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.
IntroductionToxoplasma gondii is an obligatory intracellular protozoan that causes toxoplasmosis disease. The life cycle of parasite is completed by cat and warm-blooded animals. 1 In acute form of disease the parasite reproduced inside the host blood and other organ's cells and in chronic form of disease the parasite transforms to cysts. 1 Toxoplas ma may cause different clinical forms such as asymptom atic or sever symptoms like abortion, congenital defects and death. 2 In spite of current strategies in vaccine production that are based on using living or non-living agents, it seems necessary using novel methods such as molecular methods to improve vaccine production and inhibiting of activation risk of organisms. [3][4][5] The novel strategies in production of vaccine are based on production of recombinant antigens of microorganisms. 6 Natural antigens of toxoplasma are used to identify parasite antibodies in commercial kits, and considering that the parasite is cultivated in living cell, the possible risk for contamination of parasite antigens with host-cell antigens may lead to diagnostic deviations and also the quality of this kind of antigens are not stable. 7 Considering that the production of these recombinant antigens are possible and such antigens do not have deficiencies listed for natural antigens, so nowadays the production of these types of antigens are considered. 8 Since the current antigens that are used for diagnosis or vaccination are contaminated with nonparasitic material in which the parasite is grown, a
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.