Genetic determinants of HIV-1 subtype C Nef-mediated SERINC3 down-regulation

Table 1 Amino acid variants significantly associated with altered SERINC3 down-regulation function

Codon ^a	Amino Acid ^b	ConsC ^c	Relative Nef function (%) ^d		Number of Samples ^e		Impact^f	p value	q value
Codon ^a	Amino Acid ^b	ConsC ^c	with AA	without AA	with AA	without AA	Impact^f	p value	q value
3	N	G	18	71	13	94	− 53	0.000	0.02
3	G	G	76	32	73	34	44	0.000	0.03
5	W	W	68	34	98	9	34	0.041	0.27
8	S	S	71	22	91	13	49	0.001	0.04
8	R	S	31	66	7	97	− 35	0.016	0.21
9	S	S	76	34	86	7	42	0.018	0.21
10	I	I	78	33	78	14	44	0.005	0.14
10	K	I	25	76	6	86	− 51	0.005	0.14
11	V	V	79	36	79	13	43	0.001	0.04
12	G	G	75	34	89	7	41	0.008	0.15
12	E	G	34	75	7	89	− 41	0.008	0.15
20	I	I	77	43	50	57	34	0.021	0.24
20	M	I	42	74	41	66	− 32	0.027	0.25
32	A	A	70	42	87	20	28	0.014	0.21
32	T	A	36	63	10	97	− 27	0.027	0.25
38	D	D	75	35	77	30	40	0.005	0.14
49	P	A	42	64	29	78	− 22	0.036	0.25
51	T	N	86	47	25	82	38	0.008	0.15
51	N	N	48	80	79	28	− 32	0.016	0.21
64	G	E	89	55	5	102	34	0.037	0.25
81	F	Y	88	55	15	92	33	0.018	0.21
81	Y	Y	55	87	91	16	− 32	0.035	0.25
101	V	I	89	56	5	102	33	0.045	0.28
108	E	E	75	38	62	45	37	0.030	0.25
108	D	E	38	75	45	62	− 37	0.030	0.25
116	N	H	48	74	53	54	− 27	0.033	0.25
116	H	H	74	48	54	53	27	0.033	0.25
188	L	S	17	61	6	101	− 44	0.026	0.25
205	D	D	62	26	98	8	37	0.028	0.25
205	N	D	26	62	6	100	− 37	0.047	0.28

^aCodon numbered with reference to the HIV-1 subtype B genomic reference sequence HXB2
^bAmino acids (AA) associated with altered SERINC3 down-regulation activity in participant-derived sequences, with p < 0.05, q < 0.3. Only amino acids observed at least 5 times at a given position were included in the analysis
^cThe consensus amino acid according to the 2021 consensus C Nef sequence (www.hiv.lanl.gov)
^dThe median SERINC3 down-regulation activity in Nef sequences harbouring the amino acid at that position
^eThe number of sequences with ( +) and without (−) the amino acid
^fImpact of the amino acid on Nef function, calculated as the difference in function between those expressing and not expressing the amino acid in question

ISSN: 1743-422X