Table 2b:

HLA II antigenic epitopes predicted using Rankpep.

Antigen	HLADRB10101	HLADRB10401	HLADRB10402	HLADRB10402	HLADRB10701	HLADRB10801	HLADRB11101	HLADRB11501
Nucleocapsid protein	298-305	52-60			346-354	41-49	87-95	50-58
	YKHWPQIAQ	WFTALTQHG			FKDQVILLN	RPQGLPNNT	YRRATRRIR	ASWFTALTQ
	354-362	86-94			300-308	348-356	86-94	360-368
	NKHIDAYKT	YYRRATRRI			HWPQIAQFA	DQVILLNKH	YYRRATRRI	YKTFPPTEP
	86-94	300-308					34-42
	YYRRATRRI	HWPQIAQFA					GARSKQRRP
	305-313	49-57					298-306
	AQFAPSASA	TASWFTALT					YKHWPQIAQ
	52-60						301-309
	WFTALTQHG						WPQIAQFAP
ORF3a	211-219	211-219	45-53	62-70	59-67		62-70	77-85
	YYQLYSTQL	YYQLYSTQL	WLIVGVALL	IITLKKRWQ	ASKIITLKK		IITLKKRWQ	VHFVCNLLL
	212-220	45-53	211-219	85-93	87-95		68-76	84-92
	YQLYSTQLS	WLIVGVALL	YYQLYSTQL	LLFVTVYSH	FVTVYSHLL		RWQLALSKG	LLLFVTVYS
	65-73				54-62
	LKKRWQLAL				AVFQSASKI
Membrane protein	32-40	28-36	28-36	37-45	65-73	44-52	31-39
	ICLLQFAYA	FLTWICLLQ	FLTWICLLQ	FAYANRNRF	FVLAAVYRI	RFLYIIKLI	WICLLQFAY
	65-73	55-63	49-57		48-56	55-63	39-47
	FVLAAVYRI	WLLWPVTLA	IKLIFLWLL		IIKLIFLWL	WLLWPVTLA	YANRNRFLY
	76-84	65-73				58-66	90-98
	ITGGIAIAM	FVLAAVYRI				WPVTLACFV	LMWLSYFIA
	80-88	71-79
	IAIAMACLV	YRINWITGG