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Yin W, Hu J, Chen F, Zhu L, Ma Y, Wang N, Wei H, Yang H, Chou SH, He J. Combining hybrid nanoflowers with hybridization chain reaction for highly sensitive detection of SARS-CoV-2 nucleocapsid protein. Anal Chim Acta 2023; 1279:341838. [PMID: 37827653 DOI: 10.1016/j.aca.2023.341838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND COVID-19 (coronavirus disease 2019) pandemic has had enormous social and economic impacts so far. The nucleocapsid protein (N protein) is highly conserved and is a key antigenic marker for the diagnosis of early SARS-CoV-2 infection. RESULTS In this study, the N protein was first captured by an aptamer (Aptamer 58) coupled to magnetic beads (MBs), which in turn were bound to another DNA sequence containing the aptamer (Aptamer 48-Initiator). After adding 5'-biotinylated hairpin DNA Amplifier 1 and Amplifier 2 with cohesive ends for complementary hybridization, the Initiator in the Aptamer 48-Initiator began to trigger the hybridization chain reaction (HCR), generating multiple biotin-labeled DNA concatamers. When incubated with synthetic streptavidin-invertase-Ca3(PO4)2 hybrid nanoflower (SICa), DNA concatamers could specifically bind to SICa through biotin-streptavidin interaction with high affinity. After adding sucrose, invertase in SICa hydrolyzed sucrose to glucose, whose concentration could be directly read with a portable glucometer, and its concentration was positively correlated with the amount of captured N protein. The method is highly sensitive with a detection limit as low as 1 pg/mL. SIGNIFICANCE We believe this study provided a practical solution for the early detection of SARS-CoV-2 infection, and offered a new method for detecting other viruses through different target proteins.
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Affiliation(s)
- Wen Yin
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Ji Hu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Chen
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Zhu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Nuo Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430000, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430000, China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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2
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Kelly DF, Jonaid GM, Kaylor L, Solares MJ, Berry S, DiCecco LA, Dearnaley W, Casasanta M. Delineating Conformational Variability in Small Protein Structures Using Combinatorial Refinement Strategies. MICROMACHINES 2023; 14:1869. [PMID: 37893306 PMCID: PMC10609307 DOI: 10.3390/mi14101869] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023]
Abstract
As small protein assemblies and even small proteins are becoming more amenable to cryo-Electron Microscopy (EM) structural studies, it is important to consider the complementary dynamic information present in the data. Current computational strategies are limited in their ability to resolve minute differences among low molecular weight entities. Here, we demonstrate a new combinatorial approach to delineate flexible conformations among small proteins using real-space refinement applications. We performed a meta-analysis of structural data for the SARS CoV-2 Nucleocapsid (N) protein using a combination of rigid-body refinement and simulated annealing methods. For the N protein monomer, we determined three new flexible conformers with good stereochemistry and quantitative comparisons provided new evidence of their dynamic properties. A similar analysis performed for the N protein dimer showed only minor structural differences among the flexible models. These results suggested a more stable view of the N protein dimer than the monomer structure. Taken together, the new computational strategies can delineate conformational changes in low molecular weight proteins that may go unnoticed by conventional assessments. The results also suggest that small proteins may be further stabilized for structural studies through the use of solution components that limit the movement of external flexible regions.
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Affiliation(s)
- Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - G M Jonaid
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Liam Kaylor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Maria J. Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Samantha Berry
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Liza-Anastasia DiCecco
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - William Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
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3
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Lian Z, Wu T, Wang H, Chi J, Cheng L, Xie D, Pan X, Hu Y, Tan Z, Chen S, Yang X, Yun Y, Wu W, Li C, Su M, Song Y. At-Home COVID-19 Rapid Antigen Test Down to 0.03 pg mL -1 of Nucleocapsid Protein. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2301162. [PMID: 36988021 DOI: 10.1002/smll.202301162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Rapid and ultra-sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for early screening and management of COVID-19. Currently, the real-time reverse transcription polymerase chain reaction (rRT-PCR) is the primary laboratory method for diagnosing SARS-CoV-2. It is not suitable for at-home COVID-19 diagnostic test due to the long operating time, specific equipment, and professional procedures. Here an all-printed photonic crystal (PC) microarray with portable device for at-home COVID-19 rapid antigen test is reported. The fluorescence-enhanced effect of PC amplifies the fluorescence intensity of the labeled probe, achieving detection of nucleocapsid (N-) protein down to 0.03 pg mL-1 . A portable fluorescence intensity measurement instrument gives the result (negative or positive) by the color of the indicator within 5 s after inserting the reacted PC microarray test card. The N protein in inactivated virus samples (with cycle threshold values of 26.6-40.0) can be detected. The PC microarray provides a general and easy-to-use method for the timely monitoring and eventual control of the global coronavirus pandemic.
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Affiliation(s)
- Zewei Lian
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Tingqing Wu
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Huadong Wang
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jimei Chi
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lijun Cheng
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Daixi Xie
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiangyu Pan
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yuming Hu
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhiyu Tan
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Sisi Chen
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xu Yang
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yang Yun
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Wei Wu
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Chunbao Li
- Peoples Liberat Army Gen Hosp, Med Ctr 4 Dept Orthopaed Med, Beijing, 100853, P. R. China
| | - Meng Su
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yanlin Song
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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4
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Solares MJ, Jonaid GM, Luqiu WY, Berry S, Khadela J, Liang Y, Evans MC, Pridham KJ, Dearnaley WJ, Sheng Z, Kelly DF. High-Resolution Imaging of Human Cancer Proteins Using Microprocessor Materials. Chembiochem 2022; 23:e202200310. [PMID: 35789183 PMCID: PMC9574649 DOI: 10.1002/cbic.202200310] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Indexed: 11/06/2022]
Abstract
Mutations in tumor suppressor genes, such as Tumor Protein 53 (TP53), are heavily implicated in aggressive cancers giving rise to gain- and loss-of-function phenotypes. While individual domains of the p53 protein have been studied extensively, structural information for full-length p53 remains incomplete. Functionalized microprocessor chips (microchips) with properties amenable to electron microscopy permitted us to visualize complete p53 assemblies for the first time. The new structures revealed p53 in an inactive dimeric state independent of DNA binding. Residues located at the protein-protein interface corresponded with modification sites in cancer-related hot spots. Changes in these regions may amplify the toxic effects of clinical mutations. Taken together, these results contribute advances in technology and imaging approaches to decode native protein models in different states of activation.
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Affiliation(s)
- Maria J Solares
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - G M Jonaid
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - William Y Luqiu
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Samantha Berry
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Janki Khadela
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yanping Liang
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA 24016, USA
| | - Madison C Evans
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Kevin J Pridham
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA 24016, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhi Sheng
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA 24016, USA
| | - Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA
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5
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Kelly DF, DiCecco LA, Jonaid GM, Dearnaley WJ, Spilman MS, Gray JL, Dressel-Dukes MJ. Liquid-EM goes viral - visualizing structure and dynamics. Curr Opin Struct Biol 2022; 75:102426. [PMID: 35868163 DOI: 10.1016/j.sbi.2022.102426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/27/2022] [Accepted: 06/16/2022] [Indexed: 11/27/2022]
Abstract
Liquid-electron microscopy (EM), the room temperature correlate to cryo-EM, is an exciting new technique delivering real-time data of dynamic reactions in solution. Here, we explain how liquid-EM gained popularity in recent years by examining key experiments conducted on viral assemblies and host-pathogen interactions. We describe developing workflows for specimen preparation, data collection, and computing processes that led to the first high-resolution virus structures in a liquid environment. Equally important, we review why liquid-electron tomography may become the next big thing in biomedical research due to its ability to monitor live viruses entering cells within seconds. Taken together, we pose the idea that liquid-EM can serve as a dynamic complement to current cryo-EM methods, inspiring the "real-time revolution" in nanoscale imaging.
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Affiliation(s)
- Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA; Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA.
| | - Liza-Anastasia DiCecco
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Department of Materials Science and Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada. https://twitter.com/LizaDiCecco
| | - G M Jonaid
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Center for Structural Oncology, Pennsylvania State University, University Park, PA 16802, USA; Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA. https://twitter.com/PennStateMRI
| | - Michael S Spilman
- Direct Electron, LP, San Diego, CA 92128, USA. https://twitter.com/DirectElectron
| | - Jennifer L Gray
- Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
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6
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Hou Y, Zhao S, Liu Q, Zhang X, Sha T, Su Y, Zhao W, Bao Y, Xue Y, Chen H. Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1214-1223. [PMID: 35760317 PMCID: PMC9233880 DOI: 10.1016/j.gpb.2022.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/21/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022]
Abstract
SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively through world populations since its first outbreak in December, 2019. Whether the transmissibility and pathogenicity of SARS-CoV-2 in humans after zoonotic transfer are actively evolving, and driven by adaptation to the new host and environments is still under debate. Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend, and providing guidance for disease control and treatments. Interrogating novel strategies for identifying natural selection using within-species polymorphisms and 3,674,076 SARS-CoV-2 genome sequences of 169 countries as of December 30, 2021, we demonstrate with population genetic evidence that during the course of SARS-CoV-2 pandemic in humans, 1) SARS-CoV-2 genomes are overall conserved under purifying selection, especially for the 14 genes related to viral RNA replication, transcription, and assembly; 2) ongoing positive selection is actively driving the evolution of 6 genes (e.g., S, ORF3a, and N) that play critical roles in molecular processes involving pathogen-host interactions, including viral invasion into and egress from host cells, and viral inhibition and evasion of host immune response, possibly leading to high transmissibility and mild symptom in SARS-CoV-2 evolution. According to an established haplotype phylogenetic relationship of 138 viral clusters, a spatial and temporal landscape of 556 critical mutations is constructed based on their divergence among viral haplotype clusters or repeatedly increase in frequency within at least 2 clusters, of which multiple mutations potentially conferring alterations in viral transmissibility, pathogenicity, and virulence of SARS-CoV-2 are highlighted, warranting attentions.
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Affiliation(s)
- Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilei Zhao
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Sha
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yankai Su
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenming Zhao
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongbiao Xue
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hua Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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7
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Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19042392. [PMID: 35206580 PMCID: PMC8877900 DOI: 10.3390/ijerph19042392] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/28/2022]
Abstract
Several coronaviruses (CoVs) have been identified as human pathogens, including the α-CoVs strains HCoV-229E and HCoV-NL63 and the β-CoVs strains HCoV-HKU1 and HCoV-OC43. SARS-CoV, MERS-CoV, and SARS-CoV-2 are also classified as β-coronavirus. New SARS-CoV-2 spike genomic variants are responsible for human-to-human and interspecies transmissibility, consequences of adaptations of strains from animals to humans. The receptor-binding domain (RBD) of SARS-CoV-2 binds to receptor ACE2 in humans and animal species with high affinity, suggesting there have been adaptive genomic variants. New genomic variants including the incorporation, replacement, or deletion of the amino acids at a variety of positions in the S protein have been documented and are associated with the emergence of new strains adapted to different hosts. Interactions between mutated residues and RBD have been demonstrated by structural modelling of variants including D614G, B.1.1.7, B1.351, P.1, P2; other genomic variants allow escape from antibodies generated by vaccines. Epidemiological and molecular tools are being used for real-time tracking of pathogen evolution and particularly new SARS-CoV-2 variants. COVID-19 vaccines obtained from classical and next-generation vaccine production platforms have entered clinicals trials. Biotechnology strategies of the first generation (attenuated and inactivated virus–CoronaVac, CoVaxin; BBIBP-CorV), second generation (replicating-incompetent vector vaccines–ChAdOx-1; Ad5-nCoV; Sputnik V; JNJ-78436735 vaccine-replicating-competent vector, protein subunits, virus-like particles–NVX-CoV2373 vaccine), and third generation (nucleic-acid vaccines–INO-4800 (DNA); mRNA-1273 and BNT 162b (RNA vaccines) have been used. Additionally, dendritic cells (LV-SMENP-DC) and artificial antigen-presenting (aAPC) cells modified with lentiviral vector have also been developed to inhibit viral activity. Recombinant vaccines against COVID-19 are continuously being applied, and new clinical trials have been tested by interchangeability studies of viral vaccines developed by classical and next-generation platforms.
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8
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Qi H, Hu Z, Yang Z, Zhang J, Wu JJ, Cheng C, Wang C, Zheng L. Capacitive Aptasensor Coupled with Microfluidic Enrichment for Real-Time Detection of Trace SARS-CoV-2 Nucleocapsid Protein. Anal Chem 2022; 94:2812-2819. [PMID: 34982528 PMCID: PMC8751652 DOI: 10.1021/acs.analchem.1c04296] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022]
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has lasted for almost 2 years. Stemming its spread has posed severe challenges for clinical virus detection. A long turnaround time, complicated operation, and low accuracy have become bottlenecks in developing detection techniques. Adopting a direct antigen detection strategy, we developed a fast-responding and quantitative capacitive aptasensor for ultratrace nucleocapsid protein detection based on a low-cost microelectrode array (MEA) chip. Employing the solid-liquid interface capacitance with a sensitivity of picofarad level, the tiny change on the MEA surface can be definitively detected. As a result, the limit of detection reaches an ultralow level of femtogram per milliliter in different matrices. Integrated with efficient microfluidic enrichment, the response time of this sensor from the sample to the result is shortened to 15 s, completely meeting the real-time detection demand. Moreover, the wide linear range of the sensor is from 10-5 to 10-2 ng/mL, and a high selectivity of 6369:1 is achieved. After application and evaluation in different environmental and body fluid matrices, this sensor and the detection method have proved to be a label-free, real-time, easy-to-operate, and specific strategy for SARS-CoV-2 screening and diagnosis.
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Affiliation(s)
- Haochen Qi
- College of Electrical and Electronic Engineering,
Wenzhou University, Wenzhou 325035,
China
| | - Zhiwen Hu
- School of Computer and Information Engineering,
Zhejiang Gongshang University, Hangzhou 310018,
China
| | - Zhongliang Yang
- Department of Electronic Engineering,
Tsinghua University, Beijing 100084,
China
| | - Jian Zhang
- College of Electrical and Electronic Engineering,
Wenzhou University, Wenzhou 325035,
China
- School of Food and Biological Engineering,
Hefei University of Technology, Hefei 230009,
China
| | - Jie Jayne Wu
- Department of Electrical Engineering and Computer
Science, The University of Tennessee, Knoxville, Tennessee
37996, United States
| | - Cheng Cheng
- Department of Engineering and Technology Management,
Morehead State University, Morehead, Kentucky 40351
United States
| | - Chunchang Wang
- Laboratory of Dielectric Functional Materials, School of
Materials Physics and Engineering, Anhui University, Hefei
230601, China
| | - Lei Zheng
- School of Food and Biological Engineering,
Hefei University of Technology, Hefei 230009,
China
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9
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Jonaid GM, Casasanta MA, Dearnaley WJ, Berry S, Kaylor L, Dressel-Dukes MJ, Spilman MS, Gray JL, Kelly DF. Automated Tools to Advance High-Resolution Imaging in Liquid. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-10. [PMID: 35048845 DOI: 10.1017/s1431927621013921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Liquid-electron microscopy (EM), the room-temperature correlate to cryo-EM, is a rapidly growing field providing high-resolution insights of macromolecules in solution. Here, we describe how liquid-EM experiments can incorporate automated tools to propel the field to new heights. We demonstrate fresh workflows for specimen preparation, data collection, and computing processes to assess biological structures in liquid. Adeno-associated virus (AAV) and the SARS-CoV-2 nucleocapsid (N) were used as model systems to highlight the technical advances. These complexes were selected based on their major differences in size and natural symmetry. AAV is a highly symmetric, icosahedral assembly with a particle diameter of ~25 nm. At the other end of the spectrum, N protein is an asymmetric monomer or dimer with dimensions of approximately 5–7 nm, depending upon its oligomerization state. Equally important, both AAV and N protein are popular subjects in biomedical research due to their high value in vaccine development and therapeutic efforts against COVID-19. Overall, we demonstrate how automated practices in liquid-EM can be used to decode molecules of interest for human health and disease.
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Affiliation(s)
- G M Jonaid
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Michael A Casasanta
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - William J Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Samantha Berry
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
| | - Liam Kaylor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA16802, USA
| | | | | | - Jennifer L Gray
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
| | - Deborah F Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA16802, USA
- Materials Research Institute, Pennsylvania State University, University Park, PA16802, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA16802, USA
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10
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Wu CR, Yin WC, Jiang Y, Xu HE. Structure genomics of SARS-CoV-2 and its Omicron variant: drug design templates for COVID-19. Acta Pharmacol Sin 2022; 43:3021-3033. [PMID: 35058587 PMCID: PMC8771608 DOI: 10.1038/s41401-021-00851-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/21/2021] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has brought an unprecedented public health crisis and persistently threatens to humanity. With tireless efforts from scientists around the world, understanding of the biology of coronavirus has been greatly enhanced over the past 2 years. Structural biology has demonstrated its powerful impact on uncovering structures and functions for the vast majority of SARS-CoV-2 proteins and guided the development of drugs and vaccines against COVID-19. In this review, we summarize current progress in the structural biology of SARS-CoV-2 and discuss important biological issues that remain to be addressed. We present the examples of structure-based design of Pfizer’s novel anti-SARS-CoV-2 drug PF-07321332 (Paxlovid), Merck’s nucleotide inhibitor molnupiravir (Lagevrio), and VV116, an oral drug candidate for COVID-19. These examples highlight the importance of structure in drug discovery to combat COVID-19. We also discussed the recent variants of Omicron and its implication in immunity escape from existing vaccines and antibody therapies.
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11
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Cassone A, Cauda R. Multicomponent vaccines to fight SARS-CoV-2 variants of concern. Vaccine 2021; 39:6969-6971. [PMID: 34743927 PMCID: PMC8557988 DOI: 10.1016/j.vaccine.2021.10.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/06/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Antonio Cassone
- Polo d'innovazione della genomica, genetica e biologia, c/o Toscana Life Sciences, Strada del Petriccio e Belriguardo, 53100 Siena, Italy.
| | - Roberto Cauda
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, Rome, Italy.
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