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Article

Effect of An 84-bp Deletion of the Receptor-Binding Domain on the ACE2 Binding Affinity of the SARS-CoV-2 Spike Protein: An In Silico Analysis

1
National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary
2
Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
3
Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H1117 Budapest, Hungary
4
Department of Medical Microbiology and Immunobiology, University of Szeged, H6720 Szeged, Hungary
*
Author to whom correspondence should be addressed.
Academic Editor: Kevin Sokoloski
Genes 2021, 12(2), 194; https://doi.org/10.3390/genes12020194
Received: 22 December 2020 / Revised: 21 January 2021 / Accepted: 26 January 2021 / Published: 29 January 2021
(This article belongs to the Special Issue Identifying and Characterizing Virus/Host Interactions of RNA Viruses)
SARS-CoV-2 is a recently emerged, novel human coronavirus responsible for the currently ongoing COVID-19 pandemic. Recombination is a well-known evolutionary strategy of coronaviruses, which may frequently result in significant genetic alterations, such as deletions throughout the genome. In this study we identified a co-infection with two genetically different SARS-CoV-2 viruses within a single patient sample via amplicon-based next generation sequencing in Hungary. The recessive strain contained an 84 base pair deletion in the receptor binding domain of the spike protein gene and was found to be gradually displaced by a dominant non-deleterious variant over-time. We have identified the region of the receptor-binding domain (RBD) that is affected by the mutation, created homology models of the RBDΔ84 mutant, and based on the available experimental data and calculations, we propose that the mutation has a deteriorating effect on the binding of RBD to the angiotensin-converting enzyme 2 (ACE2) receptor, which results in the negative selection of this variant. Extending the sequencing capacity toward the discovery of emerging recombinant or deleterious strains may facilitate the early recognition of novel strains with altered phenotypic attributes and understanding of key elements of spike protein evolution. Such studies may greatly contribute to future therapeutic research and general understanding of genomic processes of the virus. View Full-Text
Keywords: selection; evolution; spike-mutant; deletion; attenuated; recessive selection; evolution; spike-mutant; deletion; attenuated; recessive
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MDPI and ACS Style

Kemenesi, G.; Tóth, G.E.; Bajusz, D.; Keserű, G.M.; Terhes, G.; Burián, K.; Zeghbib, S.; Somogyi, B.A.; Jakab, F. Effect of An 84-bp Deletion of the Receptor-Binding Domain on the ACE2 Binding Affinity of the SARS-CoV-2 Spike Protein: An In Silico Analysis. Genes 2021, 12, 194. https://doi.org/10.3390/genes12020194

AMA Style

Kemenesi G, Tóth GE, Bajusz D, Keserű GM, Terhes G, Burián K, Zeghbib S, Somogyi BA, Jakab F. Effect of An 84-bp Deletion of the Receptor-Binding Domain on the ACE2 Binding Affinity of the SARS-CoV-2 Spike Protein: An In Silico Analysis. Genes. 2021; 12(2):194. https://doi.org/10.3390/genes12020194

Chicago/Turabian Style

Kemenesi, Gábor, Gábor E. Tóth, Dávid Bajusz, György M. Keserű, Gabriella Terhes, Katalin Burián, Safia Zeghbib, Balázs A. Somogyi, and Ferenc Jakab. 2021. "Effect of An 84-bp Deletion of the Receptor-Binding Domain on the ACE2 Binding Affinity of the SARS-CoV-2 Spike Protein: An In Silico Analysis" Genes 12, no. 2: 194. https://doi.org/10.3390/genes12020194

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