Next Article in Journal
Immunoinformatic Identification of Multiple Epitopes of gp120 Protein of HIV-1 to Enhance the Immune Response against HIV-1 Infection
Next Article in Special Issue
Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2
Previous Article in Journal
TGF-β1 Signaling Impairs Metformin Action on Glycemic Control
Previous Article in Special Issue
Hydroxypropyl-Beta Cyclodextrin Barrier Prevents Respiratory Viral Infections: A Preclinical Study
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 25
Issue 4
10.3390/ijms25042428
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites

by
Pedro Ferreira
1,2,3,†,
Ricardo Soares
1,2,3,4,†,
Hugo López-Fernández
5,6,
Noé Vazquez
5,6,
Miguel Reboiro-Jato
5,6,
Cristina P. Vieira
1,2 and
Jorge Vieira
1,2,*
1
Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
2
Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
3
School of Medicine and Biomedical Sciences (ICBAS), Porto University, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
4
Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
5
CINBIO, Department of Computer Science, ESEI—Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain
6
CINBIO, SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
*
Author to whom correspondence should be addressed.
†
These authors have contributed equally to this work.
Int. J. Mol. Sci. 2024, 25(4), 2428; https://doi.org/10.3390/ijms25042428
Submission received: 30 December 2023 / Revised: 3 February 2024 / Accepted: 9 February 2024 / Published: 19 February 2024
(This article belongs to the Special Issue Genetic Variability and Molecular Evolution of SARS-CoV-2)
Browse Figures
Versions Notes

Abstract

SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses.
Keywords: SARS-CoV-2; coronaviruses; positively selected amino acid sites SARS-CoV-2; coronaviruses; positively selected amino acid sites

Share and Cite

MDPI and ACS Style

Ferreira, P.; Soares, R.; López-Fernández, H.; Vazquez, N.; Reboiro-Jato, M.; Vieira, C.P.; Vieira, J. Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites. Int. J. Mol. Sci. 2024, 25, 2428. https://doi.org/10.3390/ijms25042428

AMA Style

Ferreira P, Soares R, López-Fernández H, Vazquez N, Reboiro-Jato M, Vieira CP, Vieira J. Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites. International Journal of Molecular Sciences. 2024; 25(4):2428. https://doi.org/10.3390/ijms25042428

Chicago/Turabian Style

Ferreira, Pedro, Ricardo Soares, Hugo López-Fernández, Noé Vazquez, Miguel Reboiro-Jato, Cristina P. Vieira, and Jorge Vieira. 2024. "Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites" International Journal of Molecular Sciences 25, no. 4: 2428. https://doi.org/10.3390/ijms25042428

APA Style

Ferreira, P., Soares, R., López-Fernández, H., Vazquez, N., Reboiro-Jato, M., Vieira, C. P., & Vieira, J. (2024). Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites. International Journal of Molecular Sciences, 25(4), 2428. https://doi.org/10.3390/ijms25042428

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop