TABLE 3.

Evaluation of the discrepancy results^a

Discrepancy type	Sample name	Sequence detected by:
		PANDAA (cutoff, ≥5%)	Sanger sequencing (cutoff, ≥20%)	NGS (cutoff, ≥2%)
False positive	P 053	K65R	WT	Failed
	P 082	K103N	WT	Failed
	P 096	K103N	WT	K103N
	P 025	Y181C	WT	WT
	P 033	Y181C	WT	WT
	P 040	Y181C	WT	WT
	P 061	Y181C	WT	Failed
	P 073	Y181C	WT	Failed
	P 094	Y181C	WT	WT
	P 098	Y181C	WT	Failed
	P 107	Y181C	WT	Failed
	P 113	Y181C	WT	Failed
	P 120	Y181C	WT	WT
	P 121	Y181C	WT	WT
	P 122	Y181C	WT	Y181C
	P 124	Y181C	WT	WT
	P 129	Y181C	WT	Y181C
	P 130	Y181C	WT	WT
	P 132	Y181C	WT	WT
	P 140	Y181C	WT	WT
	P 147	Y181C	WT	WT
	P 002	G190A	G190S	G190S
	P 023	G190A	G190E	Failed
	P 046	G190A	G190S	G190S
	P 060	G190A	G190S	G190AS
	P 062	G190A	WT	Failed
	P 121	G190A	G190E	G190A
	P 127	G190A	G190E	G190E
	P 129	G190A	WT	WT
	P 149	G190A	G190S	G190S
False negative	P 008	WT	K65R	K65R
	P 107	WT	K65, M184V	Failed
	P 132	WT	K103N	K103N
	P 082	WT	Y181C, G190A	Failed

^aNGS, next-generation sequencing; WT, wild-type virus. The PANDAA assay (≥5%) was assessed against Sanger sequencing for drug resistance mutations detected at ≥20%. We hypothesized that mutations detected by PANDAA and not by Sanger sequencing could represent low-abundance variants. These were later verified by NGS (≥2%). G190A/S/E mutations are nonpolymorphic mutations selected by EFV and NVP.