In Silico Design of SARS-CoV-2 Peptides to Use as Potential Biomarkers for the Diagnosis of COVID-19 in Mexican Population

The first case of COVD-19 in Mexico was reported in February 2020.Since then, different methods have been used in the world, including Mexico to detect SARS CoV-2.However, a significant number of asymptomatic cases, diagnostic tests with false positive results and different circulating variants, each with distinct patterns, have been observed, affecting different ethnicities.Considering the unique characteristics of each ethnicity, we propose in this study the design of peptides by in silico analysis of the viral proteins S, N, E, M and NSP12 of SARS CoV-2 in the context of the major histocompatibility complex class I and class II specific to the Mexican population.A bioinformatic analysis by the platforms: Immune Epitopes Data Base (IEDB) and Vaxygen was made to determine the peptides.Furthermore, GISAD platform was used to obtain the viral sequences of the most frequent variants of SARS CoV-2 circulating in our country during February 2020 to March 2021.A total of 7034 peptide sequences of SARS CoV2 viral proteins were analyzed.We identified 17 peptides from protein S (D614G), 3 peptides from protein E, 6 peptides from protein M, 1 peptide from protein N (R203K and G204R), and 13 peptides from NSP12 (P323L).All selected peptides demonstrated adequate immunogenicity and the ability to interact with the most frequent MHC alleles in our population, achieving a population coverage of 97.78% hence, they were potential biomarkers for diagnostic tests to SARS CoV-2 in our population.