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Wiriyachaiporn N, Kongrueng J, Sukkuea K, Tanrattanawong R, Vanichtanankul J, Saeyang T, Jantra T, Japrung D, Maneeprakorn W, Bamrungsap S, Janchompoo P, Pasomsub E. Characterizing a visual lateral flow device for rapid SARS-CoV-2 virus protein detection: pre-clinical and system assessment. Anal Methods 2024; 16:2740-2750. [PMID: 38634326 DOI: 10.1039/d3ay02075d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections have affected more than 769 million individuals worldwide over the last few years. Although the pandemic is transitioning into an endemic, the COVID-19 outbreak is still a global concern. A rapid screening platform is needed for effective preventive and control measures. Herein, a visual rapid lateral flow platform for SARS-CoV-2 nucleocapsid protein detection is developed. Under optimal conditions, the system demonstrated good detection sensitivity and selectivity against tested respiratory viruses. The system provides direct visual detection with a limit of 0.7 ng of the nucleocapsid protein per mL of a sample (0.7 ng mL-1) within 15 minutes. Further, a correlation between direct visual detection and semi-quantitative analysis using a reader showed a similar detection limit (R2 = 0.9571). The repeatability and reproducibility studies highlighted the potential of the system for the rapid screening of SARS-CoV-2 infection, with variations within 5% and 10% at high and low protein concentrations, respectively. Subsequent pre-clinical validation to correlate the performance with the standard molecular approach (RT-PCR) using 170 nasopharyngeal swabs demonstrated 98% estimated sensitivity (95% CI, 89.35-99.95%) and 100% specificity (95% CI, 96.38-100%). The positive and negative predictive values were reported to be 100% and 99%, respectively, with an accuracy of 99.3%. With high viral load samples (Ct value ≤25, n = 47), the system demonstrated 100% detection sensitivity and specificity. The proposed technique provides a valuable platform for potential use in rapid screening, particularly during pandemics, where diagnostic capacity and mass screening are crucial.
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Affiliation(s)
- Natpapas Wiriyachaiporn
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Jetnapang Kongrueng
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Kannika Sukkuea
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Rattana Tanrattanawong
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Jarunee Vanichtanankul
- National Center of Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Thanaya Saeyang
- National Center of Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Tararat Jantra
- National Center of Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Weerakanya Maneeprakorn
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Suwussa Bamrungsap
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Pareena Janchompoo
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar EH, Abu Zeid IM, Bouback TA, Bamagoos A, Uversky VN, Rubio-Casillas A, Redwan EM. Intrinsic factors behind long COVID: IV. Hypothetical roles of the SARS-CoV-2 nucleocapsid protein and its liquid-liquid phase separation. J Cell Biochem 2024; 125:e30530. [PMID: 38349116 DOI: 10.1002/jcb.30530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 03/12/2024]
Abstract
When the SARS-CoV-2 virus infects humans, it leads to a condition called COVID-19 that has a wide spectrum of clinical manifestations, from no symptoms to acute respiratory distress syndrome. The virus initiates damage by attaching to the ACE-2 protein on the surface of endothelial cells that line the blood vessels and using these cells as hosts for replication. Reactive oxygen species levels are increased during viral replication, which leads to oxidative stress. About three-fifths (~60%) of the people who get infected with the virus eradicate it from their body after 28 days and recover their normal activity. However, a large fraction (~40%) of the people who are infected with the virus suffer from various symptoms (anosmia and/or ageusia, fatigue, cough, myalgia, cognitive impairment, insomnia, dyspnea, and tachycardia) beyond 12 weeks and are diagnosed with a syndrome called long COVID. Long-term clinical studies in a group of people who contracted SARS-CoV-2 have been contrasted with a noninfected matched group of people. A subset of infected people can be distinguished by a set of cytokine markers to have persistent, low-grade inflammation and often self-report two or more bothersome symptoms. No medication can alleviate their symptoms efficiently. Coronavirus nucleocapsid proteins have been investigated extensively as potential drug targets due to their key roles in virus replication, among which is their ability to bind their respective genomic RNAs for incorporation into emerging virions. This review highlights basic studies of the nucleocapsid protein and its ability to undergo liquid-liquid phase separation. We hypothesize that this ability of the nucleocapsid protein for phase separation may contribute to long COVID. This hypothesis unlocks new investigation angles and could potentially open novel avenues for a better understanding of long COVID and treating this condition.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab H Mattar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Moscow Region, Russia
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, Jalisco, Mexico
- Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, Jalisco, Mexico
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
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3
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Zhao H, Wu D, Hassan SA, Nguyen A, Chen J, Piszczek G, Schuck P. A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins. Sci Adv 2023; 9:eadg6473. [PMID: 37018390 PMCID: PMC10075959 DOI: 10.1126/sciadv.adg6473] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/07/2023] [Indexed: 06/01/2023]
Abstract
The nucleocapsid (N-)protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a key role in viral assembly and scaffolding of the viral RNA. It promotes liquid-liquid phase separation (LLPS), forming dense droplets that support the assembly of ribonucleoprotein particles with as-of-yet unknown macromolecular architecture. Combining biophysical experiments, molecular dynamics simulations, and analysis of the mutational landscape, we describe a heretofore unknown oligomerization site that contributes to LLPS, is required for the assembly of higher-order protein-nucleic acid complexes, and is coupled to large-scale conformational changes of N-protein upon nucleic acid binding. The self-association interface is located in a leucine-rich sequence of the intrinsically disordered linker between N-protein folded domains and formed by transient helices assembling into trimeric coiled-coils. Critical residues stabilizing hydrophobic and electrostatic interactions between adjacent helices are highly protected against mutations in viable SARS-CoV-2 genomes, and the oligomerization motif is conserved across related coronaviruses, thus presenting a target for antiviral therapeutics.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergio A. Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Chau BA, Chen V, Cochrane AW, Parent LJ, Mouland AJ. Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication. Cell Rep 2023; 42:111968. [PMID: 36640305 PMCID: PMC9790868 DOI: 10.1016/j.celrep.2022.111968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due to their central roles in virus replication, among which is their capacity to bind their respective genomic RNAs for packaging into nascent virions. This review focuses on fundamental studies of these nucleocapsid proteins and how their intrinsic abilities to condense through liquid-liquid phase separation (LLPS) contribute to viral replication. Therapeutic targeting of these condensates and methodological advances are also described to address future questions on how phase separation contributes to viral replication.
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Affiliation(s)
- Bao-An Chau
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Venessa Chen
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alan W Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leslie J Parent
- Division of Infectious Diseases and Epidemiology, Departments of Medicine and Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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5
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Castanha PMS, Tuttle DJ, Kitsios GD, Jacobs JL, Braga-Neto U, Duespohl M, Rathod S, Marti MM, Wheeler S, Naqvi A, Staines B, Mellors J, Morris A, McVerry BJ, Shah F, Schaefer C, Macatangay BJC, Methe B, Fernandez CA, Barratt-Boyes SM, Burke D, Marques ETA. Contribution of Coronavirus-Specific Immunoglobulin G Responses to Complement Overactivation in Patients with Severe Coronavirus Disease 2019. J Infect Dis 2022; 226:766-777. [PMID: 35267024 PMCID: PMC8992249 DOI: 10.1093/infdis/jiac091] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/07/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Excessive complement activation has been implicated in the pathogenesis of coronavirus disease 2019 (COVID-19), but the mechanisms leading to this response remain unclear. METHODS We measured plasma levels of key complement markers, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and antibodies against SARS-CoV-2 and seasonal human common cold coronaviruses (CCCs) in hospitalized patients with COVID-19 of moderate (n = 18) and critical severity (n = 37) and in healthy controls (n = 10). RESULTS We confirmed that complement activation is systemically increased in patients with COVID-19 and is associated with a worse disease outcome. We showed that plasma levels of C1q and circulating immune complexes were markedly increased in patients with severe COVID-19 and correlated with higher immunoglobulin (Ig) G titers, greater complement activation, and higher disease severity score. Additional analyses showed that the classical pathway was the main arm responsible for augmented complement activation in severe patients. In addition, we demonstrated that a rapid IgG response to SARS-CoV-2 and an anamnestic IgG response to the nucleoprotein of the CCCs were strongly correlated with circulating immune complex levels, complement activation, and disease severity. CONCLUSIONS These findings indicate that early, nonneutralizing IgG responses may play a key role in complement overactivation in severe COVID-19. Our work underscores the urgent need to develop therapeutic strategies to modify complement overactivation in patients with COVID-19.
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Affiliation(s)
- Priscila M S Castanha
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dylan J Tuttle
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ulisses Braga-Neto
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Matthew Duespohl
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sanjay Rathod
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michelle M Marti
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sarah Wheeler
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brittany Staines
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Faraaz Shah
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bernard J C Macatangay
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Barbara Methe
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christian A Fernandez
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Simon M Barratt-Boyes
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Donald Burke
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ernesto T A Marques
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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6
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Ino Y, Nishi M, Yamaoka Y, Miyakawa K, Jeremiah SS, Osada M, Kimura Y, Ryo A. Phosphopeptide enrichment using Phos-tag technology reveals functional phosphorylation of the nucleocapsid protein of SARS-CoV-2. J Proteomics 2022; 255:104501. [PMID: 35093569 PMCID: PMC8800104 DOI: 10.1016/j.jprot.2022.104501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 11/28/2022]
Abstract
Phosphorylation of viral proteins serves as a regulatory mechanism during the intracellular life cycle of infected viruses. There is therefore a pressing need to develop a method to efficiently purify and enrich phosphopeptides derived from viral particles in biological samples. In this study, we utilized Phos-tag technology to analyze the functional phosphorylation of the nucleocapsid protein (N protein; NP) of severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Viral particles were collected from culture supernatants of SARS-CoV-2-infected VeroE6/TMPRSS2 cells by ultracentrifugation, and phosphopeptides were purified by Phos-tag magnetic beads for LC-MS/MS analysis. Analysis revealed that NP was reproducibly phosphorylated at serine 79 (Ser79). Multiple sequence alignment and phylogenetic analysis showed that the Ser79 was a distinct phospho-acceptor site in SARS-CoV-2 but not in other beta-coronaviruses. We also found that the prolyl-isomerase Pin1 bound to the phosphorylated Ser79 in NP and positively regulated the production of viral particles. These results suggest that SARS-CoV-2 may have acquired the potent virus-host interaction during its evolution mediated by viral protein phosphorylation. Moreover, Phos-tag technology can provide a useful means for analyzing the functional phosphorylation of viral proteins. Significance In this study, we aimed to investigate the functional phosphorylation of SARS-CoV-2 NP. For this purpose, we used Phos-tag technology to purify and enrich virus-derived phosphopeptides with high selectivity and reproducibility. This method can be particularly useful in analyzing viral phosphopeptides from cell culture supernatants that often contain high concentrations of fetal bovine serum and supplements. We newly identified an NP phosphorylation site at Ser79, which is important for Pin1 binding. Furthermore, we showed that the interaction between Pin1 and phosphorylated NP could enhance viral replication in a cell culture model.
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Affiliation(s)
- Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Graduate School of Health Sciences, Gunma Paz University, Tonyamachi 1-7-1, Takasaki-shi, Gunma 370-0006, Japan
| | - Mayuko Nishi
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yutaro Yamaoka
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Suzukawa 21, Isehara-shi, Kanagawa 259-1146, Japan
| | - Kei Miyakawa
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Sundararaj Stanleyraj Jeremiah
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Makoto Osada
- Graduate School of Health Sciences, Gunma Paz University, Tonyamachi 1-7-1, Takasaki-shi, Gunma 370-0006, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
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7
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Zhao D, Xu W, Zhang X, Wang X, Ge Y, Yuan E, Xiong Y, Wu S, Li S, Wu N, Tian T, Feng X, Shu H, Lang P, Li J, Zhu F, Shen X, Li H, Li P, Zeng J. Understanding the phase separation characteristics of nucleocapsid protein provides a new therapeutic opportunity against SARS-CoV-2. Protein Cell 2021; 12:734-740. [PMID: 33770364 PMCID: PMC7994959 DOI: 10.1007/s13238-021-00832-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China
| | - Weifan Xu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaofan Zhang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaoting Wang
- Silexon AI Technology Co., Ltd, Nanjing, 210033, China
| | - Yiyue Ge
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, 210009, China
| | - Enming Yuan
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuanpeng Xiong
- Bioinformatics Division, BNRIST/Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Shenyang Wu
- Protein Preparation and Identification Facility, Technology Center for Protein Science, Tsinghua University, Beijing, 100084, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China
| | - Nian Wu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China
| | - Tingzhong Tian
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaolong Feng
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hantao Shu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China
| | - Peng Lang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China
| | - Jingxin Li
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, 210009, China
| | - Fengcai Zhu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, 210009, China
- Center for Global Health, Nanjing Medical University, Nanjing, 210009, China
| | - Xiaokun Shen
- Convalife (Shanghai) Co., Ltd, Shanghai, 201203, China
| | - Haitao Li
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, 100084, China.
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8
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Forsythe HM, Rodriguez Galvan J, Yu Z, Pinckney S, Reardon P, Cooley RB, Zhu P, Rolland AD, Prell JS, Barbar E. Multivalent binding of the partially disordered SARS-CoV-2 nucleocapsid phosphoprotein dimer to RNA. Biophys J 2021; 120:2890-2901. [PMID: 33794152 PMCID: PMC8007181 DOI: 10.1016/j.bpj.2021.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/16/2021] [Accepted: 03/25/2021] [Indexed: 12/17/2022] Open
Abstract
The nucleocapsid phosphoprotein N plays critical roles in multiple processes of the severe acute respiratory syndrome coronavirus 2 infection cycle: it protects and packages viral RNA in N assembly, interacts with the inner domain of spike protein, binds to structural membrane (M) protein during virion packaging and maturation, and to proteases causing replication of infective virus particle. Even with its importance, very limited biophysical studies are available on the N protein because of its high level of disorder, high propensity for aggregation, and high susceptibility for autoproteolysis. Here, we successfully prepare the N protein and a 1000-nucleotide fragment of viral RNA in large quantities and purity suitable for biophysical studies. A combination of biophysical and biochemical techniques demonstrates that the N protein is partially disordered and consists of an independently folded RNA-binding domain and a dimerization domain, flanked by disordered linkers. The protein assembles as a tight dimer with a dimerization constant of sub-micromolar but can also form transient interactions with other N proteins, facilitating larger oligomers. NMR studies on the ∼100-kDa dimeric protein identify a specific domain that binds 1-1000-nt RNA and show that the N-RNA complex remains highly disordered. Analytical ultracentrifugation, isothermal titration calorimetry, multiangle light scattering, and cross-linking experiments identify a heterogeneous mixture of complexes with a core corresponding to at least 70 dimers of N bound to 1-1000 RNA. In contrast, very weak binding is detected with a smaller construct corresponding to the RNA-binding domain using similar experiments. A model that explains the importance of the bivalent structure of N to its binding on multivalent sites of the viral RNA is presented.
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Affiliation(s)
| | | | - Zhen Yu
- Department of Biochemistry and Biophysics Corvallis, Oregon
| | - Seth Pinckney
- Department of Biochemistry and Biophysics Corvallis, Oregon
| | | | | | - Phillip Zhu
- Department of Biochemistry and Biophysics Corvallis, Oregon
| | - Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon
| | - Elisar Barbar
- Department of Biochemistry and Biophysics Corvallis, Oregon.
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9
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Werner J, Kronberg RM, Stachura P, Ostermann PN, Müller L, Schaal H, Bhatia S, Kather JN, Borkhardt A, Pandyra AA, Lang KS, Lang PA. Deep Transfer Learning Approach for Automatic Recognition of Drug Toxicity and Inhibition of SARS-CoV-2. Viruses 2021; 13:v13040610. [PMID: 33918368 PMCID: PMC8066066 DOI: 10.3390/v13040610] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes COVID-19 and is responsible for the ongoing pandemic. Screening of potential antiviral drugs against SARS-CoV-2 depend on in vitro experiments, which are based on the quantification of the virus titer. Here, we used virus-induced cytopathic effects (CPE) in brightfield microscopy of SARS-CoV-2-infected monolayers to quantify the virus titer. Images were classified using deep transfer learning (DTL) that fine-tune the last layers of a pre-trained Resnet18 (ImageNet). To exclude toxic concentrations of potential drugs, the network was expanded to include a toxic score (TOX) that detected cell death (CPETOXnet). With this analytic tool, the inhibitory effects of chloroquine, hydroxychloroquine, remdesivir, and emetine were validated. Taken together we developed a simple method and provided open access implementation to quantify SARS-CoV-2 titers and drug toxicity in experimental settings, which may be adaptable to assays with other viruses. The quantification of virus titers from brightfield images could accelerate the experimental approach for antiviral testing.
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Affiliation(s)
- Julia Werner
- Department of Molecular Medicine II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (J.W.); (R.M.K.); (P.S.)
| | - Raphael M. Kronberg
- Department of Molecular Medicine II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (J.W.); (R.M.K.); (P.S.)
- Mathematical Modelling of Biological Systems, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Pawel Stachura
- Department of Molecular Medicine II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (J.W.); (R.M.K.); (P.S.)
| | - Philipp N. Ostermann
- Institute of Virology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (P.N.O.); (L.M.); (H.S.)
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (P.N.O.); (L.M.); (H.S.)
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (P.N.O.); (L.M.); (H.S.)
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.B.); (A.B.); (A.A.P.)
| | - Jakob N. Kather
- Department of Medicine III, University Hospital RWTH Aachen, 52074 Aachen, Germany;
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.B.); (A.B.); (A.A.P.)
| | - Aleksandra A. Pandyra
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (S.B.); (A.B.); (A.A.P.)
| | - Karl S. Lang
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Philipp A. Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (J.W.); (R.M.K.); (P.S.)
- Correspondence:
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10
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González-González E, Lara-Mayorga IM, Rodríguez-Sánchez IP, Zhang YS, Martínez-Chapa SO, Santiago GTD, Alvarez MM. Colorimetric loop-mediated isothermal amplification (LAMP) for cost-effective and quantitative detection of SARS-CoV-2: the change in color in LAMP-based assays quantitatively correlates with viral copy number. Anal Methods 2021; 13:169-178. [PMID: 33399137 DOI: 10.1039/d0ay01658f] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We demonstrate a loop-mediated isothermal amplification (LAMP) method to detect and amplify SARS-CoV-2 genetic sequences using a set of in-house designed initiators that target regions encoding the N protein. We were able to detect and amplify SARS-CoV-2 nucleic acids in the range of 62 to 2 × 105 DNA copies by this straightforward method. Using synthetic SARS-CoV-2 samples and RNA extracts from patients, we demonstrate that colorimetric LAMP is a quantitative method comparable in diagnostic performance to RT-qPCR (i.e., sensitivity of 92.85% and specificity of 81.25% in a set of 44 RNA extracts from patients analyzed in a hospital setting).
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Affiliation(s)
- Everardo González-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico. and Departamento de Bioingeniería, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico
| | - Itzel Montserrat Lara-Mayorga
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico. and Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico
| | - Iram Pablo Rodríguez-Sánchez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Laboratorio de Fisiología Molecular y Estructural, 66455, San Nicolás de los Garza, NL, Mexico and Alfa Medical Center, Guadalupe, CP 67100, NL, Mexico
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge 02139, MA, USA
| | - Sergio O Martínez-Chapa
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico. and Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico. and Departamento de Bioingeniería, Tecnologico de Monterrey, CP 64849, Monterrey, NL, Mexico
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11
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Fabiani L, Saroglia M, Galatà G, De Santis R, Fillo S, Luca V, Faggioni G, D'Amore N, Regalbuto E, Salvatori P, Terova G, Moscone D, Lista F, Arduini F. Magnetic beads combined with carbon black-based screen-printed electrodes for COVID-19: A reliable and miniaturized electrochemical immunosensor for SARS-CoV-2 detection in saliva. Biosens Bioelectron 2021; 171:112686. [PMID: 33086175 PMCID: PMC7833515 DOI: 10.1016/j.bios.2020.112686] [Citation(s) in RCA: 254] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/28/2020] [Accepted: 10/02/2020] [Indexed: 12/11/2022]
Abstract
The diffusion of novel SARS-CoV-2 coronavirus over the world generated COVID-19 pandemic event as reported by World Health Organization on March 2020. The huge issue is the high infectivity and the absence of vaccine and customised drugs allowing for hard management of this outbreak, thus a rapid and on site analysis is a need to contain the spread of COVID-19. Herein, we developed an electrochemical immunoassay for rapid and smart detection of SARS-CoV-2 coronavirus in saliva. The electrochemical assay was conceived for Spike (S) protein or Nucleocapsid (N) protein detection using magnetic beads as support of immunological chain and secondary antibody with alkaline phosphatase as immunological label. The enzymatic by-product 1-naphtol was detected using screen-printed electrodes modified with carbon black nanomaterial. The analytical features of the electrochemical immunoassay were evaluated using the standard solution of S and N protein in buffer solution and untreated saliva with a detection limit equal to 19 ng/mL and 8 ng/mL in untreated saliva, respectively for S and N protein. Its effectiveness was assessed using cultured virus in biosafety level 3 and in saliva clinical samples comparing the data using the nasopharyngeal swab specimens tested with Real-Time PCR. The agreement of the data, the low detection limit achieved, the rapid analysis (30 min), the miniaturization, and portability of the instrument combined with the easiness to use and no-invasive sampling, confer to this analytical tool high potentiality for market entry as the first highly sensitive electrochemical immunoassay for SARS-CoV-2 detection in untreated saliva.
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Affiliation(s)
- Laura Fabiani
- University of Rome "Tor Vergata", Department of Chemical Science and Technologies, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Marco Saroglia
- University of Insubria, Department of Biotechnologies and Life Sciences, Varese, Italy
| | - Giuseppe Galatà
- GTS Consulting S.r.l., Via Consolare Pompea 1, 98168, Messina, Italy
| | | | - Silvia Fillo
- Scientific Department, Army Medical Center, Rome, Italy
| | - Vincenzo Luca
- Scientific Department, Army Medical Center, Rome, Italy
| | | | - Nino D'Amore
- Scientific Department, Army Medical Center, Rome, Italy
| | | | | | - Genciana Terova
- University of Insubria, Department of Biotechnologies and Life Sciences, Varese, Italy
| | - Danila Moscone
- University of Rome "Tor Vergata", Department of Chemical Science and Technologies, Via della Ricerca Scientifica, 00133, Rome, Italy
| | | | - Fabiana Arduini
- University of Rome "Tor Vergata", Department of Chemical Science and Technologies, Via della Ricerca Scientifica, 00133, Rome, Italy; SENSE4MED, Via Renato Rascel 30, 00128, Rome, Italy.
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12
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Zhang Q, Zhang H, Gao J, Huang K, Yang Y, Hui X, He X, Li C, Gong W, Zhang Y, Zhao Y, Peng C, Gao X, Chen H, Zou Z, Shi ZL, Jin M. A serological survey of SARS-CoV-2 in cat in Wuhan. Emerg Microbes Infect 2020; 9:2013-2019. [PMID: 32867625 PMCID: PMC7534315 DOI: 10.1080/22221751.2020.1817796] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/11/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
COVID-19 is a new respiratory illness caused by SARS-CoV-2, and has constituted a global public health emergency. Cat is susceptible to SARS-CoV-2. However, the prevalence of SARS-CoV-2 in cats remains largely unknown. Here, we investigated the infection of SARS-CoV-2 in cats during COVID-19 outbreak in Wuhan by serological detection methods. A cohort of serum samples were collected from cats in Wuhan, including 102 sampled after COVID-19 outbreak, and 39 prior to the outbreak. Fifteen sera collected after the outbreak were positive for the receptor binding domain (RBD) of SARS-CoV-2 by indirect enzyme linked immunosorbent assay (ELISA). Among them, 11 had SARS-CoV-2 neutralizing antibodies with a titer ranging from 1/20 to 1/1080. No serological cross-reactivity was detected between SARS-CoV-2 and type I or II feline infectious peritonitis virus (FIPV). In addition, we continuously monitored serum antibody dynamics of two positive cats every 10 days over 130 days. Their serum antibodies reached the peak at 10 days after first sampling, and declined to the limit of detection within 110 days. Our data demonstrated that SARS-CoV-2 has infected cats in Wuhan during the outbreak and described serum antibody dynamics in cats, providing an important reference for clinical treatment and prevention of COVID-19.
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Affiliation(s)
- Qiang Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Huajun Zhang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Jindong Gao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Kun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yong Yang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Xianfeng Hui
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Xinglin He
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Chengfei Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Wenxiao Gong
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yufei Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Ya Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Cheng Peng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Xiaoxiao Gao
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zhong Zou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Meilin Jin
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan, People’s Republic of China
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13
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Sun B, Feng Y, Mo X, Zheng P, Wang Q, Li P, Peng P, Liu X, Chen Z, Huang H, Zhang F, Luo W, Niu X, Hu P, Wang L, Peng H, Huang Z, Feng L, Li F, Zhang F, Li F, Zhong N, Chen L. Kinetics of SARS-CoV-2 specific IgM and IgG responses in COVID-19 patients. Emerg Microbes Infect 2020; 9:940-948. [PMID: 32357808 PMCID: PMC7273175 DOI: 10.1080/22221751.2020.1762515] [Citation(s) in RCA: 337] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
The emerging COVID-19 caused by SARS-CoV-2 infection poses severe challenges to global public health. Serum antibody testing is becoming one of the critical methods for the diagnosis of COVID-19 patients. We investigated IgM and IgG responses against SARS-CoV-2 nucleocapsid (N) and spike (S) protein after symptom onset in the intensive care unit (ICU) and non-ICU patients. 130 blood samples from 38 COVID-19 patients were collected. The levels of IgM and IgG specific to N and S protein were detected by ELISA. A series of blood samples were collected along the disease course from the same patient, including 11 ICU patients and 27 non-ICU patients for longitudinal analysis. N and S specific IgM and IgG (N-IgM, N-IgG, S-IgM, S-IgG) in non-ICU patients increased after symptom onset. N-IgM and S-IgM in some non-ICU patients reached a peak in the second week, while N-IgG and S-IgG continued to increase in the third week. The combined detection of N and S specific IgM and IgG could identify up to 75% of SARS-CoV-2 infected patients in the first week. S-IgG was significantly higher in non-ICU patients than in ICU patients in the third week. In contrast, N-IgG was significantly higher in ICU patients than in non-ICU patients. The increase of S-IgG positively correlated with the decrease of C-reactive protein (CRP) in non-ICU patients. N and S specific IgM and IgG increased gradually after symptom onset and can be used for detection of SARS-CoV-2 infection. Analysis of the dynamics of S-IgG may help to predict prognosis.
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Affiliation(s)
- Baoqing Sun
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ying Feng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xiaoneng Mo
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Peiyan Zheng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Qian Wang
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Pingchao Li
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Ping Peng
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xiaoqing Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhilong Chen
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Huimin Huang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Fan Zhang
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Wenting Luo
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Peiyu Hu
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Longyu Wang
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Hui Peng
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhifeng Huang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Liqiang Feng
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Feng Li
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Fuchun Zhang
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Fang Li
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ling Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
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14
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van Tol S, Mögling R, Li W, Godeke GJ, Swart A, Bergmans B, Brandenburg A, Kremer K, Murk JL, van Beek J, Wintermans B, Reimerink J, Bosch BJ, Reusken C. Accurate serology for SARS-CoV-2 and common human coronaviruses using a multiplex approach. Emerg Microbes Infect 2020; 9:1965-1973. [PMID: 32819220 PMCID: PMC8284965 DOI: 10.1080/22221751.2020.1813636] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/19/2020] [Indexed: 01/10/2023]
Abstract
Serology is a crucial part of the public health response to the ongoing SARS-CoV-2 pandemic. Here, we describe the development, validation and clinical evaluation of a protein micro-array as a quantitative multiplex immunoassay that can identify S and N-directed SARS-CoV-2 IgG antibodies with high specificity and sensitivity and distinguish them from all currently circulating human coronaviruses. The method specificity was 100% for SARS-CoV-2 S1 and 96% for N antigen based on extensive syndromic (n=230 cases) and population panel (n=94) testing that also confirmed the high prevalence of seasonal human coronaviruses. To assess its potential role for both SARS-CoV-2 patient diagnostics and population studies, we evaluated a large heterogeneous COVID-19 cohort (n=330) and found an overall sensitivity of 89% (≥ 21 days post onset symptoms (dps)), ranging from 86% to 96% depending on severity of disease. For a subset of these patients longitudinal samples were provided up to 56 dps. Mild cases showed absent or delayed, and lower SARS-CoV-2 antibody responses. Overall, we present the development and extensive clinical validation of a multiplex coronavirus serological assay for syndromic testing, to answer research questions regarding to antibody responses, to support SARS-CoV-2 diagnostics and to evaluate epidemiological developments efficiently and with high-throughput.
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Affiliation(s)
- Sophie van Tol
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ramona Mögling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Wentao Li
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Gert-Jan Godeke
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Arno Swart
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Barbara Bergmans
- Microvida, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Afke Brandenburg
- Izore Centre for Infectious Diseases Friesland, Leeuwarden, The Netherlands
| | - Kristin Kremer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jean-Luc Murk
- Microvida, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Josine van Beek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Bas Wintermans
- Department of Medical Microbiology and Immunology, Admiral De Ruyter Hospital, Goes, The Netherlands
- Department of Medical Microbiology, Bravis Hospital, Roosendaal, The Netherlands
| | - Johan Reimerink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Chantal Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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15
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Ferretti AP, Kula T, Wang Y, Nguyen DMV, Weinheimer A, Dunlap GS, Xu Q, Nabilsi N, Perullo CR, Cristofaro AW, Whitton HJ, Virbasius A, Olivier KJ, Buckner LR, Alistar AT, Whitman ED, Bertino SA, Chattopadhyay S, MacBeath G. Unbiased Screens Show CD8 + T Cells of COVID-19 Patients Recognize Shared Epitopes in SARS-CoV-2 that Largely Reside outside the Spike Protein. Immunity 2020; 53:1095-1107.e3. [PMID: 33128877 PMCID: PMC7574860 DOI: 10.1016/j.immuni.2020.10.006] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022]
Abstract
Developing effective strategies to prevent or treat coronavirus disease 2019 (COVID-19) requires understanding the natural immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We used an unbiased, genome-wide screening technology to determine the precise peptide sequences in SARS-CoV-2 that are recognized by the memory CD8+ T cells of COVID-19 patients. In total, we identified 3-8 epitopes for each of the 6 most prevalent human leukocyte antigen (HLA) types. These epitopes were broadly shared across patients and located in regions of the virus that are not subject to mutational variation. Notably, only 3 of the 29 shared epitopes were located in the spike protein, whereas most epitopes were located in ORF1ab or the nucleocapsid protein. We also found that CD8+ T cells generally do not cross-react with epitopes in the four seasonal coronaviruses that cause the common cold. Overall, these findings can inform development of next-generation vaccines that better recapitulate natural CD8+ T cell immunity to SARS-CoV-2.
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Affiliation(s)
| | | | - Yifan Wang
- TScan Therapeutics, Waltham, MA 02451, USA
| | | | | | | | - Qikai Xu
- TScan Therapeutics, Waltham, MA 02451, USA
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16
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Ripperger TJ, Uhrlaub JL, Watanabe M, Wong R, Castaneda Y, Pizzato HA, Thompson MR, Bradshaw C, Weinkauf CC, Bime C, Erickson HL, Knox K, Bixby B, Parthasarathy S, Chaudhary S, Natt B, Cristan E, El Aini T, Rischard F, Campion J, Chopra M, Insel M, Sam A, Knepler JL, Capaldi AP, Spier CM, Dake MD, Edwards T, Kaplan ME, Scott SJ, Hypes C, Mosier J, Harris DT, LaFleur BJ, Sprissler R, Nikolich-Žugich J, Bhattacharya D. Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low-Prevalence Communities and Reveal Durable Humoral Immunity. Immunity 2020; 53:925-933.e4. [PMID: 33129373 PMCID: PMC7554472 DOI: 10.1016/j.immuni.2020.10.004] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/21/2022]
Abstract
We conducted a serological study to define correlates of immunity against SARS-CoV-2. Compared to those with mild coronavirus disease 2019 (COVID-19) cases, individuals with severe disease exhibited elevated virus-neutralizing titers and antibodies against the nucleocapsid (N) and the receptor binding domain (RBD) of the spike protein. Age and sex played lesser roles. All cases, including asymptomatic individuals, seroconverted by 2 weeks after PCR confirmation. Spike RBD and S2 and neutralizing antibodies remained detectable through 5-7 months after onset, whereas α-N titers diminished. Testing 5,882 members of the local community revealed only 1 sample with seroreactivity to both RBD and S2 that lacked neutralizing antibodies. This fidelity could not be achieved with either RBD or S2 alone. Thus, inclusion of multiple independent assays improved the accuracy of antibody tests in low-seroprevalence communities and revealed differences in antibody kinetics depending on the antigen. We conclude that neutralizing antibodies are stably produced for at least 5-7 months after SARS-CoV-2 infection.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antibodies, Neutralizing/blood
- Antibodies, Viral/blood
- Arizona/epidemiology
- Betacoronavirus/immunology
- Betacoronavirus/isolation & purification
- COVID-19
- COVID-19 Testing
- Clinical Laboratory Techniques/methods
- Coronavirus Infections/blood
- Coronavirus Infections/diagnosis
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Nucleocapsid Proteins
- Female
- Humans
- Immunity, Humoral
- Male
- Middle Aged
- Nucleocapsid Proteins/immunology
- Pandemics
- Phosphoproteins
- Pneumonia, Viral/blood
- Pneumonia, Viral/diagnosis
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Prevalence
- Protein Interaction Domains and Motifs
- SARS-CoV-2
- Seroepidemiologic Studies
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Young Adult
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Affiliation(s)
- Tyler J Ripperger
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Makiko Watanabe
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Rachel Wong
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; Division of Biological and Biomedical Sciences, Washington University, St. Louis, MO, USA
| | - Yvonne Castaneda
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Hannah A Pizzato
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; Division of Biological and Biomedical Sciences, Washington University, St. Louis, MO, USA
| | - Mallory R Thompson
- Department of Surgery, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; Department of Cellular and Molecular Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Christine Bradshaw
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Craig C Weinkauf
- Department of Surgery, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Christian Bime
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Heidi L Erickson
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Kenneth Knox
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; Department of Medicine, University of Arizona, Phoenix, Phoenix, AZ, USA
| | - Billie Bixby
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Sairam Parthasarathy
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Sachin Chaudhary
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Bhupinder Natt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Elaine Cristan
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Tammer El Aini
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Franz Rischard
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Janet Campion
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Madhav Chopra
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Michael Insel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Afshin Sam
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - James L Knepler
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Andrew P Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Tucson, AZ, USA; Functional Genomics Core, University of Arizona, Tucson, AZ, USA
| | - Catherine M Spier
- Department of Pathology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Michael D Dake
- Office of the Senior Vice-President for Health Sciences, University of Arizona, Tucson, AZ, USA
| | - Taylor Edwards
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Matthew E Kaplan
- Functional Genomics Core, University of Arizona, Tucson, AZ, USA
| | - Serena Jain Scott
- Division of Geriatrics, General Medicine and Palliative Care, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Cameron Hypes
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; Department of Emergency Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - Jarrod Mosier
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; Department of Emergency Medicine, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA
| | - David T Harris
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; University of Arizona Health Sciences Biobank, University of Arizona, Tucson, AZ, USA
| | | | - Ryan Sprissler
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Janko Nikolich-Žugich
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA.
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Tucson, AZ, USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA.
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17
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Gouveia D, Miotello G, Gallais F, Gaillard JC, Debroas S, Bellanger L, Lavigne JP, Sotto A, Grenga L, Pible O, Armengaud J. Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window. J Proteome Res 2020; 19:4407-4416. [PMID: 32697082 PMCID: PMC7640971 DOI: 10.1021/acs.jproteome.0c00535] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Indexed: 12/13/2022]
Abstract
Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.
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Affiliation(s)
- Duarte Gouveia
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Gallais
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Stéphanie Debroas
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Laurent Bellanger
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean-Philippe Lavigne
- U1047,
Institut National de la Santé et de la Recherche Médicale, Université Montpellier, Montpellier, France
- VBMI,
INSERM U1047, Université de Montpellier, Service de Microbiologie
et Hygiène Hospitalière, CHU
Nîmes, Nîmes, France
| | - Albert Sotto
- VBMI,
INSERM U1047, Université de Montpellier, Service des Maladies
Infectieuses et Tropicales, CHU Nîmes, Nîmes, France
| | - Lucia Grenga
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- INRAE,
Département Médicaments et Technologies pour la Santé
(DMTS), SPI, Université Paris Saclay,
CEA, 30200 Bagnols-sur-Cèze, France
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18
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Nikolaev EN, Indeykina MI, Brzhozovskiy AG, Bugrova AE, Kononikhin AS, Starodubtseva NL, Petrotchenko EV, Kovalev GI, Borchers CH, Sukhikh GT. Mass-Spectrometric Detection of SARS-CoV-2 Virus in Scrapings of the Epithelium of the Nasopharynx of Infected Patients via Nucleocapsid N Protein. J Proteome Res 2020; 19:4393-4397. [PMID: 32786682 PMCID: PMC7640963 DOI: 10.1021/acs.jproteome.0c00412] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Indexed: 11/30/2022]
Abstract
The detection of viral RNA by polymerase chain reaction (PCR) is currently the main diagnostic tool for COVID-19 ( Eurosurveillance 2019, 25 (3), 1). The PCR-based test, however, shows limited sensitivity, especially in the early and late stages of disease development ( Nature 2020, 581, 465-469; J. Formosan Med. Assoc. 2020, 119 (6) 1123), and is relatively time-consuming. Fast and reliable complementary methods for detecting the viral infection would be of help in the current pandemic conditions. Mass spectrometry is one of such possibilities. We have developed a mass-spectrometry-based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs based on the detection of the viral nucleocapsid N protein. Our approach shows confident identification of the N protein in patient samples, even those with the lowest viral loads, and a much simpler preparation procedure. Our main protocol consists of virus inactivation by heating and the addition of isopropanol and tryptic digestion of the proteins sedimented from the swabs followed by MS analysis. A set of unique peptides, produced as a result of proteolysis of the nucleocapsid phosphoprotein of SARS-CoV-2, is detected. The obtained results can further be used to create fast parallel mass-spectrometric approaches for the detection of the virus in the nasopharyngeal mucosa, saliva, sputum and other physiological fluids.
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Affiliation(s)
| | - Maria I. Indeykina
- Emanuel
Institute for Biochemical Physics, Russian
Academy of Sciences, Moscow 119334, Russia
| | - Alexander G. Brzhozovskiy
- Skolkovo
Institute of Science and Technology, Moscow 143025, Russia
- V. I.
Kulakov National Medical Research Center for Obstetrics, Gynecology
and Perinatology, Ministry of Healthcare
of the Russian Federation, Moscow 117997, Russia
| | - Anna E. Bugrova
- Emanuel
Institute for Biochemical Physics, Russian
Academy of Sciences, Moscow 119334, Russia
- V. I.
Kulakov National Medical Research Center for Obstetrics, Gynecology
and Perinatology, Ministry of Healthcare
of the Russian Federation, Moscow 117997, Russia
| | - Alexey S. Kononikhin
- Skolkovo
Institute of Science and Technology, Moscow 143025, Russia
- V. I.
Kulakov National Medical Research Center for Obstetrics, Gynecology
and Perinatology, Ministry of Healthcare
of the Russian Federation, Moscow 117997, Russia
| | - Natalia L. Starodubtseva
- V. I.
Kulakov National Medical Research Center for Obstetrics, Gynecology
and Perinatology, Ministry of Healthcare
of the Russian Federation, Moscow 117997, Russia
| | - Evgeny V. Petrotchenko
- Segal
Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
| | | | - Christoph H. Borchers
- Skolkovo
Institute of Science and Technology, Moscow 143025, Russia
- Segal
Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
- Gerald
Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
| | - Gennady T. Sukhikh
- V. I.
Kulakov National Medical Research Center for Obstetrics, Gynecology
and Perinatology, Ministry of Healthcare
of the Russian Federation, Moscow 117997, Russia
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19
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Goh GKM, Dunker AK, Foster JA, Uversky VN. Shell Disorder Analysis Suggests That Pangolins Offered a Window for a Silent Spread of an Attenuated SARS-CoV-2 Precursor among Humans. J Proteome Res 2020; 19:4543-4552. [PMID: 32790362 PMCID: PMC7640969 DOI: 10.1021/acs.jproteome.0c00460] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Indexed: 02/06/2023]
Abstract
A model to predict the relative levels of respiratory and fecal-oral transmission potentials of coronaviruses (CoVs) by measuring the percentage of protein intrinsic disorder (PID) of the M (Membrane) and N (Nucleoprotein) proteins in their outer and inner shells, respectively, was built before the MERS-CoV outbreak. With MPID = 8.6% and NPID = 50.2%, the 2003 SARS-CoV falls into group B, which consists of CoVs with intermediate levels of both fecal-oral and respiratory transmission potentials. Further validation of the model came with MERS-CoV (MPID = 9%, NPID = 44%) and SARS-CoV-2 (MPID = 5.5%, NPID = 48%) falling into the groups C and B, respectively. Group C contains CoVs with higher fecal-oral but lower respiratory transmission potentials. Unlike SARS-CoV, SARS-CoV-2 with MPID = 5.5% has one of the hardest outer shells among CoVs. Because the hard shell is able to resist the antimicrobial enzymes in body fluids, the infected person is able to shed large quantities of viral particles via saliva and mucus, which could account for the higher contagiousness of SARS-COV-2. Further searches have found that high rigidity of the outer shell is characteristic for the CoVs of burrowing animals, such as rabbits (MPID = 5.6%) and pangolins (MPID = 5-6%), which are in contact with the buried feces. A closer inspection of pangolin-CoVs from 2017 to 2019 reveals that pangolins provided a unique window of opportunity for the entry of an attenuated SARS-CoV-2 precursor into the human population in 2017 or earlier, with the subsequent slow and silent spread as a mild cold that followed by its mutations into the current more virulent form. Evidence of this lies in both the genetic proximity of the pangolin-CoVs to SARS-CoV-2 (∼90%) and differences in N disorder. A 2017 pangolin-CoV strain shows evidence of higher levels of attenuation and higher fecal-oral transmission associated with lower human infectivity via having lower NPID (44.8%). Our shell disorder model predicts this to be a SARS-CoV-2 vaccine strain, as lower inner shell disorder is associated with the lesser virulence in a variety of viruses.
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Affiliation(s)
| | - A. Keith Dunker
- Center
for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - James A. Foster
- Department
of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
- Institute
for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844, United States
| | - Vladimir N. Uversky
- Department
of Molecular Medicine, USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33620, United States
- Laboratory
of New Methods in Biology, Institute for Biological Instrumentation
of the Russian Academy of Sciences, Federal
Research Center “Pushchino Scientific Center for Biological
Research of the Russian Academy of Sciences”, Pushchino, Moscow 119991, Russia
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20
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Rakib A, Sami SA, Islam MA, Ahmed S, Faiz FB, Khanam BH, Marma KKS, Rahman M, Uddin MMN, Nainu F, Emran TB, Simal-Gandara J. Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2. Molecules 2020; 25:E5088. [PMID: 33147821 PMCID: PMC7663370 DOI: 10.3390/molecules25215088] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019), as a global pandemic. Additionally, the positive cases are still following an upward trend worldwide and as a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication and interferes with host immune responses. We comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we predicted the most immunogenic epitope for the T-cell and B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.
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Affiliation(s)
- Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Md. Ashiqul Islam
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
- Department of Pharmacy, Mawlana Bhashani Science & Technology University, Santosh, Tangail 1902, Bangladesh
| | - Shahriar Ahmed
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Farhana Binta Faiz
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Bibi Humayra Khanam
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Kay Kay Shain Marma
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Maksuda Rahman
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Mir Muhammad Nasir Uddin
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Tamalanrea, Kota Makassar, Sulawesi Selatan 90245, Indonesia;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo–Ourense Campus, E32004 Ourense, Spain
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21
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Huang W, Yu L, Wen D, Wei D, Sun Y, Zhao H, Ye Y, Chen W, Zhu Y, Wang L, Wang L, Wu W, Zhao Q, Xu Y, Gu D, Nie G, Zhu D, Guo Z, Ma X, Niu L, Huang Y, Liu Y, Peng B, Zhang R, Zhang X, Li D, Liu Y, Yang G, Liu L, Zhou Y, Wang Y, Hou T, Gao Q, Li W, Chen S, Hu X, Han M, Zheng H, Weng J, Cai Z, Zhang X, Song F, Zhao G, Wang J. A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection. EBioMedicine 2020; 61:103036. [PMID: 33045467 PMCID: PMC7544594 DOI: 10.1016/j.ebiom.2020.103036] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Real-time reverse transcription-PCR (rRT-PCR) has been the most effective and widely implemented diagnostic technology since the beginning of the COVID-19 pandemic. However, fuzzy rRT-PCR readouts with high Ct values are frequently encountered, resulting in uncertainty in diagnosis. METHODS A Specific Enhancer for PCR-amplified Nucleic Acid (SENA) was developed based on the Cas12a trans-cleavage activity, which is specifically triggered by the rRT-PCR amplicons of the SARS-CoV-2 Orf1ab (O) and N fragments. SENA was first characterized to determine its sensitivity and specificity, using a systematic titration experiment with pure SARS-CoV-2 RNA standards, and was then verified in several hospitals, employing a couple of commercial rRT-PCR kits and testing various clinical specimens under different scenarios. FINDINGS The ratio (10 min/5 min) of fluorescence change (FC) with mixed SENA reaction (mix-FCratio) was defined for quantitative analysis of target O and N genes, and the Limit of Detection (LoD) of mix-FCratio with 95% confidence interval was 1.2≤1.6≤2.1. Totally, 295 clinical specimens were analyzed, among which 21 uncertain rRT-PCR cases as well as 4 false negative and 2 false positive samples were characterized by SENA and further verified by next-generation sequencing (NGS). The cut-off values for mix-FCratio were determined as 1.145 for positive and 1.068 for negative. INTERPRETATION SENA increases both the sensitivity and the specificity of rRT-PCR, solving the uncertainty problem in COVID-19 diagnosis and thus providing a simple and low-cost companion diagnosis for combating the pandemic. FUNDING Detailed funding information is available at the end of the manuscript.
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Affiliation(s)
- Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Lei Yu
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Donghua Wen
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| | - Dong Wei
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yangyang Sun
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Huailong Zhao
- Jinan Center for Disease Control and Prevention, Jinan, Shandong 250021, China
| | - Yu Ye
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Chen
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Yongqiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Lijun Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Li Wang
- Jinan Infectious Diseases Hospital of Shandong University, Jinan, Shandong 250021, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| | - Qianqian Zhao
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, China
| | - Yong Xu
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Dayong Gu
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Guohui Nie
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Dongyi Zhu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| | - Zhongliang Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| | - Xiaoling Ma
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Liman Niu
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Yikun Huang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Yuchen Liu
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Bo Peng
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Renli Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xiuming Zhang
- Shenzhen Sixth People's Hospital (Nanshan Hospital), Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Dechang Li
- Yuebei Second People's Hospital, Shaoguan, Guangdong 512000, China
| | - Yang Liu
- Shanghai Institute of Quality Inspection and Technical Research/National Quality Supervision and Inspection Center for Food Products (Shanghai), Shanghai 200233, China
| | - Guoliang Yang
- Jinan Center for Disease Control and Prevention, Jinan, Shandong 250021, China
| | - Lanzheng Liu
- Jinan Center for Disease Control and Prevention, Jinan, Shandong 250021, China
| | - Yunying Zhou
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, China
| | - Yunshan Wang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, China
| | - Tieying Hou
- Laboratory of Medicine, Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou, Guangdong 510080, China
| | - Qiuping Gao
- Tolo Biotechnology Company Limited, Shanghai 200233, China
| | - Wujiao Li
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Shuo Chen
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xuejiao Hu
- Laboratory of Medicine, Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou, Guangdong 510080, China
| | - Mei Han
- Public Health Medical Centre of Chongqing Municipality, Chongqing 400036, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Jianping Weng
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Zhiming Cai
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Fei Song
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China.
| | - Guoping Zhao
- Tolo Biotechnology Company Limited, Shanghai 200233, China; CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jin Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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22
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To KK, Chua GT, Kwok KL, Wong JS, Au DCY, Lam YY, Wong WH, Ho MH, Chan GC, Chui CS, Li X, Tung KT, Wong RS, Tso WW, Wong IC, Wong CS, Fong CH, Chan KH, Yuen KY, Ip P, Kwan MY. False-positive SARS-CoV-2 serology in 3 children with Kawasaki disease. Diagn Microbiol Infect Dis 2020; 98:115141. [PMID: 32795776 PMCID: PMC7366972 DOI: 10.1016/j.diagmicrobio.2020.115141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Kawasaki disease (KD) is an acute febrile and eruptive disease with systemic vasculitis predominantly affecting young East Asian children. Recent reports showed that children with KD-like disease from KD low prevalence regions had positive SARS-CoV-2 serology despite a negative SARS-CoV-2 polymerase chain reaction (PCR) in respiratory samples. OBJECTIVES To describe 3 pediatric Kawasaki Disease patients with false positive SARS-CoV-2 serology. STUDY DESIGN We retrospectively recruited children with KD diagnosed during the COVID-19 outbreak in Hong Kong. Clinical characteristics and laboratory test results including SARS-CoV-2 PCR results were retrieved. We performed a microparticle-based immunoassay for the detection of IgG against nucleoprotein (NP) and spike protein receptor binding domain (RBD), and a microneutralization assay for the detection of neutralizing antibodies. RESULTS Three Chinese children with typical KD were identified. They had no epidemiological links with COVID-19 patients and tested negative for SARS-CoV-2 NPA PCR. They were treated with IVIG and aspirin, and were discharged without complications. Subsequently 2 of them were tested positive against anti-RBD and anti-NP antibodies and 1 was tested positive against anti- RBD antibodies. However, microneutralization assay showed that neutralizing antibodies were absent, suggesting a false-positive IgG result. CONCLUSION Detection of neutralizing antibodies is recommended to confirm previous SARS-CoV-2 infection in IgG-positive but PCR-negative patients.
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Affiliation(s)
- Kelvin Kw To
- Department of Microbiology, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Gilbert T Chua
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Ka Li Kwok
- Department of Paediatrics, Kwong Wah Hospital, Hong Kong, SAR, China
| | - Joshua Sc Wong
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, SAR, China
| | - Dennis Chi Yu Au
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, SAR, China
| | - Yuen Yu Lam
- Department of Paediatrics, Kwong Wah Hospital, Hong Kong, SAR, China
| | - Wilfred Hs Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Marco Hk Ho
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Godfrey Cf Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Celine Sl Chui
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China; Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, SAR, China
| | - Xue Li
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China; Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, SAR, China
| | - Keith Ts Tung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Rosa S Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Winnie Wy Tso
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Ian Ck Wong
- Research Department of Practice and Policy, UCL School of Pharmacy, University College, London, United Kingdom
| | | | - Carol Hy Fong
- Department of Microbiology, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Kwok Hung Chan
- Department of Microbiology, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Kwok Yung Yuen
- Department of Microbiology, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
| | - Patrick Ip
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
| | - Mike Yw Kwan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, SAR, China.
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23
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Tung HYL, Limtung P. Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein and structure model of sequestration by protein 14-3-3. Biochem Biophys Res Commun 2020; 532:134-138. [PMID: 32829876 PMCID: PMC7428706 DOI: 10.1016/j.bbrc.2020.08.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/11/2020] [Indexed: 02/09/2023]
Abstract
SARS-CoV-2 is the etiologic agent of COVID-19. There is currently no effective means of preventing infections by SARS-CoV-2, except through restriction of population movement and contact. An understanding of the origin, evolution and biochemistry (molecular biology) of SARS-CoV-2 is a prerequisite to its control. Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein isolated from various populations and locations, are described. Mutations occurred in the phosphorylation sites, all located within a stretch which forms a phosphorylation dependent interaction site, including C-TAK1 phosphorylation sites for 14-3-3. The consequences of these mutations are discussed and a structure-based model for the role of protein 14-3-3 in the sequestration and inhibition of SARS-CoV-2 nucleocapsid protein's function is presented. It is proposed that the phosphorylation of SARS-CoV-2 nucleocapsid protein and its sequestration by Protein 14-3-3 is a cellular response mechanism for the control and inhibition of the replication, transcription and packaging of the SARS-CoV-2 genome.
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Affiliation(s)
- H Y Lim Tung
- Peptide and Protein Chemistry Research Laboratory, Nacbraht Biomedical Research Institute, 3164 21st Street Suite 122, Astoria (NYC), NY, 11106, USA.
| | - Pierre Limtung
- Peptide and Protein Chemistry Research Laboratory, Nacbraht Biomedical Research Institute, 3164 21st Street Suite 122, Astoria (NYC), NY, 11106, USA
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24
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Morais IJ, Polveiro RC, Souza GM, Bortolin DI, Sassaki FT, Lima ATM. The global population of SARS-CoV-2 is composed of six major subtypes. Sci Rep 2020; 10:18289. [PMID: 33106569 PMCID: PMC7588421 DOI: 10.1038/s41598-020-74050-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022] Open
Abstract
The World Health Organization characterized COVID-19 as a pandemic in March 2020, the second pandemic of the twenty-first century. Expanding virus populations, such as that of SARS-CoV-2, accumulate a number of narrowly shared polymorphisms, imposing a confounding effect on traditional clustering methods. In this context, approaches that reduce the complexity of the sequence space occupied by the SARS-CoV-2 population are necessary for robust clustering. Here, we propose subdividing the global SARS-CoV-2 population into six well-defined subtypes and 10 poorly represented genotypes named tentative subtypes by focusing on the widely shared polymorphisms in nonstructural (nsp3, nsp4, nsp6, nsp12, nsp13 and nsp14) cistrons and structural (spike and nucleocapsid) and accessory (ORF8) genes. The six subtypes and the additional genotypes showed amino acid replacements that might have phenotypic implications. Notably, three mutations (one of them in the Spike protein) were responsible for the geographical segregation of subtypes. We hypothesize that the virus subtypes detected in this study are records of the early stages of SARS-CoV-2 diversification that were randomly sampled to compose the virus populations around the world. The genetic structure determined for the SARS-CoV-2 population provides substantial guidelines for maximizing the effectiveness of trials for testing candidate vaccines or drugs.
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Affiliation(s)
- Ivair José Morais
- Departamento de Fitopatologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Richard Costa Polveiro
- Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Gabriel Medeiros Souza
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil
| | - Daniel Inserra Bortolin
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil
| | - Flávio Tetsuo Sassaki
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Monte Carmelo, MG, 38500-000, Brazil
| | - Alison Talis Martins Lima
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, MG, 38410-337, Brazil.
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25
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Addetia A, Crawford KHD, Dingens A, Zhu H, Roychoudhury P, Huang ML, Jerome KR, Bloom JD, Greninger AL. Neutralizing Antibodies Correlate with Protection from SARS-CoV-2 in Humans during a Fishery Vessel Outbreak with a High Attack Rate. J Clin Microbiol 2020; 58:e02107-20. [PMID: 32826322 PMCID: PMC7587101 DOI: 10.1128/jcm.02107-20] [Citation(s) in RCA: 405] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022] Open
Abstract
The development of vaccines against SARS-CoV-2 would be greatly facilitated by the identification of immunological correlates of protection in humans. However, to date, studies on protective immunity have been performed only in animal models and correlates of protection have not been established in humans. Here, we describe an outbreak of SARS-CoV-2 on a fishing vessel associated with a high attack rate. Predeparture serological and viral reverse transcription-PCR (RT-PCR) testing along with repeat testing after return to shore was available for 120 of the 122 persons on board over a median follow-up of 32.5 days (range, 18.8 to 50.5 days). A total of 104 individuals had an RT-PCR-positive viral test with a cycle threshold (CT ) of <35 or seroconverted during the follow-up period, yielding an attack rate on board of 85.2% (104/122 individuals). Metagenomic sequencing of 39 viral genomes suggested that the outbreak originated largely from a single viral clade. Only three crew members tested seropositive prior to the boat's departure in initial serological screening and also had neutralizing and spike-reactive antibodies in follow-up assays. None of the crew members with neutralizing antibody titers showed evidence of bona fide viral infection or experienced any symptoms during the viral outbreak. Therefore, the presence of neutralizing antibodies from prior infection was significantly associated with protection against reinfection (Fisher's exact test, P = 0.002).
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Affiliation(s)
- Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Katharine H D Crawford
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
| | - Adam Dingens
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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26
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Cazares LH, Chaerkady R, Samuel Weng SH, Boo CC, Cimbro R, Hsu HE, Rajan S, Dall’Acqua W, Clarke L, Ren K, McTamney P, Kallewaard-LeLay N, Ghaedi M, Ikeda Y, Hess S. Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein. Anal Chem 2020; 92:13813-13821. [PMID: 32966064 PMCID: PMC7537550 DOI: 10.1021/acs.analchem.0c02288] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022]
Abstract
There is an urgent need for robust and high-throughput methods for SARS-CoV-2 detection in suspected patient samples to facilitate disease management, surveillance, and control. Although nucleic acid detection methods such as reverse transcription polymerase chain reaction (RT-PCR) are the gold standard, during the current pandemic, the deployment of RT-PCR tests has been extremely slow, and key reagents such as PCR primers and RNA extraction kits are at critical shortages. Rapid point-of-care viral antigen detection methods have been previously employed for the diagnosis of respiratory viruses such as influenza and respiratory syncytial viruses. Therefore, the direct detection of SARS-CoV-2 viral antigens in patient samples could also be used for diagnosis of active infection, and alternative methodologies for specific and sensitive viral protein detection should be explored. Targeted mass spectrometry techniques have enabled the identification and quantitation of a defined subset of proteins/peptides at single amino acid resolution with attomole level sensitivity and high reproducibility. Herein, we report a targeted mass spectrometry assay for the detection of SARS-CoV-2 spike protein and nucleoprotein in a relevant biological matrix. Recombinant full-length spike protein and nucleoprotein were digested and proteotypic peptides were selected for parallel reaction monitoring (PRM) quantitation using a high-resolution Orbitrap instrument. A spectral library, which contained seven proteotypic peptides (four from spike protein and three from nucleoprotein) and the top three to four transitions, was generated and evaluated. From the original spectral library, we selected two best performing peptides for the final PRM assay. The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in vitro derived mucus. The PRM assay provided a limit of detection of ∼200 attomoles and a limit of quantitation of ∼ 390 attomoles. Extrapolating from the test samples, the projected titer of virus particles necessary for the detection of SARS-CoV-2 spike and nucleoprotein detection was approximately 2 × 105 viral particles/mL, making it an attractive alternative to RT-PCR assays. Potentially, mass spectrometry-based methods for viral antigen detection may deliver higher throughput and could serve as a complementary diagnostic tool to RT-PCR. Furthermore, this assay could be used to evaluate the presence of SARS-CoV-2 in archived or recently collected biological fluids, in vitro-derived research materials, and wastewater samples.
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Affiliation(s)
- Lisa H. Cazares
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Raghothama Chaerkady
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Shao Huan Samuel Weng
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Chelsea C. Boo
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Raffaello Cimbro
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Hsiang-En Hsu
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Sarav Rajan
- Biological Therapeutics 1, Antibody
Discovery and Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - William Dall’Acqua
- Biological Therapeutics 1, Antibody
Discovery and Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Lori Clarke
- Cell Therapeutics, Antibody Discovery
and Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Kuishu Ren
- Discovery Anti Infection, Microbial
Sciences, R&D AstraZeneca, Gaithersburg
20878, Maryland, United States
| | - Patrick McTamney
- Discovery Anti Infection, Microbial
Sciences, R&D AstraZeneca, Gaithersburg
20878, Maryland, United States
| | - Nicole Kallewaard-LeLay
- Discovery Anti Infection, Microbial
Sciences, R&D AstraZeneca, Gaithersburg
20878, Maryland, United States
| | - Mahboobe Ghaedi
- Respiratory and Immunology,
R&D AstraZeneca, Gaithersburg
20878, Maryland, United States
| | - Yasuhiro Ikeda
- Cell Therapeutics, Antibody Discovery
and Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
| | - Sonja Hess
- Dynamic Omics, Antibody Discovery and
Protein Engineering (ADPE), R&D
AstraZeneca, Gaithersburg 20878, Maryland,
United States
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27
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Yu S, Nimse SB, Kim J, Song KS, Kim T. Development of a Lateral Flow Strip Membrane Assay for Rapid and Sensitive Detection of the SARS-CoV-2. Anal Chem 2020; 92:14139-14144. [PMID: 32967427 PMCID: PMC7539551 DOI: 10.1021/acs.analchem.0c03202] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/23/2020] [Indexed: 01/12/2023]
Abstract
The infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the coronavirus disease 2019 (COVID-19) has threatened public health worldwide. The easy human-to-human transmission of this virus has rapidly evolved into a global pandemic. Therefore, to control the community spread of the virus, it is crucial to identify the infected individuals, including asymptomatic people. Hence, a specific and rapid assay is crucial for the early diagnosis and active monitoring of individuals potentially exposed to SARS-CoV-2 for controlling the COVID-19 outbreak. In this study, we have developed the novel lateral flow strip membrane (LFSM) assay that allows the simultaneous detection of RdRp, ORF3a, and N genes using the PCR product obtained by using the single-tube reverse transcription polymerase chain reaction (RT-PCR). The LFSM assay allows detection of SARS-CoV-2 in 30 min at 25 °C after the RT-PCR with the detection limit of 10 copies/test for each gene. The clinical performance of the LFSM assay for the detection of SARS-Cov-2 was evaluated using 162 clinical samples previously detected by using the commercial assay. The percent positive agreement, percent negative agreement, and overall percent agreement of the LFSM assay with the commercial assay were 100% (94.2-100%), 99.0% (94.6-100%), and 99.4% (96.6-100%), respectively. Therefore, the results of the LFSM assay showed significantly high concordance with the commercial assay for the detection of SARS-CoV-2 in clinical specimens. Therefore, we conclude that the developed LFSM assay can be used alone or complementary to the RT-PCR or other methods for the diagnosis and monitoring of the patients to curb community transmission and the pandemic.
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Affiliation(s)
- Sangheon Yu
- Biometrix Technology, Inc.,
2-2 Bio Venture Plaza 56, Chuncheon 24232, Korea
| | - Satish Balasaheb Nimse
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
| | - Junghoon Kim
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
| | - Keum-Soo Song
- Biometrix Technology, Inc.,
2-2 Bio Venture Plaza 56, Chuncheon 24232, Korea
| | - Taisun Kim
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
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Peng Y, Du N, Lei Y, Dorje S, Qi J, Luo T, Gao GF, Song H. Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design. EMBO J 2020; 39:e105938. [PMID: 32914439 PMCID: PMC7560215 DOI: 10.15252/embj.2020105938] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
COVID-19, caused by SARS-CoV-2, has resulted in severe and unprecedented economic and social disruptions in the world. Nucleocapsid (N) protein, which is the major structural component of the virion and is involved in viral replication, assembly and immune regulation, plays key roles in the viral life cycle. Here, we solved the crystal structures of the N- and C-terminal domains (N-NTD and N-CTD) of SARS-CoV-2 N protein, at 1.8 and 1.5 Å resolution, respectively. Both structures show conserved features from other CoV N proteins. The binding sites targeted by small molecules against HCoV-OC43 and MERS-CoV, which inhibit viral infection by blocking the RNA-binding activity or normal oligomerization of N protein, are relatively conserved in our structure, indicating N protein is a promising drug target. In addition, certain areas of N-NTD and N-CTD display distinct charge distribution patterns in SARS-CoV-2, which may alter the RNA-binding modes. The specific antigenic characteristics are critical for developing specific immune-based rapid diagnostic tests. Our structural information can aid in the discovery and development of antiviral inhibitors against SARS-CoV-2 in the future.
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Affiliation(s)
- Ya Peng
- Laboratory of Animal Infectious DiseasesCollege of Animal Sciences and Veterinary MedicineGuangxi UniversityNanningChina
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ning Du
- Research Network of Immunity and Health (RNIH)Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
| | - Yuqing Lei
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Sonam Dorje
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tingrong Luo
- Laboratory of Animal Infectious DiseasesCollege of Animal Sciences and Veterinary MedicineGuangxi UniversityNanningChina
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Research Network of Immunity and Health (RNIH)Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hao Song
- Research Network of Immunity and Health (RNIH)Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
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29
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Khairkhah N, Aghasadeghi MR, Namvar A, Bolhassani A. Design of novel multiepitope constructs-based peptide vaccine against the structural S, N and M proteins of human COVID-19 using immunoinformatics analysis. PLoS One 2020; 15:e0240577. [PMID: 33057358 PMCID: PMC7561160 DOI: 10.1371/journal.pone.0240577] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
The causative agent of severe acute respiratory syndrome (SARS) reported by the Chinese Center for Disease Control (China CDC) has been identified as a novel Betacoronavirus (SARS-CoV-2). A computational approach was adopted to identify multiepitope vaccine candidates against SARS-CoV-2 based on S, N and M proteins being able to elicit both humoral and cellular immune responses. In this study, the sequence of the virus was obtained from NCBI database and analyzed with in silico tools such as NetMHCpan, IEDB, BepiPred, NetCTL, Tap transport/proteasomal cleavage, Pa3P, GalexyPepDock, I-TASSER, Ellipro and ClusPro. To identify the most immunodominant regions, after analysis of population coverage and epitope conservancy, we proposed three different constructs based on linear B-cell, CTL and HTL epitopes. The 3D structure of constructs was assessed to find discontinuous B-cell epitopes. Among CTL predicted epitopes, S257-265, S603-611 and S360-368, and among HTL predicted epitopes, N167-181, S313-330 and S1110-1126 had better MHC binding rank. We found one putative CTL epitope, S360-368 related to receptor-binding domain (RBD) region for S protein. The predicted epitopes were non-allergen and showed a high quality of proteasomal cleavage and Tap transport efficiency and 100% conservancy within four different clades of SARS-CoV-2. For CTL and HTL epitopes, the highest population coverage of the world's population was calculated for S27-37 with 86.27% and for S196-231, S303-323, S313-330, S1009-1030 and N328-349 with 90.33%, respectively. We identified overall 10 discontinuous B-cell epitopes for three multiepitope constructs. All three constructs showed strong interactions with TLRs 2, 3 and 4 supporting the hypothesis of SARS-CoV-2 susceptibility to TLRs 2, 3 and 4 like other Coronaviridae families. These data demonstrated that the novel designed multiepitope constructs can contribute to develop SARS-CoV-2 peptide vaccine candidates. The in vivo studies are underway using several vaccination strategies.
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Affiliation(s)
- Niloofar Khairkhah
- Department of Hepatitis, AIDS and Blood-borne diseases, Pasteur Institute of Iran, Tehran, Iran
- Iranian Comprehensive Hemophilia Care Center, Tehran, Iran
| | | | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis, AIDS and Blood-borne diseases, Pasteur Institute of Iran, Tehran, Iran
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30
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Algaissi A, Alfaleh MA, Hala S, Abujamel TS, Alamri SS, Almahboub SA, Alluhaybi KA, Hobani HI, Alsulaiman RM, AlHarbi RH, ElAssouli MZA, Alhabbab RY, AlSaieedi AA, Abdulaal WH, Al-Somali AA, Alofi FS, Khogeer AA, Alkayyal AA, Mahmoud AB, Almontashiri NAM, Pain A, Hashem AM. SARS-CoV-2 S1 and N-based serological assays reveal rapid seroconversion and induction of specific antibody response in COVID-19 patients. Sci Rep 2020; 10:16561. [PMID: 33024213 PMCID: PMC7538990 DOI: 10.1038/s41598-020-73491-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
As the Coronavirus Disease 2019 (COVID-19), which is caused by the novel SARS-CoV-2, continues to spread rapidly around the world, there is a need for well validated serological assays that allow the detection of viral specific antibody responses in COVID-19 patients or recovered individuals. In this study, we established and used multiple indirect Enzyme Linked Immunosorbent Assay (ELISA)-based serological assays to study the antibody response in COVID-19 patients. In order to validate the assays we determined the cut off values, sensitivity and specificity of the assays using sera collected from pre-pandemic healthy controls, COVID-19 patients at different time points after disease-onset, and seropositive sera to other human coronaviruses (CoVs). The developed SARS-CoV-2 S1 subunit of the spike glycoprotein and nucleocapsid (N)-based ELISAs not only showed high specificity and sensitivity but also did not show any cross-reactivity with other CoVs. We also show that all RT-PCR confirmed COVID-19 patients tested in our study developed both virus specific IgM and IgG antibodies as early as week one after disease onset. Our data also suggest that the inclusion of both S1 and N in serological testing would capture as many potential SARS-CoV-2 positive cases as possible than using any of them alone. This is specifically important for tracing contacts and cases and conducting large-scale epidemiological studies to understand the true extent of virus spread in populations.
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Affiliation(s)
- Abdullah Algaissi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Medical Research Center, Jazan University, Jazan, Saudi Arabia
| | - Mohamed A Alfaleh
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sharif Hala
- Pathogen Genomics Laboratory, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology, Thuwa, Saudi Arabia
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Turki S Abujamel
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sawsan S Alamri
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sarah A Almahboub
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalid A Alluhaybi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haya I Hobani
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem M Alsulaiman
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rahaf H AlHarbi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M-Z Aki ElAssouli
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rowa Y Alhabbab
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahdab A AlSaieedi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wesam H Abdulaal
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Afrah A Al-Somali
- Infectious Diseases Department, King Abdullah Medical Complex, Jeddah, Saudi Arabia
| | - Fadwa S Alofi
- Infectious Diseases Department, King Fahad Hospital, Almadinah Almunwarah, Saudi Arabia
| | - Asim A Khogeer
- Plan and Research Department, General Directorate of Health Affairs Makkah Region, Ministry of Health, Makkah, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Naif A M Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology, Thuwa, Saudi Arabia
- Research Center for Zoonosis Control, Hokkaido University, Kita-ku, Sapporo, Japan
- Nuffield Division of Clinical Laboratory Sciences (NDCLS), University of Oxford, Oxford, UK
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.
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31
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Abedin S, Paul SK, Nasreen SA, Nessa A, Ahmed S, Haque N, Ahamed F, Islam A, Ifa IA, Debnath P, Ahmed MU, Nahar S. Molecular Detection of Human Coronavirus from North Central Part of Bangladesh Depending on ORF1ab and N Gene. Mymensingh Med J 2020; 29:865-870. [PMID: 33116089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Coronavirus disease 2019 (COVID-19) resulted severe respiratory illness such as pneumonia and lung dysfunctions that was first identified at Wuhan, the capital of Hubeiin China during the end of December 2019. The etiological cause of COVID-19 has been confirmed as a novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which was similar with the zoonotic virus SARS-CoV (2002). Now a days for early diagnosis of COVID-19 the nucleic acid based test like RT PCR (real time reverse transcription polymerase chain reaction) is most consistent and used all over the world. In this study among 11,280 cases 825(7.31%) were positive by molecular RT PCR method on June 2020 at Microbiology department of Mymensingh Medical College and the samples are collected from different areas of Northern part of Bangladesh. Among this positive cases 588(71%) N gene, 10 ORF1ab (2%) and 227(27%) both N and ORF gene showed significant curve which is specific for COVID-19 positive patients. Because N and ORF gene of this virus inhibit immune system of human body especially interferon. Out of SARS-CoV-2 positive cases maximum number of N gene were found in male patients and above 40 years old aged group. So, Molecular diagnosis of this pandemic virus especially by N and ORF gene might be helpful to reduce the spread of SARS-CoV-2 as well as early treatment for saving many lives.
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Affiliation(s)
- S Abedin
- Dr Sahida Abedin, Lecturer, Department of Virology, MMC, Mymensingh, Bangladesh; E-mail:
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Nguyen-Contant P, Embong AK, Kanagaiah P, Chaves FA, Yang H, Branche AR, Topham DJ, Sangster MY. S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit. mBio 2020; 11:e01991-20. [PMID: 32978311 PMCID: PMC7520599 DOI: 10.1128/mbio.01991-20] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/08/2020] [Indexed: 01/16/2023] Open
Abstract
The high susceptibility of humans to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the cause of coronavirus disease 2019 (COVID-19), reflects the novelty of the virus and limited preexisting B cell immunity. IgG against the SARS-CoV-2 spike (S) protein, which carries the novel receptor binding domain (RBD), is absent or at low levels in unexposed individuals. To better understand the B cell response to SARS-CoV-2 infection, we asked whether virus-reactive memory B cells (MBCs) were present in unexposed subjects and whether MBC generation accompanied virus-specific IgG production in infected subjects. We analyzed sera and peripheral blood mononuclear cells (PBMCs) from non-SARS-CoV-2-exposed healthy donors and COVID-19 convalescent subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD and S2 subunit, and nucleocapsid [N]) and non-SARS-CoV-2 proteins were related to measurements of circulating IgG MBC levels. Anti-RBD IgG was absent in unexposed subjects. Most unexposed subjects had anti-S2 IgG, and a minority had anti-N IgG, but IgG MBCs with these specificities were not detected, perhaps reflecting low frequencies. Convalescent subjects had high levels of IgG against the RBD, S2, and N, together with large populations of RBD- and S2-reactive IgG MBCs. Notably, IgG titers against the S protein of the human coronavirus OC43 were higher in convalescent subjects than in unexposed subjects and correlated strongly with anti-S2 titers. Our findings indicate cross-reactive B cell responses against the S2 subunit that might enhance broad coronavirus protection. Importantly, our demonstration of MBC induction by SARS-CoV-2 infection suggests that a durable form of B cell immunity is maintained even if circulating antibody levels wane.IMPORTANCE The recent rapid worldwide spread of SARS-CoV-2 has established a pandemic of potentially serious disease in the highly susceptible human population. Key issues are whether humans have preexisting immune memory that provides some protection against SARS-CoV-2 and whether SARS-CoV-2 infection generates lasting immune protection against reinfection. Our analysis focused on pre- and postinfection IgG and IgG memory B cells (MBCs) reactive to SARS-CoV-2 proteins. Most importantly, we demonstrate that infection generates both IgG and IgG MBCs against the novel receptor binding domain and the conserved S2 subunit of the SARS-CoV-2 spike protein. Thus, even if antibody levels wane, long-lived MBCs remain to mediate rapid antibody production. Our study results also suggest that SARS-CoV-2 infection strengthens preexisting broad coronavirus protection through S2-reactive antibody and MBC formation.
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Affiliation(s)
- Phuong Nguyen-Contant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - A Karim Embong
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Preshetha Kanagaiah
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Francisco A Chaves
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Angela R Branche
- Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Mark Y Sangster
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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33
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Leuzinger K, Roloff T, Gosert R, Sogaard K, Naegele K, Rentsch K, Bingisser R, Nickel CH, Pargger H, Bassetti S, Bielicki J, Khanna N, Tschudin Sutter S, Widmer A, Hinic V, Battegay M, Egli A, Hirsch HH. Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence Amidst Community-Acquired Respiratory Viruses. J Infect Dis 2020; 222:1270-1279. [PMID: 32726441 PMCID: PMC7454752 DOI: 10.1093/infdis/jiaa464] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China as the cause of coronavirus disease 2019 in December 2019 and reached Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the World Health Organization (WHO)-recommended SARS-CoV-2 assay and analyzed the epidemiology of SARS-CoV-2 and CARVs. METHODS Nasopharyngeal/oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by the Basel S-gene and WHO-based E-gene (Roche) assays in parallel using the Basel N-gene assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex nucleic acid testing, including 1816 (75%) simultaneously for SARS-CoV-2. RESULTS The Basel S-gene and Roche E-gene assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2 positives. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2 positive, whereas children tested more frequently CARV positive. CARV coinfections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks, reaching 48% of all detected respiratory viruses followed by rhinovirus/enterovirus (13%), influenza virus (12%), coronavirus (9%), respiratory syncytial virus (6%), and metapneumovirus (6%). CONCLUSIONS Winter CARVs were dominant during the early SARS-CoV-2 pandemic, impacting infection control and treatment decisions, but were rapidly replaced, suggesting competitive infection. We hypothesize that preexisting immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.
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Affiliation(s)
- Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Laboratory Medicine, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Rainer Gosert
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Kirstin Sogaard
- Applied Microbiology Research, Laboratory Medicine, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Klaudia Naegele
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Katharina Rentsch
- Clinical Chemistry, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Roland Bingisser
- Emergency Medicine, University Hospital Basel, Basel, Switzerland
| | | | - Hans Pargger
- Intensive Care Unit, University Hospital Basel, Basel, Switzerland
| | - Stefano Bassetti
- Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Julia Bielicki
- Pediatric Infectious Diseases and Hospital Epidemiology, University Children’s Hospital Basel, Basel, Switzerland
| | - Nina Khanna
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Sarah Tschudin Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andreas Widmer
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Vladimira Hinic
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Manuel Battegay
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Laboratory Medicine, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Hans H Hirsch
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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34
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Fong CHY, Cai JP, Dissanayake TK, Chen LL, Choi CYK, Wong LH, Ng ACK, Pang PKP, Ho DTY, Poon RWS, Chung TWH, Sridhar S, Chan KH, Chan JFW, Hung IFN, Yuen KY, To KKW. Improved Detection of Antibodies against SARS-CoV-2 by Microsphere-Based Antibody Assay. Int J Mol Sci 2020; 21:E6595. [PMID: 32916926 PMCID: PMC7555114 DOI: 10.3390/ijms21186595] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 01/08/2023] Open
Abstract
Currently available COVID-19 antibody tests using enzyme immunoassay (EIA) or immunochromatographic assay have variable sensitivity and specificity. Here, we developed and evaluated a novel microsphere-based antibody assay (MBA) for detecting immunoglobulin G (IgG) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleoprotein (NP) and spike protein receptor binding domain (RBD). The seropositive cutoff value was set using a cohort of 294 anonymous serum specimens collected in 2018. The specificity was assessed using serum specimens collected from organ donors or influenza patients before 2020. Seropositive rate was determined among COVID-19 patients. Time-to-seropositivity and signal-to-cutoff (S/CO) ratio were compared between MBA and EIA. MBA had a specificity of 100% (93/93; 95% confidence interval (CI), 96-100%) for anti-NP IgG, 98.9% (92/93; 95% CI 94.2-100%) for anti-RBD IgG. The MBA seropositive rate for convalescent COVID-19 patients was 89.8% (35/39) for anti-NP IgG and 79.5% (31/39) for anti-RBD IgG. The time-to-seropositivity was shorter with MBA than EIA. MBA could better differentiate between COVID-19 patients and negative controls with higher S/CO ratio for COVID-19 patients, lower S/CO ratio with negative controls and fewer specimens in the equivocal range. MBA is robust, simple and is suitable for clinical microbiology laboratory for the accurate determination of anti-SARS-CoV-2 antibodies for diagnosis, serosurveillance, and vaccine trials.
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Affiliation(s)
- Carol Ho-Yan Fong
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Jian-Piao Cai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Thrimendra Kaushika Dissanayake
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Lin-Lei Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Charlotte Yee-Ki Choi
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Lok-Hin Wong
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Anthony Chin-Ki Ng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Polly K. P. Pang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Deborah Tip-Yin Ho
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Rosana Wing-Shan Poon
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China; (R.W.-S.P.); (T.W.-H.C.)
| | - Tom Wai-Hin Chung
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China; (R.W.-S.P.); (T.W.-H.C.)
| | - Siddharth Sridhar
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Kwok-Hung Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Jasper Fuk-Woo Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; (C.H.-Y.F.); (J.-P.C.); (T.K.D.); (L.-L.C.); (C.Y.-K.C.); (L.-H.W.); (A.C.-K.N.); (P.K.P.P.); (D.T.-Y.H.); (S.S.); (K.-H.C.); (J.F.-W.C.); (K.-Y.Y.)
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Affiliation(s)
- Carolina Rosadas
- Department of Infectious Disease, Imperial College London, London, UK
| | - Paul Randell
- Department of Infection and Immunity, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, UK
| | - Maryam Khan
- Department of Infectious Disease, Imperial College London, London, UK
| | - Myra O McClure
- Department of Infectious Disease, Imperial College London, London, UK
| | - Richard S Tedder
- Department of Infectious Disease, Imperial College London, London, UK; Jefferiss Research Trust Laboratories, Wright-Fleming Institute, Faculty of Medicine, Imperial College London, London W2 1PG, UK.
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Li T, Wang L, Wang H, Li X, Zhang S, Xu Y, Wei W. Serum SARS-COV-2 Nucleocapsid Protein: A Sensitivity and Specificity Early Diagnostic Marker for SARS-COV-2 Infection. Front Cell Infect Microbiol 2020; 10:470. [PMID: 33014893 PMCID: PMC7498565 DOI: 10.3389/fcimb.2020.00470] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Objective: To explore the diagnostic value of serum severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein assay in the early stages of SARS-COV-2 infection. Methods: Serum N protein level in SARS-COV-2 infected patients and non-SARS-COV-2 infected population was measured by enzyme-linked immunosorbent assay (ELISA) double antibody sandwich assay. Colloidal gold immunochromatography assay was used to detect serum N protein antibodies in the above populations. Results: Fifty cases of SARS-CoV-2 nucleic acid-positive and SARS-CoV-2 antibody-negative patients had a serum N protein positivity rate of 76%. Thirty-seven patients who were positive for serum SARS-CoV-2 antibody after infection had a serum SARS-CoV-2 N protein positivity rate of 2.7%. Serum N protein test results of 633 non-SARS-COV-2 infected patients, including pregnant women, patients with other respiratory infections, and individuals with increased rheumatoid factor were all negative, with serum N protein concentration <10.00 pg/mL at 100% specificity. Using SPSS 19.0 to calculate the receiver operating characteristic curve, the area under the curve was determined to be 0.9756 (95% confidence interval 0.9485-1.000, p < 0.0001), and sensitivity and specificity were 92% (95% confidence interval 81.16-96.85%) and 96.84% (95% confidence interval 95.17-97.15%), respectively. The best CUT-OFF value was 1.850 pg/mL. Conclusion: The measurement of serum SARS-COV-2 N protein has a high diagnostic value for infected patients before the antibody appears and shortens the window period of serological diagnosis. It is recommended that the manufacturer establish two different CUT-OFF values according to the purpose of the application. One CUT-OFF value is used for the diagnosis of clinical SARS-COV-2 infection, and the other is used to screen out as many suspected cases as possible.
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Affiliation(s)
- Tao Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Anti-inflammatory and Immune Medicine Innovation Team, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
| | - Li Wang
- Biohit Healthcare (Hefei) Co., Ltd, Hefei, China
| | - Huihui Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xuemei Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shubing Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei Wei
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Anti-inflammatory and Immune Medicine Innovation Team, Institute of Clinical Pharmacology, Anhui Medical University, Hefei, China
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Johnson M, Wagstaffe HR, Gilmour KC, Mai AL, Lewis J, Hunt A, Sirr J, Bengt C, Grandjean L, Goldblatt D. Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2. J Clin Virol 2020; 130:104572. [PMID: 32769024 PMCID: PMC7396134 DOI: 10.1016/j.jcv.2020.104572] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND The emergence of SARS-CoV-2 has led to the development of serological assays that could aid in an understanding of the burden of COVID-19 disease. Many available tests lack rigorous evaluation and therefore results may be misleading. OBJECTIVES The aim of this study was to assess the performance of a novel multiplexed immunoassay for the simultaneous detection of antibodies against SARS-CoV-2 trimeric spike (S), spike receptor binding domain (RBD), spike N terminal domain and nucleocapsid antigen and a novel pseudo-neutralisation assay. METHODS A multiplexed solid-phase chemiluminescence assay (Meso Scale Discovery) was evaluated for the simultaneous detection of IgG binding to four SARS-CoV-2 antigens and the quantification of antibody-induced ACE-2 binding inhibition (pseudo-neutralisation assay). Sensitivity was evaluated with a total of 196 COVID-19 serum samples (169 confirmed PCR positive and 27 anti-nucleocapsid IgG positive) from individuals with mild symptomatic or asymptomatic disease. Specificity was evaluated with 194 control serum samples collected from adults prior to December 2019. RESULTS The specificity and sensitivity of the binding IgG assay was highest for S protein with a specificity of 97.4 % and sensitivity of 96.2 % for samples taken 14 days and 97.9 % for samples taken 21 days following the onset of symptoms. IgG concentration to S and RBD correlated strongly with percentage inhibition measured by the pseudo-neutralisation assay. CONCLUSION Excellent sensitivity for IgG detection was obtained over 14 days since onset of symptoms for three SARS-CoV-2 antigens (S, RBD and N) in this multiplexed assay which can also measure antibody functionality.
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Affiliation(s)
- Marina Johnson
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Helen R Wagstaffe
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Kimberly C Gilmour
- Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Annabelle Lea Mai
- Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Joanna Lewis
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Adam Hunt
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Jake Sirr
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Christopher Bengt
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Louis Grandjean
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK; Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK; Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK.
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Pickering S, Betancor G, Galão RP, Merrick B, Signell AW, Wilson HD, Kia Ik MT, Seow J, Graham C, Acors S, Kouphou N, Steel KJA, Hemmings O, Patel A, Nebbia G, Douthwaite S, O’Connell L, Luptak J, McCoy LE, Brouwer P, van Gils MJ, Sanders RW, Martinez Nunez R, Bisnauthsing K, O’Hara G, MacMahon E, Batra R, Malim MH, Neil SJD, Doores KJ, Edgeworth JD. Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings. PLoS Pathog 2020; 16:e1008817. [PMID: 32970782 PMCID: PMC7514033 DOI: 10.1371/journal.ppat.1008817] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022] Open
Abstract
There is a clear requirement for an accurate SARS-CoV-2 antibody test, both as a complement to existing diagnostic capabilities and for determining community seroprevalence. We therefore evaluated the performance of a variety of antibody testing technologies and their potential use as diagnostic tools. Highly specific in-house ELISAs were developed for the detection of anti-spike (S), -receptor binding domain (RBD) and -nucleocapsid (N) antibodies and used for the cross-comparison of ten commercial serological assays-a chemiluminescence-based platform, two ELISAs and seven colloidal gold lateral flow immunoassays (LFIAs)-on an identical panel of 110 SARS-CoV-2-positive samples and 50 pre-pandemic negatives. There was a wide variation in the performance of the different platforms, with specificity ranging from 82% to 100%, and overall sensitivity from 60.9% to 87.3%. However, the head-to-head comparison of multiple sero-diagnostic assays on identical sample sets revealed that performance is highly dependent on the time of sampling, with sensitivities of over 95% seen in several tests when assessing samples from more than 20 days post onset of symptoms. Furthermore, these analyses identified clear outlying samples that were negative in all tests, but were later shown to be from individuals with mildest disease presentation. Rigorous comparison of antibody testing platforms will inform the deployment of point-of-care technologies in healthcare settings and their use in the monitoring of SARS-CoV-2 infections.
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Affiliation(s)
- Suzanne Pickering
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Gilberto Betancor
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Rui Pedro Galão
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Adrian W. Signell
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Mark Tan Kia Ik
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Kathryn J. A. Steel
- Centre for Inflammation Biology and Cancer Immunology (CIBCI), Dept of Inflammation Biology, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Oliver Hemmings
- Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Sam Douthwaite
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Lorcan O’Connell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Jakub Luptak
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Laura E. McCoy
- Division of Infection and Immunity, University College London (UCL), London, United Kingdom
| | - Philip Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | - Rocio Martinez Nunez
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Karen Bisnauthsing
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Geraldine O’Hara
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Eithne MacMahon
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
| | - Jonathan D. Edgeworth
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
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Li JY, Liao CH, Wang Q, Tan YJ, Luo R, Qiu Y, Ge XY. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res 2020; 286:198074. [PMID: 32589897 PMCID: PMC7309931 DOI: 10.1016/j.virusres.2020.198074] [Citation(s) in RCA: 302] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel human coronavirus causing the pandemic of severe pneumonia (Coronavirus Disease 2019, COVID-19). SARS-CoV-2 is highly pathogenic in human, having posed immeasurable public health challenges to the world. Innate immune response is critical for the host defense against viral infection and the dysregulation of the host innate immune responses probably aggravates SARS-CoV-2 infection, contributing to the high morbidity and lethality of COVID-19. It has been reported that some coronavirus proteins play an important role in modulating innate immunity of the host, but few studies have been conducted on SARS-CoV-2. In this study, we screened the viral proteins of SARS-CoV-2 and found that the viral ORF6, ORF8 and nucleocapsid proteins were potential inhibitors of type I interferon signaling pathway, a key component for antiviral response of host innate immune. All the three proteins showed strong inhibition on type I interferon (IFN-β) and NF-κB-responsive promoter, further examination revealed that these proteins were able to inhibit the interferon-stimulated response element (ISRE) after infection with Sendai virus, while only ORF6 and ORF8 proteins were able to inhibit the ISRE after treatment with interferon beta. These findings would be helpful for the further study of the detailed signaling pathway and unveil the key molecular player that may be targeted.
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Affiliation(s)
- Jin-Yan Li
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, Hunan, China.
| | - Ce-Heng Liao
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, Hunan, China.
| | - Qiong Wang
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, Hunan, China.
| | - Yong-Jun Tan
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, Hunan, China.
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Ye Qiu
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, Hunan, China.
| | - Xing-Yi Ge
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, Hunan, China.
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Khodadadi E, Maroufi P, Khodadadi E, Esposito I, Ganbarov K, Espsoito S, Yousefi M, Zeinalzadeh E, Kafil HS. Study of combining virtual screening and antiviral treatments of the Sars-CoV-2 (Covid-19). Microb Pathog 2020; 146:104241. [PMID: 32387389 PMCID: PMC7199731 DOI: 10.1016/j.micpath.2020.104241] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023]
Abstract
The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. Therefore, rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Additionally, general treatments, coronavirus-specific treatments, and antiviral treatments useful in fighting COVID-19 are addressed. This review sets out to shed light on the SARS-CoV-2 and host receptor recognition, a crucial factor for successful virus infection and taking immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein of SARS-CoV-2. A variety of improved or new approaches also have been developed. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection. Moreover, the genomic sequence of the virus responsible for COVID-19, as well as the experimentally determined three-dimensional structure of the Main protease (Mpro) is available. The reported structure of the target Mpro was described in this review to identify potential drugs for COVID-19 using virtual high throughput screening.
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Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Parham Maroufi
- Department of Orthopedy, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | | | | | | | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Facchetti F, Bugatti M, Drera E, Tripodo C, Sartori E, Cancila V, Papaccio M, Castellani R, Casola S, Boniotti MB, Cavadini P, Lavazza A. SARS-CoV2 vertical transmission with adverse effects on the newborn revealed through integrated immunohistochemical, electron microscopy and molecular analyses of Placenta. EBioMedicine 2020; 59:102951. [PMID: 32818801 PMCID: PMC7430280 DOI: 10.1016/j.ebiom.2020.102951] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND . The occurrence of trans-placental transmission of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection remains highly debated. Placental positivity for SARS-CoV-2 has been reported in selected cases, but infection or virus-associated disease of fetal tissues or newborns remains to be demonstrated. METHODS We screened for SARS-CoV-2 spike (S) protein expression placentas from 101 women who delivered between February 7 and May 15, 2020, including 15 tested positive for SARS-CoV-2 RNA, 34 tested negative, and 52 not evaluated as they did not meet testing criteria (32), or delivered before COVID-19 pandemic declaration (20). Immunostain for SARS-CoV-2 nucleocapsid (N) was performed in the placentas of all COVID-19 positive women. One placenta resulted positive for the SARS-CoV-2 S and N proteins, which was further studied by RNA-in situ hybridization and RT-PCR for S transcripts, and by electron microscopy. A comprehensive immunohistochemical and immunofluorescence analysis of the placental inflammatory infiltrate completed the investigations. FINDINGS SARS-CoV-2 S and N proteins were strongly expressed in the placenta of a COVID-19 pregnant woman whose newborn tested positive for viral RNA and developed COVID-19 pneumonia soon after birth. SARS-CoV-2 antigens, RNA and/or particles morphologically consistent with coronavirus were identified in villous syncytiotrophoblast, endothelial cells, fibroblasts, in maternal macrophages, and in Hofbauer cells and fetal intravascular mononuclear cells. The placenta intervillous inflammatory infiltrate consisted of neutrophils and monocyte-macrophages expressing activation markers. Absence of villitis was associated with an increase in the number of Hofbauer cells, which expressed PD-L1. Scattered neutrophil extracellular traps (NETs) were identified by immunofluorescence. INTERPRETATION We provide first-time evidence for maternal-fetal transmission of SARS-CoV-2, likely propagated by circulating virus-infected fetal mononuclear cells. Placenta infection was associated with recruitment of maternal inflammatory cells in the intervillous space, without villitis. PD-L1 expression in syncytiotrophoblast and Hofbaeur cells, together with limited production of NETs, may have prevented immune cell-driven placental damage, ensuring sufficient maternal-fetus nutrient exchanges.
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Affiliation(s)
- Fabio Facchetti
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy.
| | - Mattia Bugatti
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Emma Drera
- Pathology Unit, Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo School of Medicine, 90134, Palermo, Italy
| | - Enrico Sartori
- Department of Obstetrics and Gynaecology, University of Brescia, 25123, Brescia, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo School of Medicine, 90134, Palermo, Italy
| | - Marta Papaccio
- Department of Obstetrics and Gynaecology, University of Brescia, 25123, Brescia, Italy
| | - Roberta Castellani
- Department of Obstetrics and Gynaecology, University of Brescia, 25123, Brescia, Italy
| | - Stefano Casola
- The FIRC Institute of Molecular Oncology (IFOM), 20139, Milan, Italy
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (I.Z.S.L.E.R.), 25124 Brescia, Italy
| | - Patrizia Cavadini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (I.Z.S.L.E.R.), 25124 Brescia, Italy
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (I.Z.S.L.E.R.), 25124 Brescia, Italy
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42
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Gupta R, Charron J, Stenger CL, Painter J, Steward H, Cook TW, Faber W, Frisch A, Lind E, Bauss J, Li X, Sirpilla O, Soehnlen X, Underwood A, Hinds D, Morris M, Lamb N, Carcillo JA, Bupp C, Uhal BD, Rajasekaran S, Prokop JW. SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics. J Biol Chem 2020; 295:11742-11753. [PMID: 32587094 PMCID: PMC7450099 DOI: 10.1074/jbc.ra120.014873] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 06/23/2020] [Indexed: 12/28/2022] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has challenged the speed at which laboratories can discover the viral composition and study health outcomes. The small ∼30-kb ssRNA genome of coronaviruses makes them adept at cross-species spread while enabling a robust understanding of all of the proteins the viral genome encodes. We have employed protein modeling, molecular dynamics simulations, evolutionary mapping, and 3D printing to gain a full proteome- and dynamicome-level understanding of SARS-CoV-2. We established the Viral Integrated Structural Evolution Dynamic Database (VIStEDD at RRID:SCR_018793) to facilitate future discoveries and educational use. Here, we highlight the use of VIStEDD for nsp6, nucleocapsid (N), and spike (S) surface glycoprotein. For both nsp6 and N, we found highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we developed a quantitative dynamics cross-correlation matrix to gain insights into its interactions with the angiotensin I-converting enzyme 2 (ACE2)-solute carrier family 6 member 19 (SLC6A19) dimer. Using this quantitative matrix, we elucidated 47 potential functional missense variants from genomic databases within ACE2/SLC6A19/transmembrane serine protease 2 (TMPRSS2), warranting genomic enrichment analyses in SARS-CoV-2 patients. These variants had ultralow frequency but existed in males hemizygous for ACE2. Two ACE2 noncoding variants (rs4646118 and rs143185769) present in ∼9% of individuals of African descent may regulate ACE2 expression and may be associated with increased susceptibility of African Americans to SARS-CoV-2. We propose that this SARS-CoV-2 database may aid research into the ongoing pandemic.
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MESH Headings
- Amino Acid Transport Systems, Neutral/chemistry
- Amino Acid Transport Systems, Neutral/genetics
- Amino Acid Transport Systems, Neutral/metabolism
- Angiotensin-Converting Enzyme 2
- Betacoronavirus/chemistry
- Betacoronavirus/genetics
- Black People/genetics
- COVID-19
- Coronavirus Infections/metabolism
- Coronavirus Infections/virology
- Coronavirus Nucleocapsid Proteins
- Databases, Protein
- Genetic Predisposition to Disease
- Genetic Variation
- Host-Pathogen Interactions
- Humans
- Male
- Molecular Dynamics Simulation
- Nucleocapsid Proteins/chemistry
- Nucleocapsid Proteins/metabolism
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Phosphoproteins
- Pneumonia, Viral/metabolism
- Pneumonia, Viral/virology
- Protein Interaction Maps
- Protein Processing, Post-Translational
- Proteome
- SARS-CoV-2
- Sequence Homology, Amino Acid
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Ruchir Gupta
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Jacob Charron
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
- Calvin University, Grand Rapids, Michigan, USA
| | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Jared Painter
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Hunter Steward
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Taylor W Cook
- Grand Rapids Community College, Grand Rapids, Michigan, USA
| | - William Faber
- Grand Rapids Community College, Grand Rapids, Michigan, USA
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Eric Lind
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Olivia Sirpilla
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
- Walsh University, North Canton, Ohio, USA
| | - Xavier Soehnlen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
- Walsh University, North Canton, Ohio, USA
| | | | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Joseph A Carcillo
- Department of Critical Care Medicine and Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Caleb Bupp
- Spectrum Health Medical Genetics, Grand Rapids, Michigan, USA
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, Michigan, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA
- Office of Research, Spectrum Health, Grand Rapids, Michigan, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
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43
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González-González E, Trujillo-de Santiago G, Lara-Mayorga IM, Martínez-Chapa SO, Alvarez MM. Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection. PLoS One 2020; 15:e0237418. [PMID: 32790779 PMCID: PMC7425953 DOI: 10.1371/journal.pone.0237418] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/27/2020] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has crudely demonstrated the need for massive and rapid diagnostics. By the first week of July, more than 10,000,000 positive cases of COVID-19 have been reported worldwide, although this number could be greatly underestimated. In the case of an epidemic emergency, the first line of response should be based on commercially available and validated resources. Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. We used the miniPCR to detect and amplify SARS-CoV-2 DNA sequences using the sets of initiators recommended by the World Health Organization (WHO) for targeting three different regions that encode for the N protein. Prior to amplification, samples were combined with a DNA intercalating reagent (i.e., EvaGreen Dye). Sample fluorescence after amplification was then read using a commercial 96-well plate reader. This straightforward method allows the detection and amplification of SARS-CoV-2 nucleic acids in the range of ~625 to 2×105 DNA copies. The accuracy and simplicity of this diagnostics strategy may provide a cost-efficient and reliable alternative for COVID-19 pandemic testing, particularly in underdeveloped regions where RT-QPCR instrument availability may be limited. The portability, ease of use, and reproducibility of the miniPCR makes it a reliable alternative for deployment in point-of-care SARS-CoV-2 detection efforts during pandemics.
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Affiliation(s)
- Everardo González-González
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Ingeniería Mecátrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Itzel Montserrat Lara-Mayorga
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Sergio Omar Martínez-Chapa
- Departamento de Ingeniería Mecátrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
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44
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Dao Thi VL, Herbst K, Boerner K, Meurer M, Kremer LP, Kirrmaier D, Freistaedter A, Papagiannidis D, Galmozzi C, Stanifer ML, Boulant S, Klein S, Chlanda P, Khalid D, Barreto Miranda I, Schnitzler P, Kräusslich HG, Knop M, Anders S. A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples. Sci Transl Med 2020; 12:eabc7075. [PMID: 32719001 PMCID: PMC7574920 DOI: 10.1126/scitranslmed.abc7075] [Citation(s) in RCA: 404] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)-based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab-to-RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions.
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Affiliation(s)
- Viet Loan Dao Thi
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany.
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Konrad Herbst
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Kathleen Boerner
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Matthias Meurer
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Lukas Pm Kremer
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Daniel Kirrmaier
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrew Freistaedter
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | | | - Carla Galmozzi
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Megan L Stanifer
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Klein
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Dina Khalid
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | | | - Paul Schnitzler
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
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45
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Yip CCY, Sridhar S, Leung KH, Ng ACK, Chan KH, Chan JFW, Tsang OTY, Hung IFN, Cheng VCC, Yuen KY, To KKW. Development and Evaluation of Novel and Highly Sensitive Single-Tube Nested Real-Time RT-PCR Assays for SARS-CoV-2 Detection. Int J Mol Sci 2020; 21:ijms21165674. [PMID: 32784770 PMCID: PMC7461039 DOI: 10.3390/ijms21165674] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Sensitive molecular assays are critical for coronavirus disease 2019 (COVID-19) diagnosis. Here, we designed and evaluated two single-tube nested (STN) real-time RT-PCR assays, targeting SARS-CoV-2 RdRp/Hel and N genes. Both STN assays had a low limit of detection and did not cross react with other human coronaviruses and respiratory viruses. Using 213 initial respiratory specimens from suspected COVID-19 patients, the sensitivity of both the STN COVID-19-RdRp/Hel and the STN COVID-19-N assays was 100% (99/99), while that of the comparator non-nested N assay was 95% (94/99). Among 108 follow-up specimens from confirmed COVID-19 patients who tested negative by the non-nested COVID-19-RdRp/Hel assay, 28 (25.9%) were positive for SARS-CoV-2 by the STN COVID-19-RdRp/Hel or the STN COVID-19-N assay. To evaluate the performance of our novel STN assays in pooled specimens, we created four sample pools, with each pool consisting of one low positive specimen and 49 negative specimens. While the non-nested COVID-19-RdRp/Hel assay was positive in only one of four sample pools (25%), both of the STN assays were positive in two of four samples pools (50%). In conclusion, the STN assays are highly sensitive and specific for SARS-CoV-2 detection. Their boosted sensitivity offers advantages in non-traditional COVID-19 testing algorithms such as saliva screening and pooled sample screening during massive screening.
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Affiliation(s)
- Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China; (C.C.-Y.Y.); (V.C.-C.C.)
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kit-Hang Leung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
| | - Anthony Chin-Ki Ng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Owen Tak-Yin Tsang
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong, China;
| | | | | | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China; (C.C.-Y.Y.); (V.C.-C.C.)
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Correspondence: (K.-Y.Y.); (K.K.-W.T.); Tel.: +852-2255-2584 (K.-Y.Y. & K.K.-W.T.); Fax: +852-2855-1241 (K.-Y.Y. & K.K.-W.T.)
| | - Kelvin Kai-Wang To
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; (S.S.); (K.-H.L.); (A.C.-K.N.); (K.-H.C.); (J.F.-W.C.)
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Correspondence: (K.-Y.Y.); (K.K.-W.T.); Tel.: +852-2255-2584 (K.-Y.Y. & K.K.-W.T.); Fax: +852-2855-1241 (K.-Y.Y. & K.K.-W.T.)
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46
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Zhang BZ, Hu YF, Chen LL, Yau T, Tong YG, Hu JC, Cai JP, Chan KH, Dou Y, Deng J, Wang XL, Hung IFN, To KKW, Yuen KY, Huang JD. Mining of epitopes on spike protein of SARS-CoV-2 from COVID-19 patients. Cell Res 2020; 30:702-704. [PMID: 32612199 DOI: 10.1101/2020.04.23.056853] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/19/2020] [Indexed: 05/27/2023] Open
Abstract
AbstractThe ongoing coronavirus disease 2019 (COVID-19) pandemic is a serious threat to global public health, and imposes severe burdens on the entire human society. The severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) can cause severe respiratory illness and death. Currently, there are no specific antiviral drugs that can treat COVID-19. Several vaccines against SARS-CoV-2 are being actively developed by research groups around the world. The surface S (spike) protein and the highly expressed internal N (nucleocapsid) protein of SARS-CoV-2 are widely considered as promising candidates for vaccines. In order to guide the design of an effective vaccine, we need experimental data on these potential epitope candidates. In this study, we mapped the immunodominant (ID) sites of S protein using sera samples collected from recently discharged COVID-19 patients. The SARS-CoV-2 S protein-specific antibody levels in the sera of recovered COVID-19 patients were strongly correlated with the neutralising antibody titres. We used epitope mapping to determine the landscape of ID sites of S protein, which identified nine linearized B cell ID sites. Four out of the nine ID sites were found in the receptor-binding domain (RBD). Further analysis showed that these ID sites are potential high-affinity SARS-CoV-2 antibody binding sites. Peptides containing two out of the nine sites were tested as vaccine candidates against SARS-CoV-2 in a mouse model. We detected epitope-specific antibodies and SARS-CoV-2-neutralising activity in the immunised mice. This study for the first time provides human serological data for the design of vaccines against COVID-19.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Viral/blood
- Betacoronavirus/chemistry
- COVID-19
- Coronavirus Infections/blood
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Coronavirus Nucleocapsid Proteins
- Epitopes, T-Lymphocyte/immunology
- Female
- Humans
- Male
- Mice
- Mice, Inbred BALB C
- Middle Aged
- Nucleocapsid Proteins/immunology
- Pandemics/prevention & control
- Phosphoproteins
- Pneumonia, Viral/blood
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/immunology
- Viral Vaccines/immunology
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Affiliation(s)
- Bao-Zhong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Ye-Fan Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
- Department of Medicine, University of Hong Kong, 4/F Professional Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Lin-Lei Chen
- Department of Microbiology, University of Hong Kong, 19/F T Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Thomas Yau
- Department of Medicine, University of Hong Kong, 4/F Professional Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Yi-Gang Tong
- Beijing Advanced Innovation Centre for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jing-Chu Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Jian-Piao Cai
- Department of Microbiology, University of Hong Kong, 19/F T Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, University of Hong Kong, 19/F T Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Ying Dou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Jian Deng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Xiao-Lei Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, University of Hong Kong, 4/F Professional Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, University of Hong Kong, 19/F T Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China.
| | - Kwok Yung Yuen
- Department of Microbiology, University of Hong Kong, 19/F T Block, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong, China.
| | - Jian-Dong Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China.
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 3/F, Laboratory Block, 21 Sassoon Road, Hong Kong, China.
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47
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Lu X, Wang L, Sakthivel SK, Whitaker B, Murray J, Kamili S, Lynch B, Malapati L, Burke SA, Harcourt J, Tamin A, Thornburg NJ, Villanueva JM, Lindstrom S. US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis 2020; 26:1654-1665. [PMID: 32396505 PMCID: PMC7392423 DOI: 10.3201/eid2608.201246] [Citation(s) in RCA: 397] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the etiologic agent associated with coronavirus disease, which emerged in late 2019. In response, we developed a diagnostic panel consisting of 3 real-time reverse transcription PCR assays targeting the nucleocapsid gene and evaluated use of these assays for detecting SARS-CoV-2 infection. All assays demonstrated a linear dynamic range of 8 orders of magnitude and an analytical limit of detection of 5 copies/reaction of quantified RNA transcripts and 1 x 10-1.5 50% tissue culture infectious dose/mL of cell-cultured SARS-CoV-2. All assays performed comparably with nasopharyngeal and oropharyngeal secretions, serum, and fecal specimens spiked with cultured virus. We obtained no false-positive amplifications with other human coronaviruses or common respiratory pathogens. Results from all 3 assays were highly correlated during clinical specimen testing. On February 4, 2020, the Food and Drug Administration issued an Emergency Use Authorization to enable emergency use of this panel.
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48
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Van Elslande J, Decru B, Jonckheere S, Van Wijngaerden E, Houben E, Vandecandelaere P, Indevuyst C, Depypere M, Desmet S, André E, Van Ranst M, Lagrou K, Vermeersch P. Antibody response against SARS-CoV-2 spike protein and nucleoprotein evaluated by four automated immunoassays and three ELISAs. Clin Microbiol Infect 2020; 26:1557.e1-1557.e7. [PMID: 32745595 PMCID: PMC7834107 DOI: 10.1016/j.cmi.2020.07.038] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 01/10/2023]
Abstract
Objectives The aim was to determine the antibody response against SARS-CoV-2 spike protein and nucleoprotein using four automated immunoassays and three ELISAs for the detection of total Ig antibodies (Roche) or IgG (Abbott, Diasorin, Snibe, Euroimmun, Mikrogen) in COVID-19 patients. Methods Sensitivity and dynamic trend to seropositivity were evaluated in 233 samples from 114 patients with moderate, severe or critical COVID-19 confirmed with PCR on nasopharyngeal swab. Specificity was evaluated in 113 samples collected before January 2020, including 24 samples from patients with non-SARS coronavirus infection. Results Sensitivity for all assays was 100% (95% confidence interval 83.7–100) 3 weeks after onset of symptoms. Specificity varied between 94.7% (88.7–97.8) and 100% (96.1–100). Calculated at the cut-offs that corresponded to a specificity of 95% and 97.5%, Roche had the highest sensitivity (85.0% (79.8–89.0) and 81.1% (76.6–85.7), p < 0.05 except vs. Abbott). Seroconversion occurred on average 2 days earlier for Roche total Ig anti-N and the three IgG anti-N assays (Abbott, Mikrogen, Euroimmun) than for the two IgG anti-S assays (Diasorin, Euroimmun) (≥50% seroconversion day 9–10 vs. day 11–12 and p < 0.05 for percent seropositive patients day 9–10 to 17–18). There was no significant difference in the IgG antibody time to seroconversion between critical and non-critical patients. Discussion Seroconversion occurred within 3 weeks after onset of symptoms with all assays and on average 2 days earlier for assays detecting IgG or total Ig anti-N than for IgG anti-S. The specificity of assays detecting anti-N was comparable to anti-S and excellent in a challenging control population.
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Affiliation(s)
- Jan Van Elslande
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Bram Decru
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Stijn Jonckheere
- Laboratory of Microbiology, Jan Yperman Hospital, Ieper, Belgium
| | - Eric Van Wijngaerden
- General Internal Medicine & Infectious Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Els Houben
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Melissa Depypere
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Stefanie Desmet
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Emmanuel André
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Pieter Vermeersch
- Clinical Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium.
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49
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Wu T, Ge Y, Zhao K, Zhu X, Chen Y, Wu B, Zhu F, Zhu B, Cui L. A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2). Virology 2020; 549:1-4. [PMID: 32758712 PMCID: PMC7388781 DOI: 10.1016/j.virol.2020.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 11/19/2022]
Abstract
The current outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China firstly. A rapid, highly sensitive, specific, and simple operational method was needed for the detection of SARS-CoV-2. Here, we established a real-time reverse-transcription recombinase-aided amplification assay (RT-RAA) to detect SARS-CoV-2 rapidly. The primers and probe were designed based on the nucleocapsid protein gene (N gene) sequence of SARS-CoV-2. The detection limit was 10 copies per reaction in this assay, which could be conducted within 15 min at a constant temperature (39 °C), without any cross-reactions with other respiratory tract pathogens, such as other coronaviruses. Furthermore, compared with commercial real-time RT-PCR assay, it showed a kappa value of 0.959 (p < 0.001) from 150 clinical specimens. These results indicated that this real-time RT-RAA assay may be a valuable tool for detecting SARS-CoV-2.
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Affiliation(s)
- Tao Wu
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China.
| | - Yiyue Ge
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Kangchen Zhao
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Xiaojuan Zhu
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Yin Chen
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Bin Wu
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Fengcai Zhu
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Baoli Zhu
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China; From Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Lunbiao Cui
- From Institute of Pathogenic Microbiology, NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
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50
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Wang J, Cai K, Zhang R, He X, Shen X, Liu J, Xu J, Qiu F, Lei W, Wang J, Li X, Gao Y, Jiang Y, Xu W, Ma X. Novel One-Step Single-Tube Nested Quantitative Real-Time PCR Assay for Highly Sensitive Detection of SARS-CoV-2. Anal Chem 2020; 92:9399-9404. [PMID: 32438806 PMCID: PMC7299395 DOI: 10.1021/acs.analchem.0c01884] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 05/22/2020] [Indexed: 12/20/2022]
Abstract
Coronavirus disease 2019 (COVID-19) has become a public health emergency. The reverse transcriptase real-time quantitative PCR (qRT-PCR) test is currently considered as the gold standard in the laboratory for the etiological detection of COVID-19. However, qRT-PCR results could be false-negative due to the inadequate sensitivity of qRT-PCR. In this study, we have developed and evaluated a novel one-step single-tube nested quantitative real-time PCR (OSN-qRT-PCR) assay for the highly sensitive detection of SARS-CoV-2 targeting the ORF1ab and N genes. The sensitivity of the OSN-qRT-PCR assay was 1 copy/reaction and 10-fold higher than that of the commercial qRT-PCR kit (10 copies/reaction). The clinical performance of the OSN-qRT-PCR assay was evaluated using 181 clinical samples. Among them, 14 qRT-PCR-negative samples (7 had no repetitive results and 7 had no cycle threshold (CT) values) were detected by OSN-qRT-PCR. Moreover, the 7 qRT-PCR-positives in the qRT-PCR gray zone (CT values of ORF1ab ranged from 37.48 to 39.07, and CT values of N ranged from 37.34 to 38.75) were out of the gray zone and thus were deemed to be positive by OSN-qRT-PCR, indicating that the positivity of these samples is confirmative. Compared to the qRT-PCR kit, the OSN-qRT-PCR assay revealed higher sensitivity and specificity, showing better suitability to clinical applications for the detection of SARS-CoV-2 in patients with low viral load.
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Affiliation(s)
- Ji Wang
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
| | - Kun Cai
- Hubei Center for Disease
Control and Prevention, Wuhan 430000,
China
| | - Ruiqing Zhang
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
- Hebei General
Hospital, Shijiazhuang 050051,
China
| | - Xiaozhou He
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
| | - Xinxin Shen
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
| | - Jun Liu
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
| | - Junqiang Xu
- Hubei Center for Disease
Control and Prevention, Wuhan 430000,
China
| | - Feng Qiu
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
| | - Wenwen Lei
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
| | - Jinrong Wang
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
- Hebei Medical
University, Shijiazhuang 050031,
China
| | - Xinna Li
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
| | - Yuan Gao
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
- Hebei Medical
University, Shijiazhuang 050031,
China
| | - Yongzhong Jiang
- Hubei Center for Disease
Control and Prevention, Wuhan 430000,
China
| | - Wenbo Xu
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
| | - Xuejun Ma
- National Institute for
Viral Disease Control and Prevention, Chinese Center for Disease
Control and Prevention, Beijing 102206,
China
- Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan
430071, China
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