Table 2. Prolonged and substantial discordance in the prevalence of drug resistance mutations in plasma versus PBMC. Percentages represent the prevalence of the indicated resistance mutations revealed by 454 “deep” sequencing.

Patient Identifier	Days post raltegravir therapy	Log Viral Load	CD4	E92Q		E138A/K		G140S		Y143R		Q148H/R		N155H
				Plasma	PBMC	Plasma	PBMC	Plasma	PBMC	Plasma	PBMC	Plasma	PBMC	Plasma	PBMC
3180	−20	6.09	5					0%	0%			0%	0%
	78	3.53	16					0%	0%			0%	0%
	177a	4.4	18					100%	1%			100%	1%
	233	4.27	13					69%	6%			69%	6%
	331	4.11	12					1%	*			0%	*
	414	*	59					0%	*			0%	*
3242	0	4.07	331											0%	0%
	170	3.92	507											100%	*
	177	3.99	432											100%	*
	213	3.55	509											100%	*
	224a	4	470											100%	36%
	248	4.94	462											0%	*
	262	4.94	522											0%	*
	294	4.43	456											0%	*
	322	4.6	540											0%	*
	374	4.75	452											0%	0%
	497	3.81	447											0%	0%
3501	0	5.27	3			0%	*	0%	*			0%	*
	54	5.28	10			0%	0%	69%	2%			69%	1%
	113	5.39	18			2%	0%	70%	0%			69%	1%
	188	*	19			12%	0%	73%	4%			73%	5%
	226	5.68	14			20%	3%	70%	11%			70%	5%
	266	*	17			29%	8%	75%	15%			75%	15%
	338	4.59	30			61%	6%	78%	12%			78%	11%
3508	−7	4.63	3	0%	*	0%	*	0%	*	0%	*	0%	*	0%	*
	83	4.53	25	29%	0%	0%	0%	72%	33%	10%	0%	72%	33%	12%	0%
	197	4.69	7	9%	0%	2%	0%	0%	0%	100%	0%	0%	0%	0%	0%
	412	4.57	4	1%	*	0%	*	0%	*	87%	*	0%	*	0%	*

Asterisks (*) indicate unavailable samples. Bolded font indicates time points at which subjects were prescribed raltegravir-containing regimens. Superscript ^a indicates the termination of a raltegravir-containing regimen. Blank cells indicate a wildtype genotype.