A bioinformatic analysis of Staphylococcal enterotoxin B structure alteration in COVID-۱۹ variants

Background and Aim : Since the global outbreak of COVID-۱۹, amounts of papers pointed to the superantigen (SAg) activity of SARS-COV ۲. By molecular analysis, a superantigen-like motif, similar to Staphylococcal enterotoxin B (SEB), near the S۱/S۲ cleavage site of SARS-CoV-۲ Spike protein was discovered.it seems that mutations in SARS-COV ۲ Spike protein may cause different SAg activities. Here, based on bioinformatics data, SEB-like Motifs were compared in each variant.Methods : Based on CDC data, the SARS-COV ۲ variants from April ۲۰۱۹ to June ۲۰۲۱ were recognized and Variants of Concern were extracted (۴ mutations). the spike sequences and ۳-D structures especially the superantigen motif were investigated from "Uniport" and "viralzone.expasy" databases, then the sequences were compared by NICBI blast. finally, the Obtained data were evaluated.Results : the variants extracted were included: ALPHA, BETA, DELTA, and GAMMA. The original (Wuhan) SARS-COV ۲ SEB-like SAg sequences were: TNSPRRARSV. ALPHA, BETA, DELTA and GAMMA SEB like superantigens sequences were: TNSHRRARSV, TNSPRRARSV, TNSRRRARSV, TNSRRRARSV. In the ALPHA variant, Histidine replaced proline, BETA no change was observed, In DELTA, Arginine replaced proline and in gamma, Arginine replaced proline also.Conclusion : The SEB-like SAg sequence variation was observed in ALPHA, DELTA and GAMMA and interestingly the level of superantigen activity of these variants has been changed. Also, Despite the similarities between Wuhan and BETA SAg sequences, other factors may have effect on superantigen activity and lethality of BETA variant. More researches required to realize of SAg alteration impacts on virus properties.

Keywords:

SARS-CoV-۲ , super antigen , Staphylococcal enterotoxin B , Bioinformatic , spike