Table 1.

Epitopes and variants studied

Epitope	ORF	CD4/CD8	HLA	Variant	Frequency (%)	Countries	Global lineages	Loss of T cell response	References describing epitope
FTSDYYQLY207-215	3a	CD8	A∗01:01	Q213K	0.059	56	95	Yes	Ferretti et al. (2020); Kared et al., 2021; Peng et al. (2020); Schulien et al. (2021)a
QRNAPRITF9-17	N	CD8	B∗27:05	Q9H	0.289	74	176	No	Nelde et al. (2021); Peng et al. (2020)
QRNAPRITF9-17				P13L	0.978	97	194	Yes	Nelde et al. (2021); Peng et al. (2020)
QRNAPRITF9-17				P13S	0.210	83	132	Yes	Peng et al. (2020); Nelde et al. (2021)
QRNAPRITF9-17				P13T	0.102	45	81	Yes	Nelde et al. (2021); Peng et al. (2020)
MEVTPSGTWL322-331	N	CD8	B∗40:01	T325I	0.069	52	109	Partial	Nelde et al. (2021); Peng et al. (2020); Schulien et al. (2021)b
KTFPPTEPK361-369	N	CD8	A∗03:01 A∗11:01	T362I	0.293	85	165	Yes	Ferretti et al. (2020); Gangaev et al. (2020)b; Kared et al., 2021; Peng et al. (2020)
KTFPPTEPK361-369				T366I	0.237	74	154	No	Ferretti et al. (2020); Gangaev et al. (2020)b; Kared et al. (2021); Peng et al. (2020)
KTFPPTEPK361-369				P365S	0.794	73	142	Yes	Ferretti et al. (2020); Gangaev et al. (2020)b; Kared et al. (2021); Peng et al. (2020)
KCYGVSPTK378-386	S	CD8	A∗03:01	P384L	0.085	59	116	No	Ferretti et al. (2020); Peng et al. (2020)
CTFEYVSQPFLMDLE166-180	S	CD4	–	L176F	0.260	68	158	No	Peng et al. (2020)
CTFEYVSQPFLMDLE166-180				M177I	0.083	60	92	Partial	Peng et al. (2020)
NLLLQYGSFCTQLNR751-765	S	CD4	DRB1∗15:01	R765L	0.017	31	64	Partial	Peng et al. (2020)
					0.000
TTDPSFLGRY1637-1646	ORF1A	CD8	A∗01:01	T1637I	0.189	58	113	Partial	Ferretti et al. (2020); Gangaev et al. (2020)b; Nelde et al. (2021)
TTDPSFLGRY1637-1646				T1638I	0.066	52	96	Partial	Ferretti et al. (2020); Gangaev et al. (2020)b; Nelde et al. (2021)
TTDPSFLGRY1637-1646				P1640S	0.202	69	165	Partial	Ferretti et al. (2020); Gangaev et al. (2020)b; Nelde et al. (2021)
TTDPSFLGRY1637-1646				P1640L	2.540	105	156	Partial	Ferretti et al. (2020); Gangaev et al. (2020)b; Nelde et al. (2021)
TTDPSFLGRY1637-1646				P1640H	0.050	27	20	Partial	Ferretti et al. (2020); Gangaev et al. (2020)b; Nelde et al. (2021)

Mutated positions detailed in red within wild-type epitope sequence. Frequency indicates % of sequences where variant is seen within the SARS-CoV-2 mutation dataset downloaded from CoV-GLUE (http://cov-glue.cvr.gla.ac.uk/#/home) on July 30, 2021. Global Lineages refers to Pango lineage assignment.

ORF, open reading frame; HLA, human leukocyte antigen.

^aResponses to longer peptide also seen in Snyder et al. (2020).

^bResponses to longer peptide also seen in Snyder et al. (2020) and Kared et al. (2021).