EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in sili...

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Autores principales:	Cristina S. Ferreira, Yasmmin C. Martins, Rangel Celso Souza, Ana Tereza R. Vasconcelos
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	Epitopes prediction SARS-CoV-2 HLA alleles binding affinity Immunoinformatic approaches EpiCurator Medicine R
Acceso en línea:	https://doaj.org/article/69230c67c5b94501a12fe1d8cc21c8b8
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spelling	oai:doaj.org-article:69230c67c5b94501a12fe1d8cc21c8b82021-12-02T15:05:14ZEpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes10.7717/peerj.125482167-8359https://doaj.org/article/69230c67c5b94501a12fe1d8cc21c8b82021-11-01T00:00:00Zhttps://peerj.com/articles/12548.pdfhttps://peerj.com/articles/12548/https://doaj.org/toc/2167-8359The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.Cristina S. FerreiraYasmmin C. MartinsRangel Celso SouzaAna Tereza R. VasconcelosPeerJ Inc.articleEpitopes predictionSARS-CoV-2HLA alleles binding affinityImmunoinformatic approachesEpiCuratorMedicineRENPeerJ, Vol 9, p e12548 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Epitopes prediction SARS-CoV-2 HLA alleles binding affinity Immunoinformatic approaches EpiCurator Medicine R
spellingShingle	Epitopes prediction SARS-CoV-2 HLA alleles binding affinity Immunoinformatic approaches EpiCurator Medicine R Cristina S. Ferreira Yasmmin C. Martins Rangel Celso Souza Ana Tereza R. Vasconcelos EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes
description	The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.
format	article
author	Cristina S. Ferreira Yasmmin C. Martins Rangel Celso Souza Ana Tereza R. Vasconcelos
author_facet	Cristina S. Ferreira Yasmmin C. Martins Rangel Celso Souza Ana Tereza R. Vasconcelos
author_sort	Cristina S. Ferreira
title	EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes
title_short	EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes
title_full	EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes
title_fullStr	EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes
title_full_unstemmed	EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes
title_sort	epicurator: an immunoinformatic workflow to predict and prioritize sars-cov-2 epitopes
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/69230c67c5b94501a12fe1d8cc21c8b8
work_keys_str_mv	AT cristinasferreira epicuratoranimmunoinformaticworkflowtopredictandprioritizesarscov2epitopes AT yasmmincmartins epicuratoranimmunoinformaticworkflowtopredictandprioritizesarscov2epitopes AT rangelcelsosouza epicuratoranimmunoinformaticworkflowtopredictandprioritizesarscov2epitopes AT anaterezarvasconcelos epicuratoranimmunoinformaticworkflowtopredictandprioritizesarscov2epitopes
_version_	1718388894584537088

EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

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