Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq

Table 4 Association between the major drug resistance mutations emerging in treatment failures from the ALIVE cohort, the drug regimens reported at the time of failure, and expected resistance profile based on genotype results

Sample # visit #	Drug resistance mutation	Gene product	Frequency of DR mutation (coverage)*	Mutational load (copies/ml)	Treatment at time point of failure	Stanford resistance profile for major mutations
2v15	M41L	RT	13.3%(5316)	6913	ZDV, 3TC	H: 3TC, FTC
2v15	M184V	RT	99.9%(7721)	51926		L: ABC, DDI
5v20	K103N	RT	100%(5807)	513564	ZDV, 3TC,	H: 3TC, FTC,
	M184V	RT	82.8%(5266)	425231	ABC, EFV	EFV, NVP
						L: ABC
						PL: DDI
6v20	L90M	PI	16.2%(3602)	179820	TDF, FTC, DRVr, RAL	H: NFV
						I: IDV, SQV
						L: ATV, LPV, FPV,
9v33	M184V	RT	99.8%(7493)	420158	ZDV, 3TC, ABC, RTV, FTC	H: 3TC, FTC
						L: ABC
						PL: DDI
10v10	K103N	RT	100%(5979)	40200	EFV, TDF, FTC	H: 3TC, FTC, EFV, NVP
	M184V	RT	100%(5399)	40200		L: ABC
	M184V	RT	100%(5399)	40200		PL: DDI
16v11	E138K	RT	7.6%(8955)	27149	3TC, RTV, LPV	H: 3TC, FTC
	M184V	RT	56.6%(8222)	202190		I: RPV
	S147G	IN	7.0%(3123)	25006		L: ABC
	S147G	IN	7.0%(3123)	25006		PL: DDI, EFV, ETR, NVP
23v17	K103N	RT	99.8%(6110)	16168	EFV, TDF, FTC	H: 3TC, FTC, EFV, NVP
	M184V	RT	67.1%(6182)	10870		H: 3TC, FTC, EFV, NVP
						L: ABC
						PL: DDI
27v05	M46I**	PI	7.3%(3591)	1262	d4T, 3TC, ABC, IDVr	L: NFV
27v05	M46I**	PI	7.3%(3591)	1262	d4T, 3TC, ABC, IDVr	PL: ATV, FPV, IDVr, LPV (non-emerging DR related to treatment: H: 3TC, L: ABC)

Boldface: correlation between mutation, treatment and drug resistance profile in each patient sample at the time point of treatment failure. H = high level drug resistance, I = intermediate drug resistance, L = low level drug resistance, PL: potential low level drug resistance. Drug resistance mutations in italics are not associated with any reported drug taken by the patients throughout the course of this study. *Coverage refers to the number of sequencing reads representing a given nucleotide. **Patient 27 virus also harbored I54V, L90M, K103N and M184V at both time points. These mutations did not emerge between treatment success and failure, but likely contributed to overall failure.

ISSN: 1742-4690