SARS‐CoV‐2 infection is causing a pandemic disease that is reflected in challenging public health problems worldwide. HLA‐based epitope prediction and its association with disease outcomes provide an important base for treatment design. A bioinformatic prediction of T cell epitopes and their restricted HLA class I and II alleles was performed to obtain immunogenic epitopes and HLA alleles from the spike protein of the SARS‐CoV‐2 virus. Also, a correlation with the predicted fatality rate of hospitalized patients in 28 states of Mexico was done. Here, we describe a set of ten highly immunogenic epitopes, together with different HLA alleles that can efficiently present these epitopes to T cells. Most of these epitopes are located within the S1 subunit of the spike protein, suggesting that this area is highly immunogenic. A statistical negative correlation was found between the frequency of HLA‐DRB1*01 and the fatality rate in hospitalized patients in Mexico.
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Whole-genome sequencing for epidemiological investigations (genomic epidemiology) has been of paramount importance to understand the transmission dynamics of many bacterial (and nonbacterial) pathogens. Commonly, variation in the core genome, single nucleotide polymorphisms (SNPs), is employed to carry out genomic epidemiology.
SARS-CoV2 infection is causing a pandemic disease that is reflected in important public health problems worldwide. HLA-based epitope prediction and association with susceptibility provides an important base for treatment design. Hence the aim of this study is to predict the best antigen-presenting HLA-class I and II alleles in top affected populations and determine probable susceptibility associations. A bioinformatic prediction of T cell epitopes and their restricted HLA class I and II alleles was performed to predict immunogenic epitopes and HLA alleles from the spike protein of the SARS-CoV-2 virus, together with molecular modeling analysis and a correlation with the cumulative incidence of COVID-19 infection in 14 countries. Here, we describe a set of ten highly immunogenic epitopes, together with different HLA alleles that can efficiently present these epitopes to T cells. Most of these epitopes are located within the S1 subunit of the spike protein, suggesting that this area is highly immunogenic. A statistical correlation was found between the frequency of HLA-A*02:03 and HLA-A*31:01 and a low cumulative incidence in the selected countries.
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