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Table 1 Primer and probe sequences

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

Primers Primer sequence 5'-3'  
V3 evolution B1 virus
5'tripleB1_1 GAA AAT TTC ACA GAC AAT GCT 1st PCR
3'tripleB1_rt TTA ATT TTG TAA CTA TCA GTT C 1st 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 1st PCR
3'tripleB2_rt TTA ATT TTT CAA CTG TCT GAT T 1st 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 1st PCR
3'tripleAE_rt AGT GCT CTT TTA ATT TTT CAG 1st 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