Investigating the role of HLA class-1 polymorphisms within the Sub-Saharan African population, in the emergence, frequency, and persistence of SARS-CoV-2 variants.

Abstract

RATIONALE: Various studies have shown the ability of the cytotoxic T cell (by CD8+ T cells) immune response in disease control in the absence of neutralizing antibodies in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) convalescent individuals. Thus, illustrating the important role of the cytotoxic immune response in clearing coronavirus disease 2019 (COVID-19). Human Leukocyte Antigen molecules (HLA) present virus peptides to T cells during the activation of an immune response. However, only a few studies have looked at how the HLA allele repertoire of the infected population impacts immune escape, and none have looked at how the high HLA polymorphism in the Sub-Saharan African (SSA) population impacts the immune escape patterns in viruses circulating within this population. AIM: The Aim of this study was to predict the HLA-mediated cytotoxic T cell immune escape mutations present in SARS-CoV-2 structural proteins isolated from SSA populations. The SARSCoV-2 isolates for the study were analyzed from five SSA countries namely, Kenya, Democratic Republic of Congo, Nigeria, Ghana and Senegal to ask the question: Do HLA class-1 polymorphisms in SSA populations result in locally specific immune escape mutations in SARSCoV-2?