lipoprotein and long-chain fatty acid triglycerides. Serum metabolomics profiling of SARS-CoV-2-infected hamsters identified N-acetylneuraminate, a functional metabolite found to be associated with CVC, as a metabolic marker was found to be common between SARS-CoV-2-infected hamsters and COVID-19 patients. Together, we propose hamsters as a suitable animal model to study post-COVID sequelae associated with CVC which could be extended to therapeutic interventions.
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Affiliation(s)
- Zaigham Abbas Rizvi
- Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Rajdeep Dalal
- Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Srikanth Sadhu
- Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Akshay Binayke
- Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Jyotsna Dandotiya
- Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Yashwant Kumar
- Non-communicable disease centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Tripti Shrivastava
- Infection and Immunology centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Sonu Kumar Gupta
- Non-communicable disease centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Suruchi Aggarwal
- Non-communicable disease centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Manas Ranjan Tripathy
- Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Deepak Kumar Rathore
- Infection and Immunology Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Amit Kumar Yadav
- Non-communicable disease center, Translational Health Science and Technology Institute, Faridabad, India
| | - Guruprasad R Medigeshi
- Infection and Immunology Center, Translational Health Science and Technology Institute, Gurgaon, India
| | - Amit Kumar Pandey
- Infection and Immunology Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Sweety Samal
- Infection and Immunology Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Shailendra Asthana
- Non-communicable disease centre, Translational Health Science and Technology Institute, Faridabad, India
| | - Amit Awasthi
- Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, Faridabad, India
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29
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Jureka AS, Basler CF. Propagation and Quantification of SARS-CoV-2. Methods Mol Biol 2022; 2452:111-129. [PMID: 35554904 DOI: 10.1007/978-1-0716-2111-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In late 2019, the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Since its emergence, SARS-CoV-2 has been responsible for a world-wide pandemic resulting in over 80 million infections and over 1.8 million deaths. The severity of the pandemic has prompted widespread research efforts to more fully understand SARS-CoV-2 and the disease it causes, COVID-19. Research into this novel virus will be facilitated by the availability of clearly described and effective protocols that enable the propagation and quantification of infectious virus. Here, we describe protocols for the propagation of SARS-CoV-2 in Vero E6 cells as well as two human cells lines, the intestinal epithelial Caco-2 cell line and the respiratory epithelial Calu-3 cell line. Additionally, we provide protocols for the quantification of SARS-CoV-2 by plaque assays and immunofocus forming assays in Vero E6 cells utilizing liquid overlays. These protocols provide a foundation for laboratories acquiring the ability to study SARS-CoV-2 to address this ongoing pandemic.
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Affiliation(s)
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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30
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Polat O, Berber M. The Status of Healthcare Professionals’ Having COVID-19 Vaccine and Evaluation of Its Side Effects: A Pandemic Hospital Experience. EURASIAN JOURNAL OF FAMILY MEDICINE 2021. [DOI: 10.33880/ejfm.2021100406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aim: Vaccination is one of the most effective and safest preventive health services in the fight against COVID-19. Many people in society have hesitations about the COVID-19 vaccines. We evaluated the vaccination participation rates of healthcare workers to be a positive role model for society.
Methods: Between 14 January 2021 and 15 April 2021, 2637 healthcare workers who received 2 doses of 0.5 ml CoronaVac vaccine with 4 weeks intervals were classified as occupation, unit, marital status, age, and gender. Registered side effects were evaluated.
Results: It was observed that 65.6% of the healthcare workers were vaccinated and 2.4% (n=62) of the vaccinated workers developed side effects. The mean age of the vaccinated personnel was 34.37±10.04 years. 59.8% (n=1577) of the vaccinated personnel were male and 53.6% (n=1413) were single. The occupational group with the highest vaccination rate was doctors with 78% (n=658). The most common side effect was myalgia in 45.2% (n=28), followed by headache with 38.7% (n=24). About half of those who developed side effects had only one side effect.
Conclusion: It was concluded that COVID-19 vaccination differs according to age, gender, and role in the hospital, with the highest vaccination rate among physicians. The vaccination status of healthcare workers who are heavily affected by COVID-19 will positively affect society.
Keywords: health personnel, COVID-19, vaccination
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Affiliation(s)
- Ozlem Polat
- University of Health Sciences, Bakırköy Sadi Konuk Training and Research Hospital
| | - Murathan Berber
- University of Health Sciences, Bakırköy Sadi Konuk Training and Research Hospital
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31
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de Souza GAP, Le Bideau M, Boschi C, Ferreira L, Wurtz N, Devaux C, Colson P, La Scola B. Emerging SARS-CoV-2 Genotypes Show Different Replication Patterns in Human Pulmonary and Intestinal Epithelial Cells. Viruses 2021; 14:v14010023. [PMID: 35062227 PMCID: PMC8777977 DOI: 10.3390/v14010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/29/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) quickly spread worldwide following its emergence in Wuhan, China, and hit pandemic levels. Its tremendous incidence favoured the emergence of viral variants. The current genome diversity of SARS-CoV-2 has a clear impact on epidemiology and clinical practice, especially regarding transmission rates and the effectiveness of vaccines. In this study, we evaluated the replication of different SARS-CoV-2 isolates representing different virus genotypes which have been isolated throughout the pandemic. We used three distinct cell lines, including Vero E6 cells originating from monkeys; Caco-2 cells, an intestinal epithelium cell line originating from humans; and Calu-3 cells, a pulmonary epithelium cell line also originating from humans. We used RT-qPCR to replicate different SARS-CoV-2 genotypes by quantifying the virus released in the culture supernatant of infected cells. We found that the different viral isolates replicate similarly in Caco-2 cells, but show very different replicative capacities in Calu-3 cells. This was especially highlighted for the lineages B.1.1.7, B.1.351 and P.1, which are considered to be variants of concern. These results underscore the importance of the evaluation and characterisation of each SARS-CoV-2 isolate in order to establish the replication patterns before performing tests, and of the consideration of the ideal SARS-CoV-2 genotype-cell type pair for each assay.
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Affiliation(s)
- Gabriel Augusto Pires de Souza
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Marion Le Bideau
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Celine Boschi
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Lorène Ferreira
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Nathalie Wurtz
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Christian Devaux
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Correspondence: ; Tel.: +33-0413-732-401
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Enhanced apoptosis as a possible mechanism to self-limit SARS-CoV-2 replication in porcine primary respiratory epithelial cells in contrast to human cells. Cell Death Discov 2021; 7:383. [PMID: 34893585 PMCID: PMC8661338 DOI: 10.1038/s41420-021-00781-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/19/2021] [Accepted: 11/30/2021] [Indexed: 01/12/2023] Open
Abstract
The ability of SARS-CoV to infect different species, including humans, dogs, cats, minks, ferrets, hamsters, tigers, and deer, pose a continuous threat to human and animal health. Pigs, though closely related to humans, seem to be less susceptible to SARS-CoV-2. Former in vivo studies failed to demonstrate clinical signs and transmission between pigs, while later attempts using a higher infectious dose reported viral shedding and seroconversion. This study investigated species-specific cell susceptibility, virus dose-dependent infectivity, and infection kinetics, using primary human (HRECs) and porcine (PRECs) respiratory epithelial cells. Despite higher ACE2 expression in HRECs compared to PRECs, SARS-CoV-2 infected, and replicated in both PRECs and HRECs in a dose-dependent manner. Cytopathic effect was particularly more evident in PRECs than HRECs, showing the hallmark morphological signs of apoptosis. Further analysis confirmed an early and enhanced apoptotic mechanism driven through caspase 3/7 activation, limiting SARS-CoV-2 propagation in PRECs compared to HRECs. Our findings shed light on a possible mechanism of resistance of pigs to SARS-CoV-2 infection, and it may hold therapeutic value for the treatment of COVID-19.
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33
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Miao Z, Humphreys BD, McMahon AP, Kim J. Multi-omics integration in the age of million single-cell data. Nat Rev Nephrol 2021; 17:710-724. [PMID: 34417589 PMCID: PMC9191639 DOI: 10.1038/s41581-021-00463-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
An explosion in single-cell technologies has revealed a previously underappreciated heterogeneity of cell types and novel cell-state associations with sex, disease, development and other processes. Starting with transcriptome analyses, single-cell techniques have extended to multi-omics approaches and now enable the simultaneous measurement of data modalities and spatial cellular context. Data are now available for millions of cells, for whole-genome measurements and for multiple modalities. Although analyses of such multimodal datasets have the potential to provide new insights into biological processes that cannot be inferred with a single mode of assay, the integration of very large, complex, multimodal data into biological models and mechanisms represents a considerable challenge. An understanding of the principles of data integration and visualization methods is required to determine what methods are best applied to a particular single-cell dataset. Each class of method has advantages and pitfalls in terms of its ability to achieve various biological goals, including cell-type classification, regulatory network modelling and biological process inference. In choosing a data integration strategy, consideration must be given to whether the multi-omics data are matched (that is, measured on the same cell) or unmatched (that is, measured on different cells) and, more importantly, the overall modelling and visualization goals of the integrated analysis.
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Affiliation(s)
- Zhen Miao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA,Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA,Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,
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34
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Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D’Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Gitter A, Greene CS. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. mSystems 2021; 6:e0009521. [PMID: 34698547 PMCID: PMC8547481 DOI: 10.1128/msystems.00095-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. IMPORTANCE COVID-19 involves a number of organ systems and can present with a wide range of symptoms. From how the virus infects cells to how it spreads between people, the available research suggests that these patterns are very similar to those seen in the closely related viruses SARS-CoV-1 and possibly Middle East respiratory syndrome-related CoV (MERS-CoV). Understanding the pathogenesis of the SARS-CoV-2 virus also contextualizes how the different biological systems affected by COVID-19 connect. Exploring the structure, phylogeny, and pathogenesis of the virus therefore helps to guide interpretation of the broader impacts of the virus on the human body and on human populations. For this reason, an in-depth exploration of viral mechanisms is critical to a robust understanding of SARS-CoV-2 and, potentially, future emergent human CoVs (HCoVs).
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Affiliation(s)
- Halie M. Rando
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Alexandra J. Lee
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sandipan Ray
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Ashwin N. Skelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth Sell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John J. Dziak
- Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Lucy D’Agostino McGowan
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Marouen Ben Guebila
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Nils Wellhausen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Simina M. Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Stephen Capone
- St. George’s University School of Medicine, St. George’s, Grenada
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
| | - YoSon Park
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Mai
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yuchen Sun
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
| | - Joel D. Boerckel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - James Brian Byrd
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Jinhui Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - John P. Barton
- Department of Physics and Astronomy, University of California-Riverside, Riverside, California, USA
| | - Rishi Raj Goel
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Tiago Lubiana
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - COVID-19 Review Consortium
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen, Germany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Mercer University, Macon, Georgia, USA
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, North Carolina, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
- Georgia State University, Atlanta, Georgia, USA
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
- St. George’s University School of Medicine, St. George’s, Grenada
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Clinical Sciences, Lund University, Lund, Sweden
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
- Azimuth1, McLean, Virginia, USA
- Allen Institute for Immunology, Seattle, Washington, USA
- Department of Physics and Astronomy, University of California-Riverside, Riverside, California, USA
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Casey S. Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
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Karn V, Ahmed S, Tsai LW, Dubey R, Ojha S, Singh HN, Kumar M, Gupta PK, Sadhu S, Jha NK, Kumar A, Pandit S, Kumar S. Extracellular Vesicle-Based Therapy for COVID-19: Promises, Challenges and Future Prospects. Biomedicines 2021; 9:biomedicines9101373. [PMID: 34680490 PMCID: PMC8533559 DOI: 10.3390/biomedicines9101373] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/19/2021] [Accepted: 09/25/2021] [Indexed: 12/11/2022] Open
Abstract
The COVID-19 pandemic has become a serious concern and has negatively impacted public health and the economy. It primarily targets the lungs, causing acute respiratory distress syndrome (ARDS); however, it may also lead to multiple organ failure (MOF) and enhanced mortality rates. Hence, there is an urgent need to develop potential effective therapeutic strategies for COVID-19 patients. Extracellular vesicles (EVs) are released from various types of cells that participate in intercellular communication to maintain physiological and pathological processes. EVs derived from various cellular origins have revealed suppressive effects on the cytokine storm during systemic hyper-inflammatory states of severe COVID-19, leading to enhanced alveolar fluid clearance, promoted epithelial and endothelial recovery, and cell proliferation. Being the smallest subclass of EVs, exosomes offer striking characteristics such as cell targeting, being nano-carriers for drug delivery, high biocompatibility, safety, and low-immunogenicity, thus rendering them a potential cell-free therapeutic candidate against the pathogeneses of various diseases. Due to these properties, numerous studies and clinical trials have been performed to assess their safety and therapeutic efficacy against COVID-19. Hence, in this review, we have comprehensively described current updates on progress and challenges for EVs as a potential therapeutic agent for the management of COVID-19.
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Affiliation(s)
- Vamika Karn
- Department of Biotechnology, Amity University, Mumbai 410221, India;
| | - Shaista Ahmed
- Faculty of Medical and Paramedical Sciences, Aix-Marseille University, 13005 Marseille, France;
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei 11031, Taiwan; (L.-W.T.); (R.D.)
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Rajni Dubey
- Department of Medicine Research, Taipei Medical University Hospital, Taipei 11031, Taiwan; (L.-W.T.); (R.D.)
| | - Shreesh Ojha
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, UAE University, Al Ain, Abu Dhabi P.O. Box 17666, United Arab Emirates;
| | - Himanshu Naryan Singh
- Department of System Biology, Columbia University Irving Medical Center, New York, NY 10032, USA;
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India;
| | - Piyush Kumar Gupta
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201310, India; (P.K.G.); (S.S.); (S.P.)
| | - Soumi Sadhu
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201310, India; (P.K.G.); (S.S.); (S.P.)
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida 201310, India;
| | - Ashutosh Kumar
- Department of Anatomy, All India Institute of Medical Sciences, Patna 801507, India;
| | - Soumya Pandit
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201310, India; (P.K.G.); (S.S.); (S.P.)
| | - Sanjay Kumar
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201310, India; (P.K.G.); (S.S.); (S.P.)
- Correspondence: or ; Tel.: +91-120-4570-000
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36
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Jaworski E, Langsjoen RM, Mitchell B, Judy B, Newman P, Plante JA, Plante KS, Miller AL, Zhou Y, Swetnam D, Sotcheff S, Morris V, Saada N, Machado RR, McConnell A, Widen SG, Thompson J, Dong J, Ren P, Pyles RB, Ksiazek TG, Menachery VD, Weaver SC, Routh AL. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants. eLife 2021; 10:68479. [PMID: 34581669 PMCID: PMC8478411 DOI: 10.7554/elife.68479] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for next-generation sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called ‘Tiled-ClickSeq’, which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5’UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.
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Affiliation(s)
- Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,ClickSeq Technologies LLC, Galveston, United States
| | - Rose M Langsjoen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Brooke Mitchell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Barbara Judy
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Patrick Newman
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Kenneth S Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Aaron L Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Daniele Swetnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Victoria Morris
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Nehad Saada
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Rafael Rg Machado
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Allan McConnell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, United States
| | - Jill Thompson
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, United States
| | - Jianli Dong
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Ping Ren
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Rick B Pyles
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Thomas G Ksiazek
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States
| | - Vineet D Menachery
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States.,Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, United States
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37
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Zhu J, Ananthaswamy N, Jain S, Batra H, Tang WC, Lewry DA, Richards ML, David SA, Kilgore PB, Sha J, Drelich A, Tseng CTK, Chopra AK, Rao VB. A universal bacteriophage T4 nanoparticle platform to design multiplex SARS-CoV-2 vaccine candidates by CRISPR engineering. SCIENCE ADVANCES 2021; 7:eabh1547. [PMID: 34516878 PMCID: PMC8442874 DOI: 10.1126/sciadv.abh1547] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/16/2021] [Indexed: 06/02/2023]
Abstract
A “universal” platform that can rapidly generate multiplex vaccine candidates is critically needed to control pandemics. Using the severe acute respiratory syndrome coronavirus 2 as a model, we have developed such a platform by CRISPR engineering of bacteriophage T4. A pipeline of vaccine candidates was engineered by incorporating various viral components into appropriate compartments of phage nanoparticle structure. These include expressible spike genes in genome, spike and envelope epitopes as surface decorations, and nucleocapsid proteins in packaged core. Phage decorated with spike trimers was found to be the most potent vaccine candidate in animal models. Without any adjuvant, this vaccine stimulated robust immune responses, both T helper cell 1 (TH1) and TH2 immunoglobulin G subclasses, blocked virus-receptor interactions, neutralized viral infection, and conferred complete protection against viral challenge. This new nanovaccine design framework might allow the rapid deployment of effective adjuvant-free phage-based vaccines against any emerging pathogen in the future.
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Affiliation(s)
- Jingen Zhu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Neeti Ananthaswamy
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Swati Jain
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Himanshu Batra
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Wei-Chun Tang
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | | | | | | | - Paul B. Kilgore
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jian Sha
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ashok K. Chopra
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
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Gupta P, Singh MP, Goyal K, Tripti P, Ansari MI, Obli Rajendran V, Dhama K, Malik YS. Bats and viruses: a death-defying friendship. Virusdisease 2021; 32:467-479. [PMID: 34518804 PMCID: PMC8426161 DOI: 10.1007/s13337-021-00716-0] [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: 03/23/2021] [Accepted: 06/19/2021] [Indexed: 01/10/2023] Open
Abstract
Bats have a primeval evolutionary origin and have adopted various survival methods. They have played a central role in the emergence of various viral diseases. The sustenance of a plethora of virus species inside them has been an earnest area of study. This review explains how the evolution of viruses in bats has been linked to their metabolic pathways, flight abilities, reproductive abilities and colonization behaviors. The utilization of host immune response by DNA and RNA viruses is a commencement of the understanding of differences in the impact of viral infection in bats from other mammals. Rabies virus and other lyssa viruses have had long documented history as bat viruses. While many others like Ebola virus, Nipah virus, Hantavirus, SARS-CoV, MERS-CoV and other new emerging viruses like Sosuga virus, Menangle and Tioman virus are now being studied extensively for their transmission in new hosts. The ongoing pandemic SARS-CoV-2 virus has also been implicated to be originated from bats. Certain factors have been linked to spillover events while the scope of entitlement of other conditions in the spread of diseases from bats still exists. However, certain physiological and ecological parameters have been linked to specific transmission patterns, and more definite proofs are awaited for establishing these connections.
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Affiliation(s)
- Parakriti Gupta
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Mini P. Singh
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kapil Goyal
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pande Tripti
- Biological Standardization Division, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Mohd Ikram Ansari
- Department of Biosciences, Integral University, Dasauli, Kursi Road, Lucknow, Uttar Pradesh 226026 India
| | - Vinodhkumar Obli Rajendran
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Bareilly, Uttar Pradesh 243 122 India
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab 141 004 India
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Jaworski E, Langsjoen RM, Mitchell B, Judy B, Newman P, Plante JA, Plante KS, Miller AL, Zhou Y, Swetnam D, Sotcheff S, Morris V, Saada N, Machado R, McConnell A, Widen S, Thompson J, Dong J, Ren P, Pyles RB, Ksiazek T, Menachery VD, Weaver SC, Routh A. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.10.434828. [PMID: 33758846 PMCID: PMC7987005 DOI: 10.1101/2021.03.10.434828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for Next-Generation Sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called 'Tiled-ClickSeq', which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5'UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.
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Affiliation(s)
- Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- ClickSeq Technologies LLC, Galveston, TX, USA
| | - Rose M. Langsjoen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Brooke Mitchell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Barbara Judy
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Patrick Newman
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
| | - Jessica A. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Aaron L. Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Daniele Swetnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Victoria Morris
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Nehad Saada
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Rafael Machado
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Allan McConnell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Steve Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jill Thompson
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jianli Dong
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Rick B. Pyles
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas Ksiazek
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
| | - Vineet D. Menachery
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA
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Sun G, Cui Q, Garcia G, Wang C, Zhang M, Arumugaswami V, Riggs AD, Shi Y. Comparative transcriptomic analysis of SARS-CoV-2 infected cell model systems reveals differential innate immune responses. Sci Rep 2021; 11:17146. [PMID: 34433867 PMCID: PMC8387424 DOI: 10.1038/s41598-021-96462-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022] Open
Abstract
The transcriptome of SARS-CoV-2-infected cells that reflects the interplay between host and virus has provided valuable insights into mechanisms underlying SARS-CoV-2 infection and COVID-19 disease progression. In this study, we show that SARS-CoV-2 can establish a robust infection in HEK293T cells that overexpress human angiotensin-converting enzyme 2 (hACE2) without triggering significant host immune response. Instead, endoplasmic reticulum stress and unfolded protein response-related pathways are predominantly activated. By comparing our data with published transcriptome of SARS-CoV-2 infection in other cell lines, we found that the expression level of hACE2 directly correlates with the viral load in infected cells but not with the scale of immune responses. Only cells that express high level of endogenous hACE2 exhibit an extensive immune attack even with a low viral load. Therefore, the infection route may be critical for the extent of the immune response, thus the severity of COVID-19 disease status.
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Affiliation(s)
- Guihua Sun
- Department of Diabetes Complications & Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Qi Cui
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA
| | - Cheng Wang
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Mingzi Zhang
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, 90095, USA.
| | - Arthur D Riggs
- Department of Diabetes Complications & Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
| | - Yanhong Shi
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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Wu X, Zhang J. Exploration of spatial-temporal varying impacts on COVID-19 cumulative case in Texas using geographically weighted regression (GWR). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:43732-43746. [PMID: 33837938 PMCID: PMC8035058 DOI: 10.1007/s11356-021-13653-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 05/21/2023]
Abstract
Since COVID-19 is extremely threatening to human health, it is significant to determine its impact factors to curb the virus spread. To tackle the complexity of COVID-19 expansion on a spatial-temporal scale, this research appropriately analyzed the spatial-temporal heterogeneity at the county-level in Texas. First, the impact factors of COVID-19 are captured on social, economic, and environmental multiple facets, and the communality is extracted through principal component analysis (PCA). Second, this research uses COVID-19 cumulative case as the dependent variable and the common factors as the independent variables. According to the virus prevalence hierarchy, the spatial-temporal disparity is categorized into four quarters in the GWR analysis model. The findings exhibited that GWR models provide higher fitness and more geodata-oriented information than OLS models. In El Paso, Odessa, Midland, Randall, and Potter County areas in Texas, population, hospitalization, and age structures are presented as static, positive influences on COVID-19 cumulative cases, indicating that they should adopt stringent strategies in curbing COVID-19. Winter is the most sensitive season for the virus spread, implying that the last quarter should be paid more attention to preventing the virus and taking precautions. This research is expected to provide references for the prevention and control of COVID-19 and related infectious diseases and evidence for disease surveillance and response systems to facilitate the appropriate uptake and reuse of geographical data.
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Affiliation(s)
- Xiu Wu
- Department of Geography, Texas State University, 601 University drive, San Marcos, 78666 TX USA
| | - Jinting Zhang
- School of Resource and Environmental Science, Wuhan University, 129 Luoyu Rd., Wuhan, 430079 Hubei China
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42
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Saleh AA, Saad MA, Ryan I, Amin M, Shindy MI, Hassan WA, Samir M, Khattab AA, Abdelgayed SS, Seadawy MG, Fahmy HM, Amer K. Safety and immunogenicity evaluation of inactivated whole-virus-SARS-COV-2 as emerging vaccine development in Egypt. Antib Ther 2021; 4:135-143. [PMID: 34286215 PMCID: PMC8287638 DOI: 10.1093/abt/tbab012] [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: 03/15/2021] [Revised: 05/26/2021] [Accepted: 06/21/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Current worldwide pandemic coronavirus disease 2019 (COVID-19) with high numbers of mortality rates and huge economic problems require an urgent demand for safe and effective vaccine development. Inactivated SARS-CoV2 vaccine with alum. Hydroxide can play an important role in reducing the impacts of the COVID-19 pandemic. In this study, vaccine efficacy was evaluated through the detection of the neutralizing antibodies that protect mice from challenge with SARS-CoV 2 3 weeks after the second dose. We conclude that the vaccine described here has safety and desirable properties, and our data support further development and plans for clinical trials. METHODS Characterized SARS-COV-2 strain, severe acute respiratory syndrome coronavirus 2 isolates (SARS-CoV-2/human/EGY/Egy-SERVAC/2020) with accession numbers; MT981440; MT981439; MT981441; MT974071; MT974069; and MW250352 at GenBank were isolated from Egyptian patients SARS-CoV-2-positive. Development of inactivated vaccine was carried out in a BSL-3 facilities and the immunogenicity was determined in mice at two doses (55 and 100 μg per dose). RESULTS The distinct cytopathic effect induced by SARS-COV-2 propagation on Vero cell monolayers and the viral particles were identified as Coronaviridae by transmission electron microscopy and RT-PCR on infected cells cultures. Immunogenicity of the developed vaccine indicated the high antigen-binding and neutralizing antibody titers, regardless of the dose concentration, with excellent safety profiles and no deaths or clinical symptoms in mice groups. The efficacy of the inactivated vaccine formulation was tested by the wild virus challenge of the vaccinated mice and viral replication detection in lung tissues. CONCLUSIONS Vaccinated mice recorded complete protection from challenge infection via inhibition of SARS-COV-2 replication in the lung tissues of mice following virus challenge, regardless of the level of serum neutralizing antibodies. This finding will support future trials for the evaluation of an applicable SARS-CoV-2 vaccine candidate.
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Affiliation(s)
- Amani A Saleh
- A.R.C. Veterinary Serum Vaccine Research Institute (VSVRI), 131 El-Sekka El-Bidaa st. Cairo 11384, Egypt
| | - Mohamed A Saad
- A.R.C. Veterinary Serum Vaccine Research Institute (VSVRI), 131 El-Sekka El-Bidaa st. Cairo 11384, Egypt
| | - Islam Ryan
- Egyptian Army Veterinary Corps, NR Nassar City, Cairo 11765, Egypt
| | - Magdy Amin
- Military Medical Services, Kobry El Qubba. Cairo 11766, Egypt
| | - Mohamed I Shindy
- Egyptian Army Veterinary Corps, NR Nassar City, Cairo 11765, Egypt
| | - Wael A Hassan
- Egypt Center for Research and Regenerative Medicine, 3A Ramses Extension st. Cairo, 11759, Egypt
| | - Mahmoud Samir
- Egypt Center for Research and Regenerative Medicine, 3A Ramses Extension st. Cairo, 11759, Egypt
| | - Ayman A Khattab
- Egypt Center for Research and Regenerative Medicine, 3A Ramses Extension st. Cairo, 11759, Egypt
| | - Sherein S Abdelgayed
- Department of pathology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | | | - Hossam M Fahmy
- Faculty of Medicine, Ain Shams University, Abbasia, Cairo 11591, Egypt
| | - Khaled Amer
- Egypt Center for Research and Regenerative Medicine, 3A Ramses Extension st. Cairo, 11759, Egypt
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Sampaio NG, Chauveau L, Hertzog J, Bridgeman A, Fowler G, Moonen JP, Dupont M, Russell RA, Noerenberg M, Rehwinkel J. The RNA sensor MDA5 detects SARS-CoV-2 infection. Sci Rep 2021; 11:13638. [PMID: 34211037 PMCID: PMC8249624 DOI: 10.1038/s41598-021-92940-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/16/2021] [Indexed: 02/08/2023] Open
Abstract
Human cells respond to infection by SARS-CoV-2, the virus that causes COVID-19, by producing cytokines including type I and III interferons (IFNs) and proinflammatory factors such as IL6 and TNF. IFNs can limit SARS-CoV-2 replication but cytokine imbalance contributes to severe COVID-19. We studied how cells detect SARS-CoV-2 infection. We report that the cytosolic RNA sensor MDA5 was required for type I and III IFN induction in the lung cancer cell line Calu-3 upon SARS-CoV-2 infection. Type I and III IFN induction further required MAVS and IRF3. In contrast, induction of IL6 and TNF was independent of the MDA5-MAVS-IRF3 axis in this setting. We further found that SARS-CoV-2 infection inhibited the ability of cells to respond to IFNs. In sum, we identified MDA5 as a cellular sensor for SARS-CoV-2 infection that induced type I and III IFNs.
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Affiliation(s)
- Natalia G Sampaio
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Lise Chauveau
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jonny Hertzog
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Gerissa Fowler
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jurgen P Moonen
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Maeva Dupont
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Rebecca A Russell
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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44
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Campos RK, Camargos VN, Azar SR, Haines CA, Eyzaguirre EJ, Rossi SL. SARS-CoV-2 Infects Hamster Testes. Microorganisms 2021; 9:1318. [PMID: 34204370 PMCID: PMC8235703 DOI: 10.3390/microorganisms9061318] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 01/03/2023] Open
Abstract
The COVID-19 pandemic continues to affect millions of people worldwide. Although SARS-CoV-2 is a respiratory virus, there is growing concern that the disease could cause damage and pathology outside the lungs, including in the genital tract. Studies suggest that SARS-CoV-2 infection can damage the testes and reduce testosterone levels, but the underlying mechanisms are unknown and evidence of virus replication in testicular cells is lacking. We infected golden Syrian hamsters intranasally, a model for mild human COVID-19, and detected viral RNA in testes samples without histopathological changes up to one month post-infection. Using an ex vivo infection model, we detected SARS-CoV-2 replication in hamster testicular cells. Taken together, our data raise the possibility that testes damage observed in severe cases of COVID-19 could be partly explained by direct SARS-CoV-2 infection of the testicular cells.
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Affiliation(s)
- Rafael K. Campos
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (R.K.C.); (C.A.H.)
| | - Vidyleison N. Camargos
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; (V.N.C.); (S.R.A.); (E.J.E.)
| | - Sasha R. Azar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; (V.N.C.); (S.R.A.); (E.J.E.)
| | - Clint A. Haines
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (R.K.C.); (C.A.H.)
| | - Eduardo J. Eyzaguirre
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; (V.N.C.); (S.R.A.); (E.J.E.)
| | - Shannan L. Rossi
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (R.K.C.); (C.A.H.)
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; (V.N.C.); (S.R.A.); (E.J.E.)
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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45
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Sharma A, Kontodimas K, Bosmann M. Nanomedicine: A Diagnostic and Therapeutic Approach to COVID-19. Front Med (Lausanne) 2021; 8:648005. [PMID: 34150793 PMCID: PMC8211875 DOI: 10.3389/fmed.2021.648005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 virus is causing devastating morbidity and mortality worldwide. Nanomedicine approaches have a high potential to enhance conventional diagnostics, drugs and vaccines. In fact, lipid nanoparticle/mRNA vaccines are already widely used to protect from COVID-19. In this review, we present an overview of the taxonomy, structure, variants of concern, epidemiology, pathophysiology and detection methods of SARS-CoV-2. The efforts of repurposing, tailoring, and adapting pre-existing medications to battle COVID-19 and the state of vaccine developments are presented. Next, we discuss the broad concepts and limitations of how nanomedicine could address the COVID-19 threat. Nanomaterials are particles in the nanometer scale (10-100 nm) which possess unique properties related to their size, polarity, structural and chemical composition. Nanoparticles can be composed of precious metals (copper, silver, gold), inorganic materials (graphene, silicon), proteins, carbohydrates, lipids, RNA/DNA, or conjugates, combinations and polymers of all of the aforementioned. The advanced biochemical features of these nanoscale particles allow them to directly interact with virions and irreversibly disrupt their structure, which can render a virus incapable of replicating within the host. Virus-neutralizing coats and surfaces impregnated with nanomaterials can enhance personal protective equipment, hand sanitizers and air filter systems. Nanoparticles can enhance drug-based therapies by optimizing uptake, stability, target cell-specific delivery, and magnetic properties. In fact, recent studies have highlighted the potential of nanoparticles in different aspects of the fight against SARS-CoV-2, such as enhancing biosensors and diagnostic tests, drug therapies, designing new delivery mechanisms, and optimizing vaccines. This article summarizes the ongoing research on diagnostic strategies, treatments, and vaccines for COVID-19, while emphasizing the potential of nanoparticle-based pharmaceuticals and vaccines.
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Affiliation(s)
- Arjun Sharma
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Konstantinos Kontodimas
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Markus Bosmann
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
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Kanimozhi G, Pradhapsingh B, Singh Pawar C, Khan HA, Alrokayan SH, Prasad NR. SARS-CoV-2: Pathogenesis, Molecular Targets and Experimental Models. Front Pharmacol 2021; 12:638334. [PMID: 33967772 PMCID: PMC8100521 DOI: 10.3389/fphar.2021.638334] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/26/2021] [Indexed: 02/05/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recent pandemic outbreak threatening human beings worldwide. This novel coronavirus disease-19 (COVID-19) infection causes severe morbidity and mortality and rapidly spreading across the countries. Therefore, there is an urgent need for basic fundamental research to understand the pathogenesis and druggable molecular targets of SARS-CoV-2. Recent sequencing data of the viral genome and X-ray crystallographic data of the viral proteins illustrate potential molecular targets that need to be investigated for structure-based drug design. Further, the SARS-CoV-2 viral pathogen isolated from clinical samples needs to be cultivated and titrated. All of these scenarios demand suitable laboratory experimental models. The experimental models should mimic the viral life cycle as it happens in the human lung epithelial cells. Recently, researchers employing primary human lung epithelial cells, intestinal epithelial cells, experimental cell lines like Vero cells, CaCo-2 cells, HEK-293, H1299, Calu-3 for understanding viral titer values. The human iPSC-derived lung organoids, small intestinal organoids, and blood vessel organoids increase interest among researchers to understand SARS-CoV-2 biology and treatment outcome. The SARS-CoV-2 enters the human lung epithelial cells using viral Spike (S1) protein and human angiotensin-converting enzyme 2 (ACE-2) receptor. The laboratory mouse show poor ACE-2 expression and thereby inefficient SARS-CoV-2 infection. Therefore, there was an urgent need to develop transgenic hACE-2 mouse models to understand antiviral agents' therapeutic outcomes. This review highlighted the viral pathogenesis, potential druggable molecular targets, and suitable experimental models for basic fundamental research.
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Affiliation(s)
- G. Kanimozhi
- Department of Biochemistry, Dharmapuram Gnanambigai Government Arts College for Women, Mayiladuthurai, India
| | - B. Pradhapsingh
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, India
| | - Charan Singh Pawar
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, India
| | - Haseeb A. Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Salman H. Alrokayan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - N. Rajendra Prasad
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, India
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47
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Puhl AC, Fritch EJ, Lane TR, Tse LV, Yount BL, Sacramento CQ, Fintelman-Rodrigues N, Tavella TA, Maranhão Costa FT, Weston S, Logue J, Frieman M, Premkumar L, Pearce KH, Hurst BL, Andrade CH, Levi JA, Johnson NJ, Kisthardt SC, Scholle F, Souza TML, Moorman NJ, Baric RS, Madrid PB, Ekins S. Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine, and Pyronaridine: In Vitro Activity against SARS-CoV-2 and Potential Mechanisms. ACS OMEGA 2021; 6:7454-7468. [PMID: 33778258 PMCID: PMC7992063 DOI: 10.1021/acsomega.0c05996] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/02/2021] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2) is a newly identified virus that has resulted in over 2.5 million deaths globally and over 116 million cases globally in March, 2021. Small-molecule inhibitors that reverse disease severity have proven difficult to discover. One of the key approaches that has been widely applied in an effort to speed up the translation of drugs is drug repurposing. A few drugs have shown in vitro activity against Ebola viruses and demonstrated activity against SARS-CoV-2 in vivo. Most notably, the RNA polymerase targeting remdesivir demonstrated activity in vitro and efficacy in the early stage of the disease in humans. Testing other small-molecule drugs that are active against Ebola viruses (EBOVs) would appear a reasonable strategy to evaluate their potential for SARS-CoV-2. We have previously repurposed pyronaridine, tilorone, and quinacrine (from malaria, influenza, and antiprotozoal uses, respectively) as inhibitors of Ebola and Marburg viruses in vitro in HeLa cells and mouse-adapted EBOV in mice in vivo. We have now tested these three drugs in various cell lines (VeroE6, Vero76, Caco-2, Calu-3, A549-ACE2, HUH-7, and monocytes) infected with SARS-CoV-2 as well as other viruses (including MHV and HCoV 229E). The compilation of these results indicated considerable variability in antiviral activity observed across cell lines. We found that tilorone and pyronaridine inhibited the virus replication in A549-ACE2 cells with IC50 values of 180 nM and IC50 198 nM, respectively. We used microscale thermophoresis to test the binding of these molecules to the spike protein, and tilorone and pyronaridine bind to the spike receptor binding domain protein with K d values of 339 and 647 nM, respectively. Human Cmax for pyronaridine and quinacrine is greater than the IC50 observed in A549-ACE2 cells. We also provide novel insights into the mechanism of these compounds which is likely lysosomotropic.
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Affiliation(s)
- Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ethan J. Fritch
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Thomas R. Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Longping V. Tse
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Boyd L. Yount
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Carolina Q. Sacramento
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Tatyana Almeida Tavella
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Fabio Trindade Maranhão Costa
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Stuart Weston
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - James Logue
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Matthew Frieman
- Department
of Microbiology and Immunology, University
of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Lakshmanane Premkumar
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center
for Integrative Chemical Biology and Drug Discovery, Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- UNC
Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599, United States
| | - Brett L. Hurst
- Institute
for Antiviral Research, Utah State University, Logan, Utah 84322, United States
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah 84322, United States
| | - Carolina Horta Andrade
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacinto da Silva, Department
of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, São Paulo 13083-970, Brazil
- LabMol—Laboratory of Molecular Modeling
and Drug Design, Faculdade
de Farmácia, Universidade Federal
de Goiás, Goiânia,
GO 74605-170, Brazil
| | - James A. Levi
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nicole J. Johnson
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Samantha C. Kisthardt
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Frank Scholle
- Department of Biological Sciences, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thiago Moreno L. Souza
- Laboratório
de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ 21040-900, Brazil
- Centro
De Desenvolvimento Tecnológico Em Saúde (CDTS), Fiocruz, Rio de
Janeiro 21040-900, Brazil
| | - Nathaniel John Moorman
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
- Center
for Integrative Chemical Biology and Drug Discovery, Chemical Biology
and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Discovery
Initiative, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Ralph S. Baric
- Department
of Microbiology and Immunology, University
of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department
of Epidemiology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Discovery
Initiative, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Peter B. Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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48
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Synowiec A, Szczepański A, Barreto-Duran E, Lie LK, Pyrc K. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): a Systemic Infection. Clin Microbiol Rev 2021; 34:e00133-20. [PMID: 33441314 PMCID: PMC7849242 DOI: 10.1128/cmr.00133-20] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
To date, seven identified coronaviruses (CoVs) have been found to infect humans; of these, three highly pathogenic variants have emerged in the 21st century. The newest member of this group, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected at the end of 2019 in Hubei province, China. Since then, this novel coronavirus has spread worldwide, causing a pandemic; the respiratory disease caused by the virus is called coronavirus disease 2019 (COVID-19). The clinical presentation ranges from asymptomatic to mild respiratory tract infections and influenza-like illness to severe disease with accompanying lung injury, multiorgan failure, and death. Although the lungs are believed to be the site at which SARS-CoV-2 replicates, infected patients often report other symptoms, suggesting the involvement of the gastrointestinal tract, heart, cardiovascular system, kidneys, and other organs; therefore, the following question arises: is COVID-19 a respiratory or systemic disease? This review aims to summarize existing data on the replication of SARS-CoV-2 in different tissues in both patients and ex vivo models.
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Affiliation(s)
- Aleksandra Synowiec
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur Szczepański
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Emilia Barreto-Duran
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Laurensius Kevin Lie
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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49
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Castaño N, Cordts SC, Kurosu Jalil M, Zhang KS, Koppaka S, Bick AD, Paul R, Tang SKY. Fomite Transmission, Physicochemical Origin of Virus-Surface Interactions, and Disinfection Strategies for Enveloped Viruses with Applications to SARS-CoV-2. ACS OMEGA 2021; 6:6509-6527. [PMID: 33748563 PMCID: PMC7944398 DOI: 10.1021/acsomega.0c06335] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/19/2021] [Indexed: 05/07/2023]
Abstract
Inanimate objects or surfaces contaminated with infectious agents, referred to as fomites, play an important role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The long persistence of viruses (hours to days) on surfaces calls for an urgent need for effective surface disinfection strategies to intercept virus transmission and the spread of diseases. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, is important for understanding how diseases are transmitted and for developing effective intervention strategies. This review summarizes the current knowledge and underlying physicochemical processes of virus transmission, in particular via fomites, and common disinfection approaches. Gaps in knowledge and the areas in need of further research are also identified. The review focuses on SARS-CoV-2, but discussion of related viruses is included to provide a more comprehensive review given that much remains unknown about SARS-CoV-2. Our aim is that this review will provide a broad survey of the issues involved in fomite transmission and intervention to a wide range of readers to better enable them to take on the open research challenges.
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Affiliation(s)
- Nicolas Castaño
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Seth C. Cordts
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Myra Kurosu Jalil
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Kevin S. Zhang
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Saisneha Koppaka
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Alison D. Bick
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Rajorshi Paul
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Sindy K. Y. Tang
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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50
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Noval MG, Kaczmarek ME, Koide A, Rodriguez-Rodriguez BA, Louie P, Tada T, Hattori T, Panchenko T, Romero LA, Teng KW, Bazley A, de Vries M, Samanovic MI, Weiser JN, Aifantis I, Cangiarella J, Mulligan MJ, Desvignes L, Dittmann M, Landau NR, Aguero-Rosenfeld M, Koide S, Stapleford KA. Antibody isotype diversity against SARS-CoV-2 is associated with differential serum neutralization capacities. Sci Rep 2021; 11:5538. [PMID: 33692390 PMCID: PMC7946906 DOI: 10.1038/s41598-021-84913-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 02/23/2021] [Indexed: 12/23/2022] Open
Abstract
Understanding antibody responses to SARS-CoV-2 is indispensable for the development of containment measures to overcome the current COVID-19 pandemic. Recent studies showed that serum from convalescent patients can display variable neutralization capacities. Still, it remains unclear whether there are specific signatures that can be used to predict neutralization. Here, we performed a detailed analysis of sera from a cohort of 101 recovered healthcare workers and we addressed their SARS-CoV-2 antibody response by ELISA against SARS-CoV-2 Spike receptor binding domain and nucleoprotein. Both ELISA methods detected sustained levels of serum IgG against both antigens. Yet, the majority of individuals from our cohort generated antibodies with low neutralization capacity and only 6% showed high neutralizing titers against both authentic SARS-CoV-2 virus and the Spike pseudotyped virus. Interestingly, higher neutralizing sera correlate with detection of -IgG, IgM and IgA antibodies against both antigens, while individuals with positive IgG alone showed poor neutralization response. These results suggest that having a broader repertoire of antibodies may contribute to more potent SARS-CoV-2 neutralization. Altogether, our work provides a cross sectional snapshot of the SARS-CoV-2 neutralizing antibody response in recovered healthcare workers and provides preliminary evidence that possessing multiple antibody isotypes can play an important role in predicting SARS-CoV-2 neutralization.
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Affiliation(s)
- Maria G Noval
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, New York, NY, 10016, USA
| | - Maria E Kaczmarek
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, New York, NY, 10016, USA
| | - Akiko Koide
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | | | - Ping Louie
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, New York, NY, 10016, USA
| | - Takamitsu Hattori
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
- Department of Biochemistry and Pharmacology, NYU Grossman School of Medicine, 521 1st Avenue, New York, NY, 10016, USA
| | - Tatyana Panchenko
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Larizbeth A Romero
- Department of Biochemistry and Pharmacology, NYU Grossman School of Medicine, 521 1st Avenue, New York, NY, 10016, USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
| | - Andrew Bazley
- Department of Biochemistry and Pharmacology, NYU Grossman School of Medicine, 521 1st Avenue, New York, NY, 10016, USA
| | - Maren de Vries
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, New York, NY, 10016, USA
| | - Marie I Samanovic
- New York University Langone Vaccine Center and New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jeffrey N Weiser
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, New York, NY, 10016, USA
| | - Ioannis Aifantis
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Joan Cangiarella
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Mark J Mulligan
- New York University Langone Vaccine Center and New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ludovic Desvignes
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, 10016, USA
- New York University Langone Vaccine Center and New York University Grossman School of Medicine, New York, NY, 10016, USA
- Office of Science and Research, NYU Langone Health, New York, NY, 10016, USA
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, New York, NY, 10016, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, New York, NY, 10016, USA
| | | | - Shohei Koide
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA.
- Department of Biochemistry and Pharmacology, NYU Grossman School of Medicine, 521 1st Avenue, New York, NY, 10016, USA.
| | - Kenneth A Stapleford
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, New York, NY, 10016, USA.
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