Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

Retrovirology

Table 4 Frequencies of amino acids associated with altered intra-subtype Nef function

Function	Codon^a	AA	Subtype^b	+/-^c	% Frequency				p-value	q-value
Function	Codon^a	AA	Subtype^b	+/-^c	A	B	C	D	p-value	q-value
CD4	88	G	C	-	10	2	20	2	<0.0001	<0.0001
	88	S	C	+	90	97	80	98	0.0001	0.0001
HLA-I	3	G	A	-	76	95	66	81	<0.0001	<0.0001
	8-12	SSIVG	C	-	82	48^d	81	88	<0.0001	<0.0001
	8	R	B	+	10	30	7	12	<0.0001	<0.0001
	8	S	B	-	80	41	81	81	<0.0001	<0.0001
	9	R	A	+	5	9	4	0	0.05	0.06
	9	S	C	-	87	70	89	88	0.0008	0.001
	11	V	A	-	79	34	74	88	<0.0001	<0.0001
	14	P	B	-	89	63	93	94	<0.0001	<0.0001
	28	A	B	+	14	8	1	4	0.007	0.008
	40	H	C	+	86	79	51	93	<0.0001	<0.0001
	40	Y	C	-	10	14	46	5	<0.0001	<0.0001
	65	D	B	-	11	9	1	8	0.13	0.13
	65	E	B	+	86	90	97	87	0.08	0.09
	83	G	A	-	67	57	45	31	<0.0001	<0.0001
	89	F	A/B	+/-	16	5	97	5	<0.0001	<0.0001
	89	H	B	+	82	93	0	95	<0.0001	<0.0001
	98	D	B	+	85	7	47	31	<0.0001	<0.0001
	98	E	B	-	15	92	53	69	<0.0001	<0.0001
	102	H	C	-	9	25	16	1	<0.0001	<0.0001
	105	K	C	+	73	54	72	78	0.004	0.005
	105	Q	B	-	2	20	8	13	0.001	0.002
	105	R	A/C	-/-	23	26	20	9	0.03	0.04
	108	D	C	-	15	86	50	45	<0.0001	<0.0001
	108	E	C	+	84	13	50	55	<0.0001	<0.0001
	120	Y	A	-	60	93	35	62	<0.0001	<0.0001
	153	I	B	-	1	17	1	9	<0.0001	<0.0001
	153	V	B	+	99	80	99	87	<0.0001	<0.0001
	168	M	A	+	24	61	76	39	<0.0001	<0.0001
	182	Q	C	-	5	28	11	1	<0.0001	<0.0001
	191	L	A	-	61	3	0	1	<0.0001	<0.0001
	196	Q	A	-	36	0	0	0	<0.0001	<0.0001
	198	K	B	+	10	21	35	33	0.0002	0.0002
	202	F	B	+	62	10	23	62	<0.0001	<0.0001
	202	Y	B	-	35	90	69	38	<0.0001	<0.0001

^aNumbered according to HXB2.
^bIndicates the subtype in which the amino acid is associated with altered Nef function.
^cIndicates whether the amino acid is associated with increased (+) or decreased (-) Nef function.
^dThe consensus for subtype B is SSVVG and is 52% conserved.

ISSN: 1742-4690