HIV-1 sequence evolution in vivo after superinfection with three viral strains

Retrovirology

Table 1 Primer and probe sequences

Primers	Primer sequence 5'-3'
V3 evolution B1 virus
5'tripleB1_1	GAA AAT TTC ACA GAC AAT GCT	1^st PCR
3'tripleB1_rt	TTA ATT TTG TAA CTA TCA GTT C	1^st PCR
5'tripleB1_2	TAA TAG TAC AGC TGA ATG CAT	Nested PCR
3'tripleB1_3	AGT GTT ATT CCA TTT TGT TAA	Nested PCR
V3 evolution B2 virus
5'tripleB2_1	GAC AAT TTC ACA GAC AAT AAG	1^st PCR
3'tripleB2_rt	TTA ATT TTT CAA CTG TCT GAT T	1^st PCR
5'tripleB2_2	TAA TAG TAC AGC TGA AGA CAG	Nested PCR
3'tripleB2_3	AGC ATT ACC CCA TTC TAC TCC	Nested PCR
V3 evolution AE virus
5'tripleAE_1	GAA AAT CTC ACA GAT AAT ACC	1^st PCR
3'tripleAE_rt	AGT GCT CTT TTA ATT TTT CAG	1^st PCR
5'tripleAE_2	CAT AAT AGT GCA CCT TAA TAA	Nested PCR
3'tripleAE_3	CCA TTT TGT TCT ATT AAT CTC	Nested PCR
Taqman strain specific assay B1
5'B1/B2triple-taqman	TTA ATT GTA CAA GAC CCA GCA ACA
3'B1triple-taqman	AAG GTT ACA ATG TGC TTG CCT TA
B1triple-probe2rev	TCT CCT ATT ATT TCT CCT GTT GCA T	5'label 6-FAM
Taqman strain specific assay B2
5'B1/B2triple-taqman	TTA ATT GTA CAA GAC CCA GCA ACA
3'B2triple-taqman	ACT AAT GTT ACA ATG TGC CTT T
B2triple-probe	TAA AAA ATG CTT TCC CTG GTC CCA TA	5'label 6-FAM
Taqman strain specific assay AE
5'AEtriple-taqman	TCA ATT GTA CCA GAC CCT CTA AC
3'AEtriple-taqman	TTG TTC TAT TAA TCT CAC AAT A
AEtriple-probe	TAT AGA ATA CTT GTC CTG GTC CCA TA	5'label 6-FAM

ISSN: 1742-4690