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A Unique Trinucleotide-Bloc Mutation-Based Two SARS-CoV-2 Genotypes with Potential Pathogenic Impacts. Adv Virol 2022; 2022:5618222. [PMID: 35899232 PMCID: PMC9314171 DOI: 10.1155/2022/5618222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/27/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
SARS-CoV-2, the novel coronavirus behind the COVID-19 pandemic, is acquiring new mutations in its genome. Although some mutations provide benefits to the virus against human immune response, others may result in their reduced pathogenicity and virulence. By analyzing more than 3000 high-coverage, complete sequences deposited in the GISAID database up to April 2020, here I report the uniqueness of the 28881–28883: GGG > AAC trinucleotide-bloc mutation in the SARS-CoV-2 genome that results in two substrains, described here as SARS-CoV-2g (28881–28883: GGG genotype) and SARS-CoV-2a (28881–28883: AAC genotype). Computational analysis and literature review suggest that this bloc mutation would bring 203–204: RG (arginine-glycine)>KR (lysine-arginine) amino acid changes in the nucleocapsid (N) protein affecting the SR (serine-arginine)-rich motif of the protein, a critical region for the transcription of viral RNA and replication of the virus. Thus, 28881–28883: GGG > AAC bloc mutation is expected to modulate the pathogenicity of SARS-CoV-2. These analyses suggest that SARS-CoV-2 has evolved into SARS-CoV-2a affecting COVID-19 infectivity and severity. To confirm these assumptions, retrospective and prospective epidemiological studies should be conducted in different countries to understand the course of pathogenicity of SARS-CoV-2a and SARS-CoV-2g. Laboratory research should focus on the bloc mutation to understand its true impacts on the course of the pandemic. Potential drug and vaccine development should also keep the 28881–28883 region of the N protein under consideration.
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Identification of a SARS-CoV-2 Lineage B1.1.7 Virus in New York following Return Travel from the United Kingdom. Microbiol Resour Announc 2021; 10:10/9/e00097-21. [PMID: 33664151 PMCID: PMC7936631 DOI: 10.1128/mra.00097-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Here, we report the identification and coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain (NYI.B1-7.01-21) obtained from a patient with symptoms of COVID-19 who had a recent travel history to the United Kingdom. The sample was tested by the Cayuga Health Systems laboratory as part of New York State’s travel testing guidance and was sequenced at Cornell University after testing positive. Here, we report the identification and coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain (NYI.B1-7.01-21) obtained from a patient with symptoms of COVID-19 who had a recent travel history to the United Kingdom. The sample was tested by the Cayuga Health Systems laboratory as part of New York State’s travel testing guidance and was sequenced at Cornell University after testing positive.
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Tsai CW, Jheng SL, Chen WY, Ruaan RC. Strategy of Fc-Recognizable Peptide Ligand Design for Oriented Immobilization of Antibody. Anal Chem 2014; 86:2931-8. [DOI: 10.1021/ac4029467] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Ching-Wei Tsai
- Department
of Chemical and Materials Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
| | - Siang-Long Jheng
- Department
of Chemical and Materials Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
| | - Wen-Yih Chen
- Department
of Chemical and Materials Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
- Institute
of Biomedical Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
| | - Ruoh-Chyu Ruaan
- Department
of Chemical and Materials Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
- Institute
of Biomedical Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
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Tsai CW, Ruaan RC, Liu CI. Adsorption of antimicrobial indolicidin-derived peptides on hydrophobic surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10446-10452. [PMID: 22721449 DOI: 10.1021/la301401v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The hydrophobic interaction between antimicrobial peptides and membrane hydrophobic cores is usually related to their cytotoxicity. In this study, the adsorption mechanism of five plasma membrane-associated peptides, indolicidin (IL) and its four derivatives, with hydrophobic ligands was investigated to understand the relationship between peptide hydrophobicity and bioactivity. The hydrophobic adsorption mechanisms of IL and its derivatives were interpreted thermodynamically and kinetically by reversed-phase chromatography (RPC) analysis and surface plasmon resonance (SPR) measurement, respectively. IL and its derivatives possess a similar random coil structure in both aqueous and organic solvents. Thermodynamic analysis showed that the binding enthalpy of peptides with higher electropositivity was lower than those with lower electropositivity and exhibited unfavorable binding entropy. Higher electropositivity peptides adsorbed to the hydrophobic surface arising from the less bound solvent on the peptide surface. A comparison with the kinetic analysis showed that IL and its derivatives adopt a two-state binding model (i.e., adsorption onto and self-association on the hydrophobic acyl chain) to associate with the hydrophobic surface, and the binding affinity of peptide self-association correlates well with peptide hemolysis. Consequently, this study provided a novel concept for understanding the action of plasma membrane-associated peptides.
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Affiliation(s)
- Ching-Wei Tsai
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, Taiwan
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Tsai CW, Liu CI, Chan YC, Tsai HHG, Ruaan RC. Study of Conformation Effects on the Retention of Small Peptides in Reversed-Phase Chromatography by Thermodynamic Analysis and Molecular Dynamics Simulation. J Phys Chem B 2010; 114:11620-7. [DOI: 10.1021/jp101846n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ching-W Tsai
- Department of Chemical and Materials Engineering, and Department of Chemistry, National Central University, Jhong-Li, Taiwan 320, R&D Center for Membrane Technology, Department of Chemical Engineering, Chung Yuan Christian University, Jhong-Li, Taoyuan 320, Taiwan, and Department of Nursing, Mei-Ho Institute of Technology, Pintung 912, Taiwan
| | - Chih-I Liu
- Department of Chemical and Materials Engineering, and Department of Chemistry, National Central University, Jhong-Li, Taiwan 320, R&D Center for Membrane Technology, Department of Chemical Engineering, Chung Yuan Christian University, Jhong-Li, Taoyuan 320, Taiwan, and Department of Nursing, Mei-Ho Institute of Technology, Pintung 912, Taiwan
| | - Ying-C Chan
- Department of Chemical and Materials Engineering, and Department of Chemistry, National Central University, Jhong-Li, Taiwan 320, R&D Center for Membrane Technology, Department of Chemical Engineering, Chung Yuan Christian University, Jhong-Li, Taoyuan 320, Taiwan, and Department of Nursing, Mei-Ho Institute of Technology, Pintung 912, Taiwan
| | - Hui-H G Tsai
- Department of Chemical and Materials Engineering, and Department of Chemistry, National Central University, Jhong-Li, Taiwan 320, R&D Center for Membrane Technology, Department of Chemical Engineering, Chung Yuan Christian University, Jhong-Li, Taoyuan 320, Taiwan, and Department of Nursing, Mei-Ho Institute of Technology, Pintung 912, Taiwan
| | - Ruoh-C Ruaan
- Department of Chemical and Materials Engineering, and Department of Chemistry, National Central University, Jhong-Li, Taiwan 320, R&D Center for Membrane Technology, Department of Chemical Engineering, Chung Yuan Christian University, Jhong-Li, Taoyuan 320, Taiwan, and Department of Nursing, Mei-Ho Institute of Technology, Pintung 912, Taiwan
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