Table 3.

Ultradeep pyrosequencing of discordant samples phenotyped as CXCR4-using but as CCR5-using by direct sequencing

Patient	HIV-1 subtype	Plasma HIV-1 RNA (log10 copies/ml)	Phenotype (TTT)	Genotype by direct sequencing	Ultradeep pyrosequencing on the GS Junior
					No. of reads	Geno2pheno 5.75		Combined 11/25 and net charge rule
						% CXCR4-using clones	Tropism	% CXCR4-using clones	Tropism
6	B	2.88	R5X4	R5	5,704	4.59	X4-containing	4.59	X4-containing
8	B	3.82	R5X4	R5	2,875	3.20	X4-containing	0	Pure R5
11	B	4.75	R5X4	R5	2,689	3.05	X4-containing	10.52	X4-containing
24	B	5.50	R5X4	R5	2,641	5.11	X4-containing	5.11	X4-containing
25	B	3.31	R5X4	R5	3,476	5.84	X4-containing	5.84	X4-containing
26	B	4.93	R5X4	R5	2,357	8.70	X4-containing	0	Pure R5
27	B	4.78	R5X4	R5	2,881	0	Pure R5	0	Pure R5
28	B	5.83	R5X4	R5	2,665	0	Pure R5	0	Pure R5
29	B	3.34	R5X4	R5	4,425	0	Pure R5	0	Pure R5