Table 2. Epitopes and escape rate of epitopes from chronic progressors with fixation events where positive IFN-γ ELISPOT response was detected on the T/F virus.

Subject ID	GT	Epitope (MT)*,†	Epitope (WT)†	Start aa	End aa	Region	ELISPOT‡	DPI§	Matching Subject Allele	Predicted Rank (WT)	Rank Change	Epsilon Estimate¶	p-Value	Fitness Estimated
300023	1a	RAEAHLHAW	RAEAQLHAW	852	860	NS2	91	60	HLA-B*57:01	0.3	0	0.0625	0.0001	Yes
		NSKRTPMGF	KSKRTPMGF	2629	2637	NS5B	484	60	HLA-B*57:01	0.45	–2.2	0.1243	0.0036	Yes
300240	3a	RAQALPPSW	RAQAPPPSW	1602	1610	NS3	55	44	HLA-B*57:01	0.2	0	0.1025	0.0236	Yes
		RLGPVQNEI	RLGPVQNEV	1633	1641	NS3	300	71	HLA-A*02:01	1.6	–2.1	0.0303	0.0001	Yes
300256	1a	DYPYRLWHY	HYPYRLWHY	610	618	E2	750	58	HLA-A*24:02	1.45	–0.5	0.4813	0.0242	N/A
		GPKMGVRAT	GPRLGVRAT	41	49	Core	25	58	HLA-B*07:02	0.4	–1.4	0.0532	0.0413	N/A
		HPSIEEVAL	HPNIEEVAL	1359	1367	NS3	150	58	HLA-B*35:01	0.5	0	0.0565	0.0001	Yes
HOKD0485FX	1b	HSRRKCDEL	HSKKKCDEL	1395	1403	NS3	55	79	HLA-B*08:01	3.3	0.5	0.2685	0.972	Yes
THDS1086MX	1a	KLVAMGLNAV	KLVAMGINAV	1406	1415	NS3	85	72	HLA-A*02:01	0.75	0.5	0.5098	0.0005	Yes
		TLSPYYKRHI	TLSPYYKRYI	830	839	NS2	30	72	HLA-A*02:01	3.35	–6.05	0.0689	0.0003	Yes
		VRMVMMTHF	ARMVMMTHF	2841	2849	NS5B	25	72	HLA-B*27:05	0.2	–0.1	0.2582	0.0034	Yes
THGS0684MX	1a	TSILGIGTV	TSILGIGTA	1324	1332	NS3	230	58	HLA-A*02:01	32	17	0.2861	0.0145	Yes
		SILGIGTVL	SILGIGTAL	1325	1333	NS3	405	58	HLA-A*02:01	5.6	–1.2	0.2861	0.0145	Yes
		AWETARYTPV	AWETARHTPV	2816	2825	NS5B	50	58	HLA-A*02:01	36.5	3.5	0.1082	0.0484	Yes

^*Final most dominant escape variant is shown (i.e. frequency of occurrence >70%).

^†Red shows the positions which undergo amino acid change.

^‡ IFN-γ ELISPOT test of autologous PBMC measured in SFU per million PBMC against wild type epitope at earliest sample time point with a positive assay (shown in DPI column). WT - Wild Type and MT - Mutant Mutant epitopes are sourced from the final available deep sequenced data point.

^§Days post infection.

^¶The epsilon estimate is the rate of escape given in per day.