The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against COVID-19

Bishajit Sarkar; Md. Asad Ullah; Fatema Tuz Johora; Masuma Afrin Taniya; Yusha Araf

The antigenicity of protein sequences was determined using an online tool called VaxiJen v2.0 (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.htm). During the antigenicity prediction, the prediction accuracy parameter threshold was set at 0.4 in the tumor model [103] - [105] . The tumor model was used in prediction because it generated excellent results (when compared to other models) in both the leave-on-out cross-validation (LOO-CV) and external validation in numerous studies. The accuracy, sensitivity, and specificity of a prediction (by the VaxiJen v2.0 server) depends on the prediction accuracy threshold. For this reason, to improve the accuracy of the prediction, the threshold 0.4 was used. The server is a user-friendly web tool for effective . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.05.935072 doi: bioRxiv preprint prediction of the antigenicity of proteins [106] - [108] . Only the highly antigenic protein sequences were selected for further analysis. Next, the selected antigenic protein sequences were analyzed by ExPASy's online tool and ProtParam (https://web.expasy.org/protparam/) to determine their physicochemical properties i.e., the number of amino acids, theoretical pI, extinction co-efficient, aliphatic index and grand average of hydropathicity (GRAVY) etc. [109] .