Considering epitopes conservity in targeting SARS-CoV-2 mutations in variants: a novel immunoinformatics approach to vaccine design

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has gained mutations at an alarming rate in the past years. Developing mutations can increase the virus's pathogenicity and virulence; reduce the efficacy of vaccines, antibodies neutralization, and even challenge adaptive immunity. So, it is essential to identify conserved epitopes (with fewer mutations) in different variants with appropriate antigenicity to target the variants by an appropriate vaccine design. Yet as, 3369 SARS-CoV-2 genomes were collected from global initiative on sharing avian flu data. Then, mutations in the immunodominant regions (IDRs), immune epitope database (IEDB) epitopes, and also predicted epitopes were calculated. In the following, epitopes conservity score against the total number of events (mutations) and the number of mutated sites in each epitope was weighted by Shannon entropy and then calculated by the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS). Based on the TOPSIS conservity score and antigenicity score, the epitopes were plotted. The result demonstrates that almost all epitopes and IDRs with various lengths have gained different numbers of mutations in dissimilar sites. Herein, our two-step calculation for conservity recommends only 8 IDRs, 14 IEDB epitopes, and 10 predicted epitopes among all epitopes. The selected ones have higher conservity and higher immunogenicity. This method is an open-source multi-criteria decision-making platform, which provides a scientific approach to selecting epitopes with appropriate conservity and immunogenicity; against ever-changing viruses.

Significance of Conserved Regions in Coronavirus Spike Protein for Developing a Novel Vaccine against SARS-CoV-2 Infection

“…Their study further identified conserved common neutralizing epitopes on the SARS-CoV-2, including YLTPGDSSSGWTAGAAAYYV (247–267 aa), TFKCYGVSPTKLNDL (376–390 aa) on S1 and LNEVAKNLNESLIDLQELGK (1186–1205 aa) on the S2 [ 116 ]. A recent immunoinformatic study predicted conserved and highly immunogenic CTL-induced epitopes on S1 VRFPNITNL (327–335 aa) and PYRVVVLSF (507–515 aa) ( Table 1 ), while the CTL-induced epitopes on S2 were identified to be VVFLHVTYV (1060–1068 aa) and GVVFLHVTY (1059–1067 aa) ( Table 2 ) [ 117 ]. Based on the conservancy, antigenicity, allergenicity, population coverage and transmembrane location, another study chose potential conserved epitopes from the S1 (FNATRFASVYAWNRK, 342–356 aa) ( Table 1 ), S2 (FLHVTYVPAQEKNFT, 1062–1072 aa) ( Table 2 ) and the E/M protein to construct a SARS-CoV-2 vaccine and revealed that it had high immunogenicity and broad neutralizing activity against the SARS-CoV-2 RBD ( Figure 3 ) [ 118 ].…”

Bioinformatics approach for the construction of multiple epitope vaccine against omicron variant of SARS-CoV-2

“…The conservity was checked by predicting epitopes with the help of immune epitope database (IEDB). This method provides a scientific approach for selecting epitopes with good immunogenicity and conservity against any virus 40 . Currently, immune system stimulation triggers allergic reaction in response to the vaccines developed.…”

Significance of Conserved Regions in Coronavirus Spike Protein for Developing a Novel Vaccine against SARS-Cov-2 Infection

“…Their study further identified conserved common neutralizing epitopes on the SARS-CoV-2 including YLTPGDSSSGWTAGAAAYYV (247-267 aa), TFKCYGVSPTKLNDL (376-390 aa) on S1 and LNEVAKNLNESLID-LQELGK (1186-1205 aa) on the S2 [106]. A recent immunoinformatic study predicted conserved and highly immunogenic CTL-induced epitopes on S1 VRFPNITNL (327-335 aa), and PYRVVVLSF (507 -515 aa) (Table 1), while the CTL-induced epitopes on S2 were identified to be VVFLHVTYV (1060-1068 aa) and GVVFLHVTY (1059-1067 aa) (Table 2) [107].…”