309 Effects of SARS-CoV-2 Variants on CD8+ T cell Epitope Diversity: Estimating Clinical Severity in the United States

Abstract

OBJECTIVES/GOALS: Our goal was to distinguish SARS-CoV-2 CD8+ T cell epitopes of spike, membrane, and nucleocapsid products in 27 of the most frequent HLA-Aand -B alleles.We hypothesize that differences mediated by variation in SARS-CoV-2 and host HLA genetics affect the differential clinical severity and presentation of acute infection and PASC. METHODS/STUDY POPULATION: Genomic sequences of SARS-CoV-2 variants were blasted against the original Wuhan strain using Ensembl’s SARS-CoV-2 browser. We examined 16 COVID variants: 2 Alpha (B.1 and B.1.1.7), 5 Delta (AY.100, AY.25, AY.3, AY.3.1, and AY.44), and 9 Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, and XBB.1.5), sequenced from the Louisiana patient population. cDNA sequences were translated using the Expasy tool. To predict MHC-I epitope binding, we used the Immune Epitope Database and Analysis Resource, via TepiTool utilizing the IEDB recommended default prediction and the 27 most frequent HLA-A and -B alleles. In silico peptide docking was conducted on FoldX, utilizing HLA-B*15:01 structures (n= 7) from the Protein Data Bank. RESULTS/ANTICIPATED RESULTS: CD8+ epitope conservation was estimated at 87.6-96.5% in S, 92.5-99.6% in M, and 94.6-99% for N. As the virus mutated, an increasing proportion of S epitopes experienced reduced predicted binding affinity: 70% of Omicron BQ.1- XBB.1.5 S epitopes experienced decreased predicted binding, as compared to ~ 3% and ~15% in Delta AY.100-AY.44 and Omicron BA.1-BA.5 respectively. Additionally, we identified several novel candidate haplotypes that may be susceptible to severe disease, notably HLA-A*32:01, -A*26:01, -B*58:01, and -B*53:01, and relatively protected from disease, such as -A*01:01, -A*02:01,-A*31:01, -B*15:01, -B*40:01, -B*44:03, and -B*57:01. In silico analysis of COVID peptides and HLA-B*15:01, a common allotype in the United States, largely matched predicted binding patterns. DISCUSSION/SIGNIFICANCE: To elicit long term COVID-19 immunity and prevent PASC, it is important to understand the relationship between T-cells, viral variants, and HLA genetics. This project is one of the first to explore the interaction between CD8+ epitope diversity and viral genetics for the majority of the United States population.