REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited Data
HLA haplotype population frequency data	This paper, Mendeley Data	Mendeley Data: https://doi.org/10.17632/cfxkfy9zp4.1
SARS-CoV-2 vaccine designs	This paper	Table S3
SARS-CoV-2 proteome	GISAID (Elbe and Buckland-Merrett, 2017)	Sequence entry Wuhan/IPBCAMS-WH-01/2019
SARS-CoV proteome	UniProt (Consortium, 2019)	UniProt: UP000000354 (Proteome ID)
HLA population frequency data	dbMHC, as obtained from the IEDB Population Coverage Tool download (Bui et al., 2006)	http://tools.iedb.org/population/
Human proteome	UniProt (Consortium, 2019)	UniProt: UP000005640 (Proteome ID)
SARS-CoV-2 experimental peptide stability data (Immunitrack)	(Prachar et al., 2020)	Data S1. COVID19-Intavis-Immunitrack-dataset: https://www.immunitrack.com/wp/wp-content/uploads/Covid19-Intavis-Immunitrack-datasetV2.xlsx
SARS-CoV-2 cleavage regions: ORF1a and ORF1b	UniProt (Consortium, 2019)	UniProt: P0DTD1; https://covid-19.uniprot.org/uniprotkb/P0DTD1#Protein%20Processing
SARS-CoV-2 cleavage regions: Spike (S)	(Wang et al., 2020)	Figure 1
Additional SARS-CoV-2 proteomes for mutation analysis	GISAID (Elbe and Buckland-Merrett, 2017)	Acknowledgements and detailed GISAID accessions in Table S4 (this paper)
Experimental data of Spike N-glycosylation: Cryo-EM	(Walls et al., 2020)	Table 2
Experimental data of Spike N-glycosylation: tandem mass spectrometry	(Zhang et al., 2020b)	https://www.biorxiv.org/content/10.1101/2020.03.28.013276v1.upplementary-material, Figures S5A and S5B
Baseline vaccine MHC I: (Srivastava et al., 2020)	(Srivastava et al., 2020)	Figure 2
Baseline vaccine MHC I: (Herst et al., 2020)	(Herst et al., 2020)	Data S1; Table 6
Baseline vaccine MHC I: (Herst et al., 2020)-top16	(Herst et al., 2020)	Table 4
Baseline vaccine MHC I: (Baruah and Bose, 2020)	(Baruah and Bose, 2020)	Table 1
Baseline vaccine MHC I: (Fast et al., 2020)	(Fast et al., 2020)	Table 2
Baseline vaccine MHC I: (Poran et al., 2020)	(Poran et al., 2020)	Table S5
Baseline vaccine MHC I: (Vashi et al., 2020)	(Vashi et al., 2020)	Table 5
Baseline vaccine MHC I: (Abdelmageed et al., 2020)	(Abdelmageed et al., 2020)	Table 2
Baseline vaccine MHC I: (Lee and Koohy, 2020)	(Lee and Koohy, 2020)	Table 4
Baseline vaccine MHC I: (Akhand et al., 2020)	(Akhand et al., 2020)	Table 2
Baseline vaccine MHC I: (Singh et al., 2020)	(Singh et al., 2020)	Table 2
Baseline vaccine MHC I: (Bhattacharya et al., 2020)	(Bhattacharya et al., 2020)	Table 2
Baseline vaccine MHC I: (Ahmed et al., 2020)	(Ahmed et al., 2020)	Table 2
Baseline vaccine MHC I: (Saha and Prasad, 2020)	(Saha and Prasad, 2020)	Table 1
Baseline vaccine MHC I: (Gupta et al., 2020)	(Gupta et al., 2020)	Table 4a
Baseline vaccine MHC I: (Khan et al., 2020)	(Khan et al., 2020)	Sub-Section 2 in Results of the Main Text
Baseline vaccine MHC I: (Mitra et al., 2020)	(Mitra et al., 2020)	Table 1(C)
Baseline vaccine MHC I: (Nerli and Sgourakis, 2020)	(Nerli and Sgourakis, 2020)	Tables S1 and S2
Baseline vaccine MHC I: (Yarmarkovich et al., 2020)	(Yarmarkovich et al., 2020)	Table S5 (65 33-mers, to which we applied sliding windows of lengths 8–10 to obtain the peptide set considered for MHC class I)
Baseline vaccine MHC I: (Yazdani et al., 2020)	(Yazdani et al., 2020)	Table 1 (peptides created by sliding windows of length 8–10)
Baseline vaccine MHC I: (Ismail et al., 2020)	(Ismail et al., 2020)	Section 3.2 "MEPVC Designing" (peptides created by sliding windows of length 8–10)
Baseline vaccine MHC II: (Ramaiah and Arumugaswami, 2020)	(Ramaiah and Arumugaswami, 2020)	Table S2 - "Unique Mean HBA T-Cell Epitopes" for each protein Subunit
Baseline vaccine MHC II: (Fast et al., 2020)	(Fast et al., 2020)	Table 2
Baseline vaccine MHC II: (Banerjee et al., 2020)	(Banerjee et al., 2020)	Table 3
Baseline vaccine MHC II: (Akhand et al., 2020)	(Akhand et al., 2020)	Table 2
Baseline vaccine MHC II: (Poran et al., 2020)	(Poran et al., 2020)	Table S7
Baseline vaccine MHC II: (Singh et al., 2020)	(Singh et al., 2020)	Table 2
Baseline vaccine MHC II: (Ahmed et al., 2020)	(Ahmed et al., 2020)	Table 2
Baseline vaccine MHC II: (Tahir ul Qamar et al., 2020)	(Tahir ul Qamar et al., 2020)	Table 1
Baseline vaccine MHC II: (Mitra et al., 2020)	(Mitra et al., 2020)	Table 1(B)
Baseline vaccine MHC II: (Abdelmageed et al., 2020)	(Abdelmageed et al., 2020)	Table 3
Baseline vaccine MHC II: (Vashi et al., 2020)	(Vashi et al., 2020)	Table 6
Baseline vaccine MHC II: (Baruah and Bose, 2020)	(Baruah and Bose, 2020)	Table 2
Baseline vaccine MHC II: (Yarmarkovich et al., 2020)	(Yarmarkovich et al., 2020)	Table S5 (65 33-mers, to which we applied sliding windows of lengths 13–25 to obtain the peptide set considered for MHC class II)
Baseline vaccine MHC II: (Yazdani et al., 2020)	(Yazdani et al., 2020)	Table 1 (peptides created by sliding windows of length 13–25)
Megapool MHC I: (Grifoni et al., 2020a)	(Grifoni et al., 2020a)	Table S6
Megapool MHC II: (Grifoni et al., 2020a)	(Grifoni et al., 2020a)	Table S3
Software and Algorithms
OptiVax	This paper, GitHub	https://github.com/gifford-lab/optivax
EvalVax	This paper, GitHub	https://github.com/gifford-lab/optivax
NetMHCpan-4.0	(Jurtz et al., 2017)	http://www.cbs.dtu.dk/services/NetMHCpan-4.0/
NetMHCpan-4.1	(Reynisson et al., 2020a)	http://www.cbs.dtu.dk/services/NetMHCpan-4.1/
NetMHCIIpan-4.0	(Reynisson et al., 2020b)	http://www.cbs.dtu.dk/services/NetMHCIIpan-4.0/
NetMHCIIpan-3.2	(Jensen et al., 2018)	http://www.cbs.dtu.dk/services/NetMHCIIpan-3.2/
MHCflurry 1.6.0	(O’Donnell et al., 2020)	Version 1.6.0, https://github.com/openvax/mhcflurry
PUFFIN	(Zeng and Gifford, 2019); https://github.com/gifford-lab/PUFFIN	GitHub commit a63f6c563b7e2f7b04eac28 a6cf09d8078ac3a2a with pre-trained model
Hapferret	https://github.com/nilsboar/HapFerret	GitHub commit e2381dc567cec97373acb 49c09f167e46ea0bb53
Nextstrain	(Hadfield et al., 2018); https://github.com/nextstrain/ncov	GitHub commit 639c63f25e0bf30c900f8d 3d937de4063d96f791
NetNGlyc	(Gupta et al., 2004)	http://www.cbs.dtu.dk/services/NetNGlyc/