Table 1.

Oligonucleotide probes used in OLA to detect mutations in HIV pol

Subtype B Amplicons
SPX OLA			MPX OLA
Codon	Genotype	Oligonucleotide Sequence	Codon	Genotype	Oligonucleotide Sequence	Concentration per reaction [uM]	Ratio of Probe per codon set	Probe Mixture
K65R	wta	digb-CTCCAGTATTTGCCATAAAGAA	K65R	wt	CTCCAGTATTTGCCATAAARAA	0.13	1
	mutant	fc-CTCCAGTATTTGCCATAAAGAG		mutant	dig-CTCCAGTATTTGCCATAAAGAG		4
	common	pd-RAAAGACRGTACTAAATGGAGAA-bio		common	p-RAAAGACRGTACTAAATGGAGAA-bio		2
M184V	wt	dig-AGACATAGTTATCTATCAATACA	M184V	wt	AGACATAGTTATCTATCAATACA	0.03	1	Sub B/C
	mutant	f-AGACATAGTTATCTATCAATAYG		mutant	f-AGACATAGTTATCTATCAATAYG		4	Sub B/C
	common	p-TGGATGATTTGTATGTAGGATC-bio		common	p-TGGATGATTTGTATGTAGGATC-bio		4
K103N	wt	dig-ACATCCCGCAGGGTTAAAAAAGAAR	K103N	wt	ACATCCCGCAGGGTTAAAAAAGAAR	0.03	1
	mutant	f-ACATCCCGCAGGGTTAAAAAAGAAC		mutant	dig-ACATCCCGCAGGGTTAAAAAAGAAC		4
	common	p-AAATCAGTAACAGTACTGGATGTGGGT-bio		common	p-AAATCAGTAACAGTACTGGATGTGGGT-bio		4
Y181C	wt	dig-ACAAAATCCAGACATAGTTATCTA	Y181C	wt	ACAAAATCCAGACATAGTTATCTA		1
	mutant	f-ACAAAATCCAGACATAGTTATCTG		mutant	f-ACAAAATCCAGACATAGTTATCTG	0.16	8
	common	p-TCAATACATGGATGATTTGTATGTA-bio		common	p-TCAATACATGGATGATTTGTATGTA-bio		8	Sub B/C

Subtype C Amplicons
SPX OLA			MPX OLA
Codon	Genotype	Oligonucleotide Sequence	Codon	Genotype	Oligonucleotide Sequence	Concentration per reaction [uM]	Ratio of Probe per codon set	Probe Mixture
K65R	wt	dig-CTCCAGTATTTGCCATAAARAA	K65R	wt	CTCCAGTATTTGCCATAAARAA	0.06	1
	mutant	f-CTCCAGTATTTGCCATAAARAG		mutant	dig-CTCCAGTATTTGCCATAAARAG		4
	common	p-RAARGACAGTACTAAATGGAGAA-bio		common	p-RAARGACAGTACTAAATGGAGAA-bio		4	Sub B/C
M184V	wt	dig-AGACATAGTTATCTATCAATATA	M184V	wt	AGACATAGTTATCTATCAATATA	0.06	1
	mutant	f- AGACATAGTTATCTATCAATATG		mutant	f-AGACATAGTTATCTATCAATAYG		8	Sub B/C
	common	p-TGGATGATTTGTATGTAGGATC-bio		common	p-TGGATGATTTGTATGTAGGATC-bio		8
K103N	wt	dig-ACATCCCGCAGGGTTAAAAAAGAAR	K103N	wt	ACATCCCGCAGGGTTAAAAAAGAAR	0.06	1
	mutant	f-ACATCCCGCAGGGTTAAAAAAGAAC		mutant	f-ACATCCCGCAGGGTTAAAAAAGAAC		4
	common	p-AAATCAGRAACAGTACTGGATGTGGGGGAT-bio		common	p-AAATCAGTRACAGTACTGGATGTGGG-bio		4
	commonf	p-AAATCAGRAACAGTACTGGATGTGGG-bio
Y181C	wt	dig-ACAAAATCCAGAAATAGTCATCTA	Y181C	wt	ACAAAATCCAGAAATAGTCATCTA	0.20	1
	mutant	f-AMAAAATCCAGAAATAGTCATCTG		mutant	dig-AMAAAATCCAGAAATAGTCATCTG		4
	common	p-TCAATACATGGATGATTTGTATGTA-bio		common	p-TCAATATATGGATGACTTGTATGTA-bio		8	Sub B/C
V106M	wt	dig-CCAGCAGGGTTAAAAAAGAAAAAATCAG	V106M	wt	CCAGCAGGGTTAAAAAAGAAAAAATCAG	0.06	1
	mutant	f-CCAGCAGGGTTAAAAAAGAAAAAATCAA		mutant	f-CCAGCAGGGTTAAAAAAGAAAAAATCAA		4
	common	p-TRACAGTACTGGATGTGGGGGATGCATAT-bio		common	p-TRACAGTACTGGATGTGGGGGATGCATAT-bio		4
G190A	wt	dig-CATGGATGACTTGTATGTAGG	G190A	wt	CATGGATGACTTGTATGTAGG	0.12	1
	mutant	f-CATGGATGACTTGTATGTAGC		mutant	dig-CATGGATGACTTGTATGTAGC		8
	common	p-ATCTGAYTTAGAAATAGGGCAG-bio		common	p- ATCTGAYTTAGAAATAGGGCAG-bio		8

^awt, wild-type;

^bdig, digoxigenin;

^cf, fluorescein;

^dp, phosphate;

^ebio, biotin;

^falternative probe