Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19

Detalhes bibliográficos
Autor(a) principal: Pretti, Marco Antônio M.
Data de Publicação: 2020
Outros Autores: Gavani, Rômulo G., Vieira, Gustavo Fioravanti, Bonomo, Adriana, Bonamino, Martín H., Boroni, Mariana
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/46255
Resumo: Instituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Laboratório de Bioinformática e Biologia Computacional. Rio de Janeiro, RJ, Brasil / Instituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Programa de Imunologia e Biologia Tumoral. Rio de Janeiro, RJ, Brasil.
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spelling Pretti, Marco Antônio M.Gavani, Rômulo G.Vieira, Gustavo FioravantiBonomo, AdrianaBonamino, Martín H.Boroni, Mariana2021-03-04T13:35:48Z2021-03-04T13:35:48Z2020PRETTI, Marco Antônio M. et al. Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19. Frontiers in Immunology, v. 11, Article 564730, p. 1-14, Dec. 2020.1664-3224https://www.arca.fiocruz.br/handle/icict/4625510.3389/fimmu.2020.5657301664-022XengFrontiers MediaCOVID-19SARS-CoV-2BetacoronavírusLiigandomeLiigandomeAnálise de cobertura populacionalImunidade de rebanhoCOVID-19SARS-CoV-2BetacoronavirusLiigandomePopulation coverage analysisHerd immunityClass I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleInstituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Laboratório de Bioinformática e Biologia Computacional. Rio de Janeiro, RJ, Brasil / Instituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Programa de Imunologia e Biologia Tumoral. Rio de Janeiro, RJ, Brasil.Instituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Laboratório de Bioinformática e Biologia Computacional. Rio de Janeiro, RJ, Brasil / Universidade Veiga de Almeida. Faculdade de Biomedicina. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa sobre o Timo. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio Grande do Sul. Instituto de Biociências. Departamento de Genética. Laboratório de Imunoinformárica. Porto Alegre, RS, Brasil / Universidade La Salle. Programa de Pós-Graduação em Saúde e Desenvolvimento Humano. Laboratório de Saúde Humana de Silico. Canoas, RS, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa sobre o Timo. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Presidência. Vice-Presidência de Pesquisa e Biologia Coleções. Rio de Janeiro, RJ, Brasil.Instituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Programa de Imunologia e Biologia Tumoral. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Presidência. Vice-Presidência de Pesquisa e Biologia Coleções. Rio de Janeiro, RJ, Brasil.Instituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Laboratório de Bioinformática e Biologia Computacional. Rio de Janeiro, RJ, Brasil.The world is dealing with one of the worst pandemics ever. SARS-CoV-2 is the etiological agent of COVID-19 that has already spread to more than 200 countries. However, infectivity, severity, and mortality rates do not affect all countries equally. Here we consider 140 HLA alleles and extensively investigate the landscape of 3,723 potential HLA-I A and B restricted SARS-CoV-2-derived antigens and how 37 countries in the world are predicted to respond to those peptides considering their HLA-I distribution frequencies. The clustering of HLA-A and HLA-B allele frequencies partially separates most countries with the lowest number of deaths per million inhabitants from the other countries. We further correlated the patterns of in silico predicted population coverage and epidemiological data. The number of deaths per million inhabitants correlates to the predicted antigen coverage of S and N derived peptides and its module is influenced if a given set of frequent or rare HLA alleles are analyzed in a given population. Moreover, we highlighted a potential risk group carrying HLAs associated with an elevated number of deaths per million inhabitants. In addition, we identified three potential antigens bearing at least one amino acid of the four-length insertion that differentiates SARS-CoV-2 from previous coronavirus strains. We believe these data can contribute to the search for peptides with the potential to be used in vaccine strategies considering the role of herd immunity to hamper the spread of the disease. Importantly, to the best of our knowledge, this work is the first to use a populational approach in association with COVID- 19 outcome.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/46255/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALPretti_Marco_etal_IOC_2021_COVID-19.pdfPretti_Marco_etal_IOC_2021_COVID-19.pdfapplication/pdf2388786https://www.arca.fiocruz.br/bitstream/icict/46255/2/Pretti_Marco_etal_IOC_2021_COVID-19.pdfe469ab0478d22613a457614fb92622f8MD52TEXTPretti_Marco_etal_IOC_2021_COVID-19.pdf.txtPretti_Marco_etal_IOC_2021_COVID-19.pdf.txtExtracted texttext/plain68871https://www.arca.fiocruz.br/bitstream/icict/46255/3/Pretti_Marco_etal_IOC_2021_COVID-19.pdf.txte92142e36023ff5217aead89f0250afeMD53icict/462552021-03-05 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dc.title.pt_BR.fl_str_mv Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
title Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
spellingShingle Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
Pretti, Marco Antônio M.
COVID-19
SARS-CoV-2
Betacoronavírus
LiigandomeLiigandome
Análise de cobertura populacional
Imunidade de rebanho
COVID-19
SARS-CoV-2
Betacoronavirus
Liigandome
Population coverage analysis
Herd immunity
title_short Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
title_full Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
title_fullStr Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
title_full_unstemmed Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
title_sort Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
author Pretti, Marco Antônio M.
author_facet Pretti, Marco Antônio M.
Gavani, Rômulo G.
Vieira, Gustavo Fioravanti
Bonomo, Adriana
Bonamino, Martín H.
Boroni, Mariana
author_role author
author2 Gavani, Rômulo G.
Vieira, Gustavo Fioravanti
Bonomo, Adriana
Bonamino, Martín H.
Boroni, Mariana
author2_role author
author
author
author
author
dc.contributor.author.fl_str_mv Pretti, Marco Antônio M.
Gavani, Rômulo G.
Vieira, Gustavo Fioravanti
Bonomo, Adriana
Bonamino, Martín H.
Boroni, Mariana
dc.subject.other.pt_BR.fl_str_mv COVID-19
SARS-CoV-2
Betacoronavírus
LiigandomeLiigandome
Análise de cobertura populacional
Imunidade de rebanho
topic COVID-19
SARS-CoV-2
Betacoronavírus
LiigandomeLiigandome
Análise de cobertura populacional
Imunidade de rebanho
COVID-19
SARS-CoV-2
Betacoronavirus
Liigandome
Population coverage analysis
Herd immunity
dc.subject.en.pt_BR.fl_str_mv COVID-19
SARS-CoV-2
Betacoronavirus
Liigandome
Population coverage analysis
Herd immunity
description Instituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Laboratório de Bioinformática e Biologia Computacional. Rio de Janeiro, RJ, Brasil / Instituto Nacional de Câncer. Divisão de Pesquisa Experimental e Translacional. Programa de Imunologia e Biologia Tumoral. Rio de Janeiro, RJ, Brasil.
publishDate 2020
dc.date.issued.fl_str_mv 2020
dc.date.accessioned.fl_str_mv 2021-03-04T13:35:48Z
dc.date.available.fl_str_mv 2021-03-04T13:35:48Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv PRETTI, Marco Antônio M. et al. Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19. Frontiers in Immunology, v. 11, Article 564730, p. 1-14, Dec. 2020.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/46255
dc.identifier.issn.pt_BR.fl_str_mv 1664-3224
dc.identifier.doi.none.fl_str_mv 10.3389/fimmu.2020.565730
dc.identifier.eissn.none.fl_str_mv 1664-022X
identifier_str_mv PRETTI, Marco Antônio M. et al. Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19. Frontiers in Immunology, v. 11, Article 564730, p. 1-14, Dec. 2020.
1664-3224
10.3389/fimmu.2020.565730
1664-022X
url https://www.arca.fiocruz.br/handle/icict/46255
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
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instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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https://www.arca.fiocruz.br/bitstream/icict/46255/2/Pretti_Marco_etal_IOC_2021_COVID-19.pdf
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