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Immunoinformatic analysis of structural and epitope variations in the spike and Orf8 proteins of SARS-CoV-2/B.1.1.7.
Hussain, Mushtaq; Shabbir, Sanya; Amanullah, Anusha; Raza, Fozia; Imdad, Muhammad J; Zahid, Sahar.
  • Hussain M; Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.
  • Shabbir S; Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.
  • Amanullah A; Department of Microbiology, University of Karachi, Karachi, Pakistan.
  • Raza F; Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.
  • Imdad MJ; Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.
  • Zahid S; Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.
J Med Virol ; 93(7): 4461-4468, 2021 07.
Article in English | MEDLINE | ID: covidwho-1263095
ABSTRACT
A newly emerged strain of SARS-CoV-2 of B.1.1.7 lineage has caused a significant surge in the SARS-CoV-2 infections in the UK. In this study, changes in the epitopes of spike and orf8 proteins in SARS-CoV-2 of B.1.1.7 lineage were investigated. Genomic alignment of the SARS-CoV-2/B.1.1.7 with SARS-CoV-2/Wuhan showed the presence of several mutations in orf1a/b, spike, orf8, and N proteins of SARS-CoV-2/B.1.1.7. Molecular models of spike and orf8 proteins were constructed by homology modeling. Superimposition between the spike proteins of SARS-CoV-2/Wuhan and SARS-CoV-2/B.1.1.7 showed noticeable variations in the spatial orientation in Val70-Asn74 and Thr250-Ser255 regions. This may have also resulted in the extension of the epitopic region at Ser244-Gly249 in the SARS-CoV-2/B.1.1.7 spike protein. Superimposition of the SARS-CoV-2/B.1.1.7 spike protein over Fab-spike protein complexes of SARS-CoV-2/Wuhan also showed subtle variations in the antibody binding affinity targeting the N-terminal domain of the spike protein. Epitopic variations were also observed between the corresponding orf8 regions of SARS-CoV-2/Wuhan and SARS-CoV-2/B.1.1.7. Moreover, the presence of a stop codon at position 27 in orf8 connotes the emergence of two frames (orf8a and orf8b) in SARS-CoV-2, which further hampers its extracellular secretion, and in turn, immunogenicity. The findings of the present study could further be used to develop targeted immunotherapeutics.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Proteins / Spike Glycoprotein, Coronavirus / SARS-CoV-2 / COVID-19 Limits: Humans Country/Region as subject: Europa Language: English Journal: J Med Virol Year: 2021 Document Type: Article Affiliation country: Jmv.26931

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Proteins / Spike Glycoprotein, Coronavirus / SARS-CoV-2 / COVID-19 Limits: Humans Country/Region as subject: Europa Language: English Journal: J Med Virol Year: 2021 Document Type: Article Affiliation country: Jmv.26931