Dataset Information

Utility of in silico-identified-peptides in spike-S1 domain and nucleocapsid of SARS-CoV-2 for antibody detection in COVID-19 patients and antibody production.

ABSTRACT: SARS-CoV-2 contains four structural proteins, two of which, the spike and nucleocapsid, are commonly used for the standardization of novel methods for antibody detection; however, some limitations in their use have been observed due to the homology of this virus with other phylogenetically-related viruses. We performed in silico analysis to search for novel immunogenic and antigenic peptides. A total of twenty-five peptides were preliminarily selected, located in the 3D structure of both proteins. Finally, eight peptides were selected: one located in the N protein and seven in the S1 domain of the spike protein. Additionally, the localization of selected peptides in 2D structures and possible changes in the sequences of these peptides in SARS-CoV-2 variants of concern were analyzed. All peptides were synthetized in MAP8 format, and recombinant S (trimer and RBD) and N proteins were used as antigens to search for antibodies in serum samples derived from COVID-19 patients, and for antibody response in New Zealand rabbits. Results showed high recognition of the serum derived from COVID-19 patients to all selected peptides; however, only the RBD3 peptide induced antibody production. In conclusion, this work provides evidence for a new strategy in peptide selection and its use for antibody detection or antibody production in animals.

SUBMITTER: Cortes-Sarabia K

PROVIDER: S-EPMC9442563 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Utility of in silico-identified-peptides in spike-S1 domain and nucleocapsid of SARS-CoV-2 for antibody detection in COVID-19 patients and antibody production.

Cortés-Sarabia Karen K Luna-Pineda Víctor Manuel VM Rodríguez-Ruiz Hugo Alberto HA Leyva-Vázquez Marco Antonio MA Hernández-Sotelo Daniel D Beltrán-Anaya Fredy Omar FO Vences-Velázquez Amalia A Del Moral-Hernández Oscar O Illades-Aguiar Berenice B

Scientific reports 20220905 1

SARS-CoV-2 contains four structural proteins, two of which, the spike and nucleocapsid, are commonly used for the standardization of novel methods for antibody detection; however, some limitations in their use have been observed due to the homology of this virus with other phylogenetically-related viruses. We performed in silico analysis to search for novel immunogenic and antigenic peptides. A total of twenty-five peptides were preliminarily selected, located in the 3D structure of both protein ...[more]

PMID: 36064951

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Project description:The clue behind the SARS-CoV-2 origin is still a matter of debate. Here, we report that SARS-CoV-2 has gained a novel spike protein S1-N-terminal domain (S1-NTD). In our CLuster ANalysis of Sequences (CLANS) analysis, SARS-CoV/SARS-CoV-2 S1-NTDs displayed a close relationship with OC43 and HKU1. However, in the complete and S1-NTD-free spike protein, SARS-CoV/SARS-CoV-2 revealed closeness with MERS-CoV. Further, we have divided the S1-NTD of SARS-CoV-2 related viruses into three distinct types (Type-I to III S1-NTD) and the S1-NTD of viruses associated with SARS-CoVs into another three classes (Type-A to C S1-NTD) using CLANS and phylogenetic analyses. In particular, the results of our study indicate that SARS-CoV-2, RaTG13, and BANAL-20-52 viruses carry Type-I-S1-NTD and other SARS-CoV-2-related-bat viruses have Type-II and III. In addition, it was revealed that the Pangolin-GX and Pangolin-Guangdong lineages inherited Type-I-like and Type-II-like S1-NTD, respectively. Then our CLANS study shows the potential for evolution of Type-I and Type-III S1-NTD from SARS-CoV-related viruses Type-A and Type-B S1-NTDs, respectively. Furthermore, our analysis clarifies the possibility that Type-II S1-NTDs may have evolved from Type-A-S1-NTD of SARS-CoV-related viruses through Type-I S1-NTDs. We also observed that BANAL-20-103, BANAL-20-236, and Pangolin-Guangdong-lineage viruses containing Type-II-like S1-NTD are very close to SARS-CoV-2 in spike genetic areas other than S1-NTD. Possibly, it suggests that the common ancestor spike gene of SARS-CoV-2/RaTG13/BANAL-20-52-like virus may have evolved by recombining the Pangolin-Guangdong/BANAL-20-103/BANAL-20-236-like spike gene to Pangolin-GX-like Type-I-like-S1-NTD in the unsampled bat or undiscovered intermediate host or possibly pangolin. These may then have evolved into SARS-CoV-2, RaTG13, and BANAL-20-52 virus spike genes by host jump mediated evolution. The potential function of the novel Type-I-S1-NTD and other types of S1-NTDs needs to be studied further to understand better its importance in the ongoing COVID-19 outbreak and for future pandemic preparedness.

Dataset Information

Utility of in silico-identified-peptides in spike-S1 domain and nucleocapsid of SARS-CoV-2 for antibody detection in COVID-19 patients and antibody production.

Publications

Utility of in silico-identified-peptides in spike-S1 domain and nucleocapsid of SARS-CoV-2 for antibody detection in COVID-19 patients and antibody production.

Similar Datasets

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