Comparison of Immunological Profiles of SARS-CoV-2 Variants in the COVID-19 Pandemic Trends: An Immunoinformatics Approach

Abstract

The current dynamics of the COVID-19 pandemic have become a serious concern with the emergence of a series of mutant variants of the SARS-CoV-2 virus. Unlike the previous strain, it is reported that the descendants are associated with increased risk of transmission yet causing less impact in terms of hospital admission, the severity of illness, or mortality. Moreover, the vaccine efficacy is also not believed to vary among the population depending on the variants of the virus and ethnicity. It has been determined that the mutations recorded in the spike gene and protein of the newly evolved viruses are specificallyresponsible for this transformation in the behavior of the virus and its disease condition. Hence, this study aimed to compare the immunogenic profiles of the spike protein from the latest variants of the SARS-CoV-2 virus concerning the probability of COVID-19 severity. Genome sequences of the latest SARS-CoV-2 variants were obtained from GISAID and NCBI repositories. The translated protein sequences were run against T-cell and B-cell epitope prediction tools. Subsequently, antigenicity, immunogenicity, allergenicity, toxicity, and conservancy of the identified epitopes were ascertained using various prediction servers. Only the non-allergic and non-toxic potential epitopes were matched for population relevance by using the Human Leucocyte Antigen population registry in IEDB. Finally, the selected epitopes were validated by docking and simulation studies. The evaluated immunological parameters would concurrently reveal the severity of COVID-19, determining the infection rate of the pathogen. Our immunoinformatics approach disclosed that spike protein of the five variants was capable of forming potential T and B-cell epitopes with varying immune responses. Although the Wuhan strain showed a high number of epitope/HLA combinations, relatively less antigenicity and higher immunogenicity results in poor neutralizing capacity, which could be associated with increased disease severity. Our data demonstrate that increased viral antigenicity with moderate to high immunogenicity, and several potential epitope/HLA combinations in England strain, the USA, India, and South Africa variants,could possess a high neutralizing ability. Therefore, our findings reinforce that the newly circulating variants of SARS-CoV-2 might be associated with more infectiousness and less severe disease condition despite their greater viremia, as reported in the recent COVID-19 cases, whichconsequently determine their increased epidemiological fitness.

EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

“…Thereby, it is plausible to assume that these epitopes could be responsible for the strong activation of the cell-mediated immune response ( Patronov et al, 2011 ; Sarma, Olotu & Soliman, 2021 ) in case of an experimental assay. In addition, the RBD epitopes have a broad populational coverage consistent with studies for SARS-CoV-2 epitopes identified in lineages isolated from India, England and the United States ( Mallavarpu Ambrose et al, 2021 ). These findings combined with the high conservancy, antigenicity and immunogenicity suggest these epitopes’ in silico immunogen profile ( Zheng & Song, 2020 ; Mallavarpu Ambrose et al, 2021 ; Jahangirian et al, 2021 ), validating the accurate selection of EpiCurator.…”

Age and Sex Modulate SARS-CoV-2 Viral Load Kinetics: A Longitudinal Analysis of 1735 Subjects

“…On this subject, the individual (epi)genetic make-up was investigated looking for specific variants and genes able to contribute to the susceptibility and progression to severe forms of COVID-19 [36]. In particular, an interesting role of immune genes (such as the HLA make-up) in the differential activation of host immune responses by SARS-CoV-2 variants was investigated, pointing out the importance of specific virus-host molecular interactions [37]. Therefore, studies at (epi)genome-wide level will certainly help to characterize groups of individuals with the same pattern of viral kinetics, providing useful insights for a more tailored and effective management of infected patients.…”

Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population

“…The promising epitope YQPYRVVVL has been reported to exhibit high antigenicity against the beta variant from South Africa (GSAID ID: EPI_ISL_1706561) and another variant from India (GSAID ID: EPI_ISL_1708422) [ 53 ]. Furthermore, this peptide exhibited high binding affinity for several HLAs in silico and has been proposed as candidate epitope for vaccine design [ 54 ].…”