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Khan SS, Ullah A. Comparative genomics of spike, envelope, and nucleocapsid protein of severe acute respiratory syndrome coronavirus 2. Afr Health Sci 2023; 23:384-399. [PMID: 38357143 PMCID: PMC10862604 DOI: 10.4314/ahs.v23i3.45] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) upsurge sprang up in Wuhan, China, in late December 2019. Objectives Due to the exceptionally high mutation frequency, comparative genomics of viruses isolated throughout time and in various geographical locations are crucial. To better understand how SARS-CoV-2 heterogeneity has changed around the globe, this research was conducted. Methods Nucleotide and protein sequences of SARS-CoV-2, SARS-CoV, and bat SARS-like CoV were extracted from the NCBI Virus database. The Wuhan SARS-CoV-2 variant was used as a reference. Molecular Evolutionary Genetics Study performed the phylogenetic analysis, while the Genome Detective Coronavirus Typing Tool performed the mutational analysis. Results The evolutionary research has revealed that bats are the primary host for coronavirus evolution and the origin of the formation of SARS-CoV and SARS-CoV-2. Numerous mutations have been discovered in the spike, envelope, and nucleocapsid protein. Conclusions The current research findings may have an implication that facilitates the development of prospective immunization candidates/small pharmacological compounds targeting COVID-19.
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Affiliation(s)
- Sufyan Sohail Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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Pei F, Feng S, Hu W, Liu B, Mu X, Hao Q, Cao Y, Lei W, Tong Z. Sandwich mode lateral flow assay for point-of-care detecting SARS-CoV-2. Talanta 2023; 253. [PMCID: PMC9612878 DOI: 10.1016/j.talanta.2022.124051] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The global corona virus disease 2019 (COVID-19) has been announced a pandemic outbreak, and has threatened human life and health seriously. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as its causative pathogen, is widely detected in the screening of COVID-19 patients, infected people and contaminated substances. Lateral flow assay (LFA) is a popular point-of-care detection method, possesses advantages of quick response, simple operation mode, portable device, and low cost. Based on the above advantages, LFA has been widely developed for detecting SARS-CoV-2. In this review, we summarized the articles about the sandwich mode LFA detecting SARS-CoV-2, classified according to the target detection objects indicating genes, nucleocapsid protein, spike protein, and specific antibodies of SARS-CoV-2. In each part, LFA is further classified and summarized according to different signal detection types. Additionally, the properties of the targets were introduced to clarify their detection significance. The review is expected to provide a helpful guide for LFA sensitization and marker selection of SARS-CoV-2.
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Affiliation(s)
- Fubin Pei
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, Jiangsu, China,State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Shasha Feng
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, Jiangsu, China,State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Wei Hu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Bing Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Xihui Mu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Qingli Hao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, Jiangsu, China
| | - Yang Cao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, Jiangsu, China
| | - Wu Lei
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, Jiangsu, China,Corresponding author
| | - Zhaoyang Tong
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China,Corresponding author
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Elssaig EH, Alnour TM, Ullah MF, Ahmed-Abakur EH. Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern. Pol J Microbiol 2022; 71:577-587. [PMID: 36537060 PMCID: PMC9944972 DOI: 10.33073/pjm-2022-053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/12/2022] [Indexed: 12/24/2022] Open
Abstract
This study aimed to determine the genetic alterations in the Omicron variants compared to other variants of concern (VOCs) to trace the evolutionary genetics of the SARS-CoV-2 variants responsible for the multiple COVID-19 waves globally. The present study is an in silico analysis determining the evolution of selected 11 VOCs compared to the original Wuhan strain. The variants included six Omicrons and one variant of Alpha, Beta, Delta, Gamma, and Mu. The pairwise alignment with the local alignment search tool of NCBI Nucleotide-BLAST and NCBI Protein-BLAST were used to determine the nucleotide base changes and corresponding amino acid changes in proteins, respectively. The genomic analysis revealed 210 nucleotide changes; most of these changes (127/210, 60.5%) were non-synonymous mutations that occurred mainly in the S gene (52/127, 40.1%). The remaining 10.5% (22/210) and 1.9% (4/210) of the mutations were frameshift deletions and frameshift insertions, respectively. The frameshift insertion (Ins22194T T22195G) led to frameshift deletion (Δ211N). Only four mutations (C241T, C3037T, C14408T, and A23403G) were shared among all the VOCs. The nucleotide changes among Omicron variants resulted in 61 amino acid changes, while the nucleotide changes in other VOCs showed 11 amino acid changes. The present study showed that most mutations (38/61, 62.3%) among Omicron variants occurred in the S gene; and 34.2% of them (13/38) occurred in the receptor-binding domain. The present study confirmed that most of mutations developed by Omicron variants occurred in the vaccine target gene (S gene).
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Affiliation(s)
- Elmutuz H. Elssaig
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan
| | - Tarig M.S. Alnour
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan, T.M.S. Alnour, Department of Medical Laboratory Technology (FAMS), University of Tabuk, Saudi Arabia; Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia; Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan;
| | - Mohammad Fahad Ullah
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | - Eltayib H. Ahmed-Abakur
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan
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