Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing

Table 1 Samples subjected to ultra-deep pyrosequencing in this study

Patient Number	Sampling Time-point	NRTI mutations	NNRTI mutations	Primary PCR	Secondary PCR
Patient 2	Baseline			9	9
	8 Months		K103KN
	11 Months		Y181C	10	20
	14 Months			3	20
Patient 32	Baseline		V90I	6	9
	7 Months	T215ST		2	20
	8 Months	M184I
	14 Months
	15 Months		G190AE
	16 Months		V108AV	3	20
	24 Months			2	20
Patient 42	Baseline 1 (2008)			2	7
	Baseline 2 (2009)	V118IV		5	20
	5 Months	V118I
Patient 45	Baseline		V106I, E138A, G190A	9	20
	8 Months		V106I, E138A, G190A	10	20
	13 Months		Sequence Failed	10	20
Patient 76	Baseline		V90I, Y181CY, H221HY	10	20
	3 Months
	6 Months		Y181C	10	15
	9 Months		Sequence Failed	10	19

Consensus sequencing of reverse transcriptase from five patients had previously revealed discrepancies in the presence/absence of DRMs [6, 7]. Baseline describes the sampling time-point prior to ART initiation with subsequent samples being described as the number of months post ART initiation. Mutations shown in the table are those observed in the consensus sequencing of each sampling time-point with DRMs to current therapy marked in bold. The sample time-point names for samples selected for subsequent ultra-deep pyrosequencing are marked in bold and the success rate for multiple PCRs for these samples are also shown. The remaining six samples were not chosen due to difficulty/failure with PCR amplification or consensus sequencing.

ISSN: 1471-2334