State of the Art in Epitope Mapping and Opportunities in COVID-19

Figures & data

Table 1. In silico prediction tools of T and B-cell epitopes.

Epitope type	Method of measurement	Description of method	Prediction tool	URL	Ref.
T-cell epitope mapping	Data driven	Prediction of peptide-MHC binding based on sequence motif (SM) that depends on detection of MHC-binding amino acid motifs which are called anchor residues	MotifScan	https://myhits.sib.swiss/cgi-bin/motif_scan	[46]
		Evaluate the contribution of all peptide positions to MHC molecule binding	Rankpep	http://imed.med.ucm.es/Tools/rankpep.html	[199]
			SYFPEITHI	http://www.syfpeithi.de/
			PEPVAC	http://imed.med.ucm.es/PEPVAC/
			EPISOPT	http://bio.med.ucm.es/episopt.html
			Vaxign	https://violinet.org/vaxign2
		This approach is quantitative affinity matrices (QAMs) which involves peptide binding affinity scores	BIMAS2	https://edumetrisis.com/bimas-2/	[200,201]
			Propred	https://mybiosoftware.com/propred1-propred-predict-mhc-class-i-class-ii-binding-regions-antigen-sequence.html
			EpiJen	http://www.ddg-pharmfac.net/epijen/EpiJen/EpiJen.htm
	Structure based method	In the QSAR model, the binding affinity of peptides to MHC is computed as the sum of amino acid contributions at each position plus the contribution of adjacent peptide to anchor site	MHCPred	http://www.ddg-pharmfac.net/mhcpred/MHCPred/	[202,203]
			EpiDOCK,	http://www.ddg-pharmfac.net/epidock/
	Machine learning models	Pan-MHC specific methods made by training artifical neural network (ANNs) on input data including MHC residues that contact the peptide and peptide-binding affinity which can be used in predicting peptide-binding affinities to uncharacterized human leukocyte antigen (HLA) alleles	NetCTL	https://services.healthtech.dtu.dk/service.php?NetCTL-1.2	[204]
B-cell epitope mapping	Machine learning models	3D structure-based methods	DiscoTOP	http://tools.iedb.org/discotope/
			ElliPRO	http://tools.iedb.org/ellipro/
			SEPPA	http://www.badd-cao.net/seppa3/index.html
			EPITOPIA	http://epitopia.tau.ac.il/
			CBTOPE	http://crdd.osdd.net/raghava/cbtope/
			EPCES	http://sysbio.unl.edu/EPCES/
			PEASE	https://maayanlab.cloud/datasets2tools/landing/tool/PEASE

Figure 1. Representation for epitope mapping techniques and its significance in understanding disease severity, preparation of diagnostics, vaccines as well as therapeutics.

Both in silico epitope prediction tools and experimental epitope mapping are used for identification of SARS-CoV-2 epitopes. Epitope prediction and analysis tools are fed by protein sequences available in protein databases for prediction of potential epitopes that are then filtered for selected features. For experimental epitope mapping, SARS-CoV-2-specific antibodies, B-cells or T-cells may be isolated from COVID-19 patients, vaccinated persons or immunized animals. The interaction with whole, fragmented, synthetic, or recombinant antigens as well as phage display libraries can be analyzed using several experimental methods such as: ELISA, ELISpot, Cryo-electron microscope, etc.

ADE: Antibody-dependent enhancement.

Figure 2. SARS-CoV-2 genome showing the produced structural and non-structural protein with focus on some major findings of epitope mapping.

Epitope mining has revealed the presence of several immunodominant epitopes on the RBD as well as other regions of the Spike protein. Mutations in these epitopes have resulted in new variants of SARS-COV-2. Mimicry of some viral epitopes with other human proteins could provide an explanation for hyperinflammatory response.

CTD: C-terminal domain; NTD: N-terminal domain; RBD: Receptor binding domain.

Figure 3. Mechanism of proposed molecular mimicry of SARS-CoV-2 epitopes and human proteins.

This can lead to cross reaction with the immune cells resulting in hyperinflammatory response, cytokine storm and respiratory failure.

Table 2. List of some recent epitope-based vaccine studies, techniques used, and study outcomes.

Study	Epitope prediction method	Epitopes identified ^† (Location ^‡ )	Multiepitope vaccine construction	Immunogenicity validation/Epitope mapping of elicited immune response	Ref.
Smith et al.	Immuno-informatic tools	6 B (S) 10 T (S, M, and N)	Yes	In vivo animal model in mice/ELISA and ELISpot assays.	[106]
Feng et al.		19 B (S) 499 T (S, M, and E)			[117]
Qiao et al.		7 B (S) 3 T (S)			[138]
Kar et al.		15 T (S) 21 B (S)	Yes	In silico immune simulation	[125]
Tahir Ul Qamar et al.		69 B (M, N, E, ORF6, ORF7a, ORF8, and ORF10) 27 T (M, N, E, ORF6, ORF7, and ORF8)			[133]
Chukwudozie et al.		32 B (S) 15 T (S)			[119]
Saba et al.		3 B (S) 13 T (ORF1ab, S, M, and E)			[139]
Devi et al.		20 B (S, M, N, and E) 79 T (S, M, N, and E)			[127]
Ferreira et al.		5 B (S) 6 T (S)			[141]
Adam		1 B (N) 31 T (ORF1a, S, M, and N)			[142]
Rouzbahani et al.		14 B (S and N) 14 T (S and N)			[143]
Gustiananda et al.		12 T (ORF1ab)	No		[131]
Naz et al.		12 T (S) 1 B (S)	Yes	Not tested	[104]
Jyotisha et al.		1 B (S) 5 T (S)			[134]
Sanami et al.		6 B (S) 12 T (S)			[137]
Fatoba et al.		37 T (Orf1ab, S, ORF3a, M, and N) 8 B (Orf1ab, S, ORF3a, M, and N)			[120]
Khan et al.		5 B (S, M, N, and E) 21 T (S, M, N, E, ORF1ab, ORF3, ORF6, ORF7, and ORF8)			[121]
Crooke et al.		6 B (S, M, and N) 41 T (S, M, ORF1ab, ORF3, ORF6, ORF7, and ORF8)	No		[116]
Alam et al.		6 B (S) / 9 T (S)			[132]
Aparicio et al.	Experimental Tools	B (S) T (S)	Yes	In vivo animal model in mice/ELISA and ELISpot assays	[140]

† B, B-cell epitopes; T, T-cell epitopes.

‡ Viral proteins.

Table 3. List of some recent studies focusing on epitope-based therapeutics and epitope mapping techniques used in each study.

Study	Publication date	Source of mAbs	In vivo testing	Epitope mapping method	Ref.
Ju et al.	May 2020	Single B cells from individuals infected with SARS-CoV-2	Mouse model	X-ray crystallography	[169]
Brouwer et al.	June 2020	Convalescent sera of COVID-19 patients	Not done	Electron microscopy	[155]
Liu et al.	July 2020	Convalescent sera of COVID-19 patients	Hamster model	Cryo-electron microscopy	[74]
Tai et al.	July 2020	RBD-immunized mice	Not done	ELISA	[163]
Cao et al.	July 2020	Convalescent sera of COVID-19 patients	hACE2-transgenic mice	Cryo-Electron Microscopy	[151]
Zost et al.	July 2020	Convalescent sera of COVID-19 patients	Mouse model - non-human primate (NHP) model	ELISA	[154]
Baum et al./Hansen et al.	August 2020	Convalescent sera of COVID-19 patients and humanized mice immunized by DNA vaccines	Not done	Hydrogen-deuterium exchange mass spectrometry (HDX-MS)	[152,161]
Parray et al.	September 2020	Naive human semisynthetic phage library against RBD	Not done	Molecular modeling and docking	[167]
Zhang et al.	January 2021	Immunized mice	Mouse model	ELISA	[174]
Kim et al.	January 2021	Convalescent sera of COVID-19 patients	Ferret, hamster, and rhesus monkey models	X-ray crystallography	[148]
Piepenbrink et al.	March 2021	Convalescent sera of COVID-19 patients	Hamster model	CM-5 sensor chips to which RBD-FC were captured.	[157]
Xie et al.	August 2021	Convalescent sera of COVID-19 patients	Not done	ELISA	[153]
Schmitz et al.	September 2021	SARS-CoV-2 mRNA vaccine-elicited germinal center B cells	Hamster model	Bio-layer interferometry (BLI)-based competition assays	[205]
Tan et al.	November 2021	Naive human phage display antibody libraries	Not done	enzyme-linked immunosorbent assays and surface plasmon resonance analysis	[166]
Yuan et al.	December 2021	Large-scale phage libraries for nAbs	Hamster model	Site-directed mutagenesis in RBD followed by screening for mAb binding to cells expressing the mutants.	[165]
Wang et al.	December 2021	Convalescent sera of COVID-19 patients	Not done	Cryo-electron microscopy	[175]
Shan et al.	December 2021	Convalescent sera of COVID-19 patients	hACE2 Transgenic Mice	Competitive binding of mAbs to SARS-CoV-2 RBD immobilized to a CM5 sensor chip. measured by surface plasmon resonance (SPR)/Cryo-electron microscopy	[158]
Huang et al.	January 2022	Convalescent sera of COVID-19 patients	a Syrian hamster model	Cryo-electron microscopy/X-ray crystallography	[184]
Li et al.	January 2022	Convalescent sera of COVID-19 patients	Mouse model	Cryo-electron microscopy/cryo-electron tomography/peptide competition/X-ray crystallography	[183]
Kovacech et al.	February 2022	Mice immunized with either recombinant S protein or RBD	Mouse model	HDX-MS	[162]
Ueno et al.	March 2022	Convalescent sera of COVID-19 patients	Mouse model	ELISA	[156]
Lai et al.	March 2022	Mice immunized by purified RBD	Not done	Site-direct mutagenesis in RBD followed by western blot	[164]

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