Multi-epitope vaccine against SARS-CoV-2 targeting the spike RBD: an immunoinformatics approach

Figures & data

Table 1. The T-cell epitopes prediction.

Epitopes	Antigenisity	Allergenicity and toxicity	Accessibility prediction	Beta-turn prediction	Flexibility	Hydrophobicity
SNNRIYQTSNFRVQP	0.6622	Non	1.0	1.063	1.015	2.327
PSNCLWTLKSLLIW	0.4775	Non	1.0	0.940	0.969	-2.071
KKFLLFHKFGQRHCHYCCPSTDTDSQ	0.5375	Non	1.0	1.058	0.987	1.498
QGTNTSKQVAAPLSGVTAQKSFAL	0.7786	Non	1.0	0.985	1.015	2.621

Table 2. The B-cell epitopes prediction.

Epitopes	Antigenicity	Allergenicity and toxicity	Accessibility	Flexibility	Hydrophobicity
APLTPSSSENKSVPLKSFHLEKK	0.7773	Non	2.144	1.137	6.643
APLTPSSSENKSV	0.6955	Non	1.594	1.137	6.643
RGDEVRQIAPGQTGKFADYNYKLPD	1.0425	Non	2.171	1.112	6.643
VRQIAPGQTGKFAD	1.2211	Non	1.865	1.112	4.643

Table 3. Population coverage analysis.

Population/area	Class combined
	Coverage	Average hit	pc90
In this study	86.94%	6.25	3.06
Average	86.94	6.25	3.06
Standard deviation	0.0	0.0	0.0

Table 4. Epitope conservancy analysis results.

Epitopes	Length	Protein sequence matches at identity (%)	Minimum identity (%)	Maximum identity
SNNRIYQTSNFRVQP	15	100.00 (1/1)	100.00	100.00
PSNCLWTLKSLLIW	14	100.00 (1/1)	100.00	100.00
KKFLLFHKFGQRHCHYCCPSTDTDSQ	26	100.00 (1/1)	100.00	100.00
QGTNTSKQVAAPLSGVTAQKSFAL	24	100.00 (1/1)	100.00	100.00

Table 5. Epitope clustering results.

Cluster number	Peptide number	Alignment
1.1	Singleton	SNNRIYQTSNFRVQP
2.1	Singleton	PSNCLWTLKSLLIW
3.1	Singleton	KKFLLFHKFGQRHCHYCCPSTDTDSQ
4.1	Singleton	QGTNTSKQVAAPLSGVTAQKSFAL

Figure 1. Secondary structure prediction of the RBD region of SARS-CoV-2.

Figure 2. Structure of the SARS-CoV-2 spike receptor-binding domain.

(A) 3D structure of receptor-binding domain region of SARS-CoV-2. (B) Nucleotide sequence of receptor-binding domain region in S gene.

Table 6. Physicochemical properties of amino acid sequences of the RBD region.

Target	Amino acids (n)	Theoretical pI	Negatively charged residues (n)	Positively charged residues (n)	Extinction coefficient	Estimated half-life	Instability index	Aliphatic index
RBD region	344	10.07	21	55	55305	2.8 hours	43.88	98.23