SARS-CoV-2 Omicron and Delta variants conserve epitopes present in Abdala and Soberana Cuban anti-covid-19 vaccines

Abstract

Background: a new SARS-CoV-2 variant, known as omicron, has been classified as “of concern” by the World Health Organization, due to the high number of mutations and its increased ability to disseminate worldwide. Objective: to evaluate in silico the protection that the Cuban anti-covid-19 vaccines may offer against omicron variant, through the identification of shared epitopes. Methods: with the use of bioinfomatic tools, T y B epitopes from the receptor-binding domain of SARS-CoV-2 S protein, were compared in primary sequences from Abdala and Soberana vaccines, as well as in variants alpha, beta, gamma, delta and omicron, all obtained from GenBank and aligned in the region between residues 319-541. The percent of identical epitopes, those with some change in the sequence and different were all calculated. Results: conserved T epitopes were found between the vaccines and delta and omicron variants: FTNVYADSFVIRGDE (392-406), SFVIRGDEVRQIAPG (399-413), NLKPFERDI (460-468), ELLHAPATV (516-524) and STNLVKNKCVNFNFN (530-544). The region spanning from residues 522 and 540 included B epitopes identified by three algorithms, both in the vaccines and all the variants. Among several isolations of the omicron variant, a number of sequence changes occurs, leading to heterogeneous lines and potential modifications in their immunogenicity. Conclusions: epitopes shared between Cuban vaccines and ómicron variant justify the usefulness of vaccination with the immunogens used in Cuba, as well as boosters that will lead to some partial protection.

Keywords

• glicoproteínas
• virus del sras
• sars-cov-2
• covid-19
• vacunas
• inmunogenicidad vacunal