Table 1.

Technologic approaches for HIV drug resistance testing

Category	Type	Assay	Application	Unique features	Status	References
Population-based	Sanger ‘Standard’ sequencing	Viroseq	Centralized	Genotyping HIV-1 protease gene from codons 1–99 and RT gene from codons 1–335	Commercially available	[5,6■■]
				Cost 120 USD per sample, VL threshold =2000cpm, Sensitivity >20%
	Sanger ‘Standard’ sequencing	TruGene	Centralized	Genotyping HIV-1 protease gene from codons 4–99 and RT codons 38–248	Discontinued	[7]
				Cost 150 USD per sample, VL threshold = 200cpm
	Sanger ‘Standard’ sequencing	In-house	Centralized	Genotyping for non-B subtypes and flexible amplification of resistance codons	In development	[5,8–10]
				Cost 50–150 USD per sample
Sensitive	NGS	Illumina	Centralized	Detection of minor variants using unique tagging of individual virion genomes	In development	[11■]
				High number of reads per run, but the read lengths are shorter than 454
	NGS	454 Pyrosequencing	Centralized	Longer read lengths, but limited to 1 million reads, high error rates with polybases >6	In development	[12]
	Point mutation assay PCR primer amplification	ASPCR	Point-of-care	Selective amplification of PCR product by match or mismatch of 3’ end of primer	In development	[13]
				Cost <5 USD per sample, low VL threshold, problems with specificity (polymorphisms)
	Point mutation assay PCR primer ligation	OLA	Point-of-care	Selective ligation of tagged-oligonucleotides on HIV PCR product by match or mismatch of 3’ end of primer, ligated-oligonucleotides can be identified with ELISA, plate or paper capture detection methods	Currently field testing in Kenya: Clinical trial: NCT01898754	[14–16]
	Point mutation assay PCR primer ligation	LRA	Point-of-care	Simplified ligation amplification assay using a one-step single-buffer method and sequence-specific dual-labeled probe for detection	In development	[17,18]

ASPCR, allele-specific PCR; LRA, one-step ligation on RNA amplification; NGS, next-generation sequencing; OLA, oligonucleotide ligation assay; RT, reverse transcriptase; VL, viral load.