Attenuation of multiple Nef functions in HIV-1 elite controllers

Retrovirology

Table 1 Analysis of Nef residues associated with EC Nef functions (all N>5 and q<0.4)

Nef activity	Position on HXB2	AA^a	No. of subjects^b		Relative Nef activity (%)		p-value	q-value
Nef activity	Position on HXB2	AA^a	With AA	Without AA	With AA	Without AA	p-value	q-value
HLA-I down-regulation	8	S	17	27	83.6	97.2	0.01	0.3
	8	R	14	30	106.1	91.1	0.02	0.3
	11	V	20	21	87.2	98.9	0.01	0.3
	14	P	34	11	91.1	108	0.004	0.3
	46	S	36	8	96.7	77.1	0.01	0.3
	108	D	34	11	91.1	105.8	0.02	0.3
	108	E	11	34	105.8	91.1	0.02	0.3
	138	C	5	40	79.8	96.5	0.02	0.3
	138	T	40	5	96.5	79.8	0.02	0.3
	192	H	36	9	97	78.1	0.01	0.3
	192	R	6	39	84	96.8	0.04	0.4
	205	N	22	23	101	83.6	0.02	0.3
	205	D	22	23	85.9	98.9	0.03	0.3
CD74 up-regulation	8	S	17	27	37.7	60	0.004	0.3
	28	E	14	31	73.7	42.4	0.008	0.3
	28	D	29	16	40.4	65.3	0.009	0.3
	135	F	10	35	35	57.5	0.003	0.3
	135	Y	34	11	57.1	35.1	0.01	0.3
CD4 down-regulation	8	S	17	27	84.8	92.6	0.007	0.3
	14	P	34	11	86.1	97.9	0.003	0.1
	14	S	5	40	102.9	87.2	0.02	0.4
	15	A	11	34	76.9	91.3	0.02	0.4
	21	K	11	34	70.7	91.6	0.002	0.1
	21	R	28	17	91.6	76.9	0.02	0.4
	105	R	12	33	76.6	91.9	0.003	0.1
	163	C	9	36	98.1	86.6	0.02	0.4

^a AA, amino acid.
^b Row totals vary depending on the codon position because sequences with gaps in the alignment are considered missing data.

ISSN: 1742-4690