Table 1.

Analysis of conformational epitopes on the SARS-CoV-2 mutations. The results of the conformational epitope analysis were compared mutation by mutation, and only regions of concordance were excerpted. Mutations consistent with all three analyses are indicated in bold letters. Mutations consistent with positive selection by selection pressure analysis are shown in red letters, and mutations unique to conformational epitope analysis are shown in blue letters. The areas highlighted in a pale yellow color indicate the RBD regions.

BA.2		BA.4		BA.5
Position	Predicted epitopes	Position	Predicted epitopes	Position	Predicted epitopes
109–114	TLDSKT	108–114	TTLDSKT	109–114	TLDSKT
144–154	YYHKNNKSWME	142–152	DVYYHKNNKSW	145–152	YHKNNKSW
160–169	YSSANNCTFE	164–167	NNCT	160–167	YSSANNCT
177–185	MDLEGKQGN	182–185	KQGN	182–185	KQGN
436–452	WNSNKLDSKVGGNYNYL	437–450	NSNKLDSKVGGNYN	443–450	SKVGGNYN
458–460	KSN	455–460	LFRKSN	457–460	RKSN
474–488	QAGNKPCNGVAGFNC	468–494	ISTEIYQAGNKPCNGVAGVNCYFPLQS	472–489	IYQAGNKPCNGVAG VNCY
498–506	RPTYGVGHQ	497–506	FRPTYGVGHQ	496–506	GFRPTYGVGHQ
703–705	NSV	703–705	NSV	703–705	NSV
834–842	IKQYGDCLG	836–841	QYGDCL	836–841	QYGDCL
890–897	AGAALQIP	890–895	AGAALQ	890–897	AGAALQIP
1140–1162	PLQPELDSFKEELDKYFKNHTSP	1140–1162	PLQPELDSFKEELDKYFKNHTSP	1140–1162	PLQPELDSFKEELDKYFKNHTSL
BA.4		XBB.1.5		XBB.1.16
Position	Predicted epitopes	Position	Predicted epitopes	Position	Predicted epitopes
142–152	DVYYHKNNKSW	146–151	QKNNKS	147–151	KNNKS
164–167	NNCT	164–166	NNC	162–166	SANNC
182–185	KQGN	182–185	KEGN	182–185	KEGN
437–450	NSNKLDSKVGGNYN	436–452	WNSNKLDSKPSGNYNYL	436–452	WNSNKLDSKPSGNYNYL
455–460	LFRKSN	455–460	LFRKSK	455–460	LFRKSK
468–494	ISTEIYQAGNKPCNGVAGVNCYFPLQS	472–494	IYQAGNKPCNGVAGP NCYSPLQS	469–494	STEIYQAGNRPCNGVAGP NCYSPLQS
497–506	FRPTYGVGHQ	498–506	RPTYGVGHQ	496–506	GFRPTYGVGHQ
703–705	NSV	703–705	NSV	703–705	NSV
836–841	QYGDCL	836–843	QYGDCLGD	834–841	IKQYGDCL
890–895	AGAALQ	890–895	AGAALQ	890–894	AGAAL
1140–1162	PLQPELDSFKEELDKYFKNHTSP	1140–1162	PLQPELDSFKEELDKYFKNHTSP	1140–1162	PLQPELDSFKEELDKYFKNHTSP
BA.5		XBB.1.5		XBB.1.16
Position	Predicted epitopes	Position	Predicted epitopes	Position	Predicted epitopes
142–152	YHKNNKSW	146–151	QKNNKS	147–151	KNNKS
160–167	YSSANNCT	164–166	NNC	162–166	SANNC
182–185	KQGN	182–185	KEGN	182–185	KEGN
443–450	SKVGGNYN	436–452	WNSNKLDSKPSGNYNYL	436–452	WNSNKLDSKPSGNYNYL
457–460	RKSN	455–460	LFRKSK	455–460	LFRKSK
472–489	IYQAGNKPCNGVAGV NCY	472–494	IYQAGNKPCNGVAGP NCYSPLQS	469–494	STEIYQAGNRPCNGVAGP NCYSPLQS
496–506	GFRPTYGVGHQ	498–506	RPTYGVGHQ	496–506	GFRPTYGVGHQ
703–705	NSV	703–705	NSV	703–705	NSV
836–841	QYGDCL	836–843	QYGDCLGD	834–841	IKQYGDCL
890–897	AGAALQIP	890–895	AGAALQ	890–894	AGAAL
1140–1162	PLQPELDSFKEELDKYFKNHTSL	1140–1162	PLQPELDSFKEELDKYFKNHTSP	1140–1162	PLQPELDSFKEELDKYFKNHTSP