In-silico design of a multi-epitope for developing sero-diagnosis detection of SARS-CoV-2 using spike glycoprotein and nucleocapsid antigens

Abstract

COVID-19 is a pandemic disease caused by novel corona virus, SARS-CoV-2, initially originated from China. In response to this serious life-threatening disease, designing and developing more accurate and sensitive tests are crucial. The aim of this study is designing a multi-epitope of spike and nucleocapsid antigens of COVID-19 virus by bioinformatics methods. The sequences of nucleotides obtained from the NCBI Nucleotide Database. Transmembrane structures of proteins were predicted by TMHMM Server and the prediction of signal peptide of proteins was performed by Signal P Server. B-cell epitopes' prediction was performed by the online prediction server of IEDB server. Beta turn structure of linear epitopes was also performed using the IEDB server. Conformational epitope prediction was performed using the CBTOPE and eventually, eight antigenic epitopes with high physicochemical properties were selected, and then, all eight epitopes were blasted using the NCBI website. The analyses revealed that α-helices, extended strands, β-turns, and random coils were 28.59%, 23.25%, 3.38%, and 44.78% for S protein, 21.24%, 16.71%, 6.92%, and 55.13% for N Protein, respectively. The S and N protein three-dimensional structure was predicted using the prediction I-TASSER server. In the current study, bioinformatics tools were used to design a multi-epitope peptide based on the type of antigen and its physiochemical properties and SVM method (Machine Learning) to design multi-epitopes that have a high avidity against SARS-CoV-2 antibodies to detect infections by COVID-19.

Designing an Epitope-Based Peptide Vaccine Derived from RNA-Dependent RNA Polymerase (RdRp) against Dengue Virus Serotype 2

“…Figure 2 depicts the outcomes of the prediction. Residues with a score greater than 0.35 are displayed in yellow and are candidates for predicted epitopes [ 63 ].…”

A Promising Tool in Serological Diagnosis: Current Research Progress of Antigenic Epitopes in Infectious Diseases

“…These have both become major foci in the development of diagnostic epitopes for new coronaviruses. As computational tools are convenient and enable the development of new detection methods to be accelerated, a number of studies have used them to predict the epitopes of proteins that diagnostic performance has been initially characterized as well [ 90 , 92 , 93 , 95 ]. For example, the synthetic peptides from S protein, predicted by online servers, were developed into a magnetic chemiluminescence enzyme immunoassay for the detection of SARS-CoV-2 antibodies, greatly enhancing the diagnostic accuracy of COVID-19 [ 90 ].…”

Demographic and clinical characteristics and outcomes of COVID-19 patients admitted to a university hospital in the west of Iran: a retrospective study in the third wave

“…In December 2019, the first cases of COVID-19 infection, an emerging respiratory infection caused by SARS-CoV-2, were reported from Wuhan, China ( 1. , 2. , 3.…”

“…, 8. )) and 7 (Javadi Mamaghani et al, 2021; Abdolahnejad et al, 2022; Nojomi et al, 2021; Flores-Vega et al, 2022; Fattahi et al, 2021; Cusinato et al, 2022; Avatef Fazeli et al, 2021; Sayad et al, 2021; Hesni et al, 2022; Buttenschøn et al, 2022; Smits et al, 2022; Rosenberger et al, 2021; Shi et al, 2022 ( 2. , 3.…”