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Brudenell EL, Pohare MB, Zafred D, Phipps J, Hornsby HR, Darby JF, Dai J, Liggett E, Cain KM, Barran PE, de Silva TI, Sayers JR. Efficient overexpression and purification of severe acute respiratory syndrome coronavirus 2 nucleocapsid proteins in Escherichia coli. Biochem J 2024; 481:669-682. [PMID: 38713013 DOI: 10.1042/bcj20240019] [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: 01/22/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
The fundamental biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and its potential application as a vaccine component have received considerable attention since the outbreak of the Covid19 pandemic in late 2019. Here we report the scalable expression and purification of soluble, immunologically active, SARS-CoV-2 Ncap in Escherichia coli. Codon-optimised synthetic genes encoding the original Ncap sequence and four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into an inducible expression vector carrying a regulated bacteriophage T5 synthetic promoter controlled by lac operator binding sites. The constructs were used to express Ncap proteins and protocols developed which allow efficient production of purified Ncap with yields of over 200 mg per litre of culture media. These proteins were deployed in ELISA assays to allow comparison of their responses to human sera. Our results suggest that there was no detectable difference between the 6His-tagged and untagged original Ncap proteins but there may be a slight loss of sensitivity of sera to other Ncap isolates.
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Affiliation(s)
- Emma L Brudenell
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Manoj B Pohare
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Domen Zafred
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Janine Phipps
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Hailey R Hornsby
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - John F Darby
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Junxiao Dai
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Ellen Liggett
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Kathleen M Cain
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Thushan I de Silva
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
| | - Jon R Sayers
- Sheffield Institute for Nucleic Acids and Florey Institute, Section of Infection and Immunity, Division of Clinical Medicine, School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, U.K
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You R, Wu R, Wang X, Fu R, Xia N, Chen Y, Yang K, Chen J. Systematic Genomic Surveillance of SARS-CoV-2 at Xiamen International Airport and the Port of Xiamen Reveals the Importance of Incoming Travelers in Lineage Diversity. Viruses 2024; 16:132. [PMID: 38257832 PMCID: PMC10821529 DOI: 10.3390/v16010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Sever Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is still a threat to human health globally despite the World Health Organization (WHO) announcing the end of the COVID-19 pandemic. Continued surveillance of SARS-CoV-2 at national borders would be helpful in understanding the epidemics of novel imported variants and updating local strategies for disease prevention and treatment. This study focuses on the surveillance of imported SARS-CoV-2 variants among travelers entering Xiamen International Airport and the Port of Xiamen from February to August 2023. A total of 97 imported SARS-CoV-2 sequences among travelers from 223 cases collected from 12 different countries and regions were identified by real-time RT-PCR. Next-generation sequencing was used to generate high-quality complete sequences for phylogenetic and population dynamic analysis. The study revealed a dominant shift in variant distribution, in which the XBB subvariant (XBB.1.5, XBB.1.16, XBB.1.9, XBB.2.3, and EG.5.1) accounted for approximately 88.8% of the sequenced samples. In detail, clades 23D and 23E accounted for 26.2% and 21.4% of the sequenced samples, respectively, while clades 23B (13.6%) and 23F (10.7%) took the third and fourth spots in the order of imported sequences, respectively. Additionally, the XBB.2.3 variants were first identified in imported cases from the mainland of Xiamen, China on 27 February 2023. The spatiotemporal analyses of recent viral genome sequences from a limited number of travelers into Xiamen provide valuable insights into the situation surrounding SARS-CoV-2 and highlight the importance of sentinel surveillance of SARS-CoV-2 variants in the national border screening of incoming travelers, which serves as an early warning system for the presence of highly transmissible circulating SARS-CoV-2 lineages.
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Affiliation(s)
- Ruiluan You
- Xiamen International Travel Healthcare Center, Xiamen Entry-Exit Inspection and Quarantine Bureau, Xiamen 361001, China;
| | - Ruotong Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
| | - Xijing Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
| | - Rao Fu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, China
| | - Yixin Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, China
| | - Kunyu Yang
- Xiamen International Travel Healthcare Center, Xiamen Entry-Exit Inspection and Quarantine Bureau, Xiamen 361001, China;
| | - Junyu Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health & School of Life Sciences, Xiamen University, Xiamen 361102, China; (R.W.); (N.X.); (Y.C.)
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, China
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Feng Y, Yi J, Yang L, Wang Y, Wen J, Zhao W, Kim P, Zhou X. COV2Var, a function annotation database of SARS-CoV-2 genetic variation. Nucleic Acids Res 2024; 52:D701-D713. [PMID: 37897356 PMCID: PMC10767816 DOI: 10.1093/nar/gkad958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species transmission, viral immune escape, immune response level, viral transmission capability, viral evolution, host adaptability, viral protein structure, viral protein function, viral protein stability and concurrent mutations. Deep understanding the relationship between mutation sites and these factors is crucial for advancing our knowledge of SARS-CoV-2 and for developing effective responses. To fill this gap, we built COV2Var, a function annotation database of SARS-CoV-2 genetic variation, available at http://biomedbdc.wchscu.cn/COV2Var/. COV2Var aims to identify common mutations in SARS-CoV-2 variants and assess their effects, providing a valuable resource for intensive functional annotations of common mutations among SARS-CoV-2 variants.
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Affiliation(s)
- Yuzhou Feng
- Department of Laboratory Medicine and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Jiahao Yi
- School of Big Health, Guizhou Medical University, Guiyang 550025, China
| | - Lin Yang
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yanfei Wang
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianguo Wen
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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