Mutations in SARS-CoV-2 structural proteins: a global analysis

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Abstract

Background

Emergence of new variants mainly variants of concerns (VOC) is caused by mutations in main structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, we aimed to investigate the mutations among structural proteins of SARS-CoV-2 globally.

Methods

We analyzed samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the declaration of the coronavirus 2019 (COVID-19) as pandemic to January 2022. The presence and location of mutations were then investigated by aligning the sequences to the reference sequence and categorizing them based on frequency and continent. Finally, the related human genes with the viral structural genes were discovered, and their interactions were reported.

Results

The results indicated that the most relative mutations among the E, M, N, and S AASs occurred in the regions of 7 to 14, 66 to 88, 164 to 205, and 508 to 635 AAs, respectively. The most frequent mutations in E, M, N, and S proteins were T9I, I82T, R203M/R203K, and D614G. D614G was the most frequent mutation in all six geographical areas. Following D614G, L18F, A222V, E484K, and N501Y, respectively, were ranked as the most frequent mutations in S protein globally. Besides, A-kinase Anchoring Protein 8 Like (AKAP8L) was shown as the linkage unit between M, E, and E cluster genes.

Conclusion

Screening the structural protein mutations can help scientists introduce better drug and vaccine development strategies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01951-7.

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Most cited references 56

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World Medical Association Declaration of Helsinki: ethical principles for medical research involving human subjects.

(2013)

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A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing

David E Gordon, Gwendolyn M Jang, Mehdi Bouhaddou … (2020)

SUMMARY The novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 2.3 million people, killed over 160,000, and caused worldwide social and economic disruption 1,2 . There are currently no antiviral drugs with proven clinical efficacy, nor are there vaccines for its prevention, and these efforts are hampered by limited knowledge of the molecular details of SARS-CoV-2 infection. To address this, we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), identifying 332 high-confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (29 FDA-approved drugs, 12 drugs in clinical trials, and 28 preclinical compounds). Screening a subset of these in multiple viral assays identified two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the Sigma1 and Sigma2 receptors. Further studies of these host factor targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.

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Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus

B Korber, W.M. Fischer, S. Gnanakaran … (2020)

Summary A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to the introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to higher titer as pseudotyped virions. In infected individuals G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, although not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus, and support continuing surveillance of Spike mutations to aid in the development of immunological interventions.

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Author and article information

Contributors

Mohammadamin Mahmanzar: Mahmanzar.ma@ut.ac.ir

Zahra Meshkat: zmeshkat@gmail.com

Journal

Journal ID (nlm-ta): Virol J

Journal ID (iso-abbrev): Virol J

Title: Virology Journal

Publisher: BioMed Central (London )

ISSN (Electronic): 1743-422X

Publication date (Electronic): 18 December 2022

Publication date PMC-release: 18 December 2022

Publication date Collection: 2022

Volume: 19

Electronic Location Identifier: 220

Affiliations

[1 ]GRID grid.411583.a, ISNI 0000 0001 2198 6209, Student Research Committee, , Mashhad University of Medical Sciences, ; Mashhad, Iran

[2 ]GRID grid.411583.a, ISNI 0000 0001 2198 6209, Department of Microbiology and Virology, School of Medicine, Faculty of Medicine, , Mashhad University of Medical Sciences, ; Mashhad, Iran

[3 ]GRID grid.46072.37, ISNI 0000 0004 0612 7950, Institute of Biochemistry and Biophysics (IBB), , University of Tehran, ; Tehran, Iran

[4 ]GRID grid.417689.5, Department of Molecular Biotechnology, Cell Science Research Center, , Royan Institute for Biotechnology, ACECR, ; Isfahan, Iran

[5 ]GRID grid.411463.5, ISNI 0000 0001 0706 2472, Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, , Islamic Azad University, ; Tehran, Iran

[6 ]GRID grid.5645.2, ISNI 000000040459992X, Department of Biochemistry, , Erasmus University Medical Center, ; P.O. Box 2040, 3000 CA Rotterdam, The Netherlands

[7 ]GRID grid.412462.7, ISNI 0000 0000 8810 3346, Department of Biology, , Payame Noor University, ; Tehran, Iran

[8 ]GRID grid.510756.0, ISNI 0000 0004 4649 5379, Non Communicable Diseases Research Center, , Bam University of Medical Sciences, ; Bam, Iran

[9 ]GRID grid.46072.37, ISNI 0000 0004 0612 7950, Department of Bioinformatics, , Kish International Campus University of Tehran, ; Kish, Iran

Article

Publisher ID: 1951

DOI: 10.1186/s12985-022-01951-7

PMC ID: 9759450

PubMed ID: 36528612

SO-VID: 6798b7c7-ef9c-4e70-b194-b68f17c8abdb

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 5 July 2022

Date accepted : 8 December 2022

Custom metadata

ScienceOpen disciplines: Microbiology & Virology

Keywords: covid-19,evolutionary analysis,genome-wide mutations,mutations,sars-cov-2

Data availability:

ScienceOpen disciplines: Microbiology & Virology

Keywords: covid-19, evolutionary analysis, genome-wide mutations, mutations, sars-cov-2

Mutations in SARS-CoV-2 structural proteins: a global analysis

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Abstract

Background

Methods

Results

Conclusion

Supplementary Information

Related collections

Novel Coronavirus Disease COVID-19

Most cited references 56

World Medical Association Declaration of Helsinki: ethical principles for medical research involving human subjects.

A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing

Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus

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