Table 1.

Prediction of CD4⁺ and CD8 + T cell binding epitopes of the selected SARS Cov2 proteins

Software	Parameter	Envelope (E) protein	Membrane (M)protein	Spike (S) protein	Nucleocapsid (N) protein
NETMHC4.0 [Prediction of MHC Class I binders]	Overlapping nonamers	67	214	1265	411
	Total number of binding epitopes	33	103	411	101
	Number of alleles bound	62	61	70	64
	Number of promiscuous epitopes	23	26	90	20
	Number of promiscuous antigenic epitopes	17	13	50	9
IEDB [Prediction of MHC Class II binders]	Overlapping nonamers	67	214	1265	411
	Total number of binding epitopes	37	75	349	68
	Number of alleles bound	14	15	15	15
	Number of promiscuous epitopes	3	7	29	3
	Number of promiscuous antigenic epitopes	3	4	14	1
Vaxijen 2.0 [Prediction of whole protein antigenicity]	Antigenic score	0.6025	0.5102	0.4646	0.5059

Spike protein (S) generated maximum number of overlapping nonamers and binding epitopes among all the four proteins. Because of its smallest size, Envelope (E) protein generated least overlapping nonamers and binding epitopes. Using NetMHC4.0: Spike protein (S) and Nucleocapsid (N) phosphoprotein bound to maximum number and Membrane (M) glycoprotein to least number of alleles. A total of 89 promiscuous antigenic epitopes were found in all the 4 proteins. Using IEDB: Surface glycoprotein or (S) Spike protein, Nucleocapsid (N) phosphoprotein and Membrane (M) glycoprotein bound to 15 class II alleles. A total of 22 promiscuous antigenic epitopes were found in all the 4 proteins. Vaxijen score of > 0.4 in all the 4 proteins shows their probable antigenic nature