HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity

Retrovirology

Table 7 Nef amino acids significantly associated with altered SERINC5 down-regulation activity

Codon^a	AA^b	Cons^c	Relative Nef function (%)^d		Number of samples^e		Impact^f	p value	q value
Codon^a	AA^b	Cons^c	With AA	Without AA	With AA	Without AA	Impact^f	p value	q value
10	K	I	57.6	88.3	6	86	− 31	0.008	0.3
10	I	I	88.6	60.9	78	14	28	0.01	0.3
11	V	V	89.5	58.0	79	13	32	0.003	0.3
38	D	D	89.5	65.9	77	29	24	0.005	0.3
38	E	D	55.1	86.7	13	93	− 32	0.01	0.3
51	T	N	92.7	79.9	25	81	13	0.01	0.3
65	E	E	81.3	95.1	94	12	− 14	0.0005	0.1
65	D	E	95.2	83.2	9	97	12	0.003	0.2
101	V	I	97.7	83.2	5	101	15	0.01	0.3
135	F	Y	59.8	85.9	13	93	− 26	0.03	0.4
173	T	M	54.6	85.9	5	101	− 31	0.02	0.3
176	T	E	58.8	86.7	9	97	− 28	0.02	0.4
188	H	S	94.4	83.2	6	100	12	0.01	0.3
191	H	R	91.0	81.3	16	90	10	0.03	0.4
191	R	R	81.3	91.0	88	18	− 10	0.03	0.4

Amino acids (AA) at n ≥ 5 in the dataset, p < 0.05, q ≤ 0.4
^aNumbered according to HXB2
^bThe amino acids associated with increased or decreased SERINC5 down-regulation activity
^cThe consensus amino acid (Cons) at a particular codon from the reference 2004 consensus C Nef sequence from the Los Alamos HIV sequence database
^dThe median percentage SERINC5 down-regulation activity which was expressed relative to SF2 control (100% down-regulation activity) of the Nef clones with (+) and without (−) the amino acid
^eThe number of sequences with (+) and without (−) the amino acid
^fThe median Nef activity of the clones with the amino acid minus the median Nef activity of the clones without amino acid

ISSN: 1742-4690