Table 1.

V3 sequence alignment and PSSM viral phenotype prediction^a

Strain	V3 sequence	CD4+ PBL %CCR5 useb	SI/NSIc	X4R5d
Bal	CTRPNNNTRKSIHIGPGRALYTTGEIIGDIRQAHC	100	0	0
C2-16	............TM....VY..............	52	0	0
C2-22	............TM....VY...............	39	0	0
NR10	............A.....SF.A..R..........	39	0	0
NR8	............A.....SF.A..R..........	35	0	0
NR11	............A.....SF.A..R..........	26	0	0
DH12	..........G.TL....VF......V....K...	12	1	0
R3A	....G.....RVTL....VY....Q......K...	11	1	1
DR1	.I.........MTL...KVF....-VT....K...	15	1	0
DR17	.I.........MTL...KVF....-VT....K...	8	1	0
DR8	.I.........MTL...KVF....-VT....K...	4	1	0
89.6	.........RRLS......F.ARRN..........	4	1	1

^aPosition specific scoring matrix (Jensen et al., 2003)

^bPercentage of total primary lymphocyte entry in the presence of CXCR4 blocking

^cPredicted SI phenotype based on SI/NSI PSSM algorithm; 0=NSI, 1=SI

^dPredicted coreceptor phenotype based on X4R5 PSSM algorithm; 0=R5, 1=X4 or R5X4