Table 1.
ASPE primers for HIV-1 group M subtype C
| Primer no. | Typea | Sequence (5′ to 3′) | Tag IDb | Positionc |
|---|---|---|---|---|
| 1 | M41 | Tag-AAG ARA AAA TAA AAG CAT TAA YAG MAA TTT GTG AWG ARA | 45 | 2632→2670 |
| 2 | 41L | Tag-AAG ARA AAA TAA AAG CAT TAA YAG MAA TTT GTG AWG ARC | 38 | 2632→2670 |
| 3 | K65 | Tag-AAA TCC ATA TAA CAC TCC ART ATT TGC YAT AAA RAA | 12 | 2708→2743 |
| 4 | 65R | Tag-AAA TCC ATA TAA CAC TCC ART ATT TGC YAT AAA RAG | 13 | 2708→2743 |
| 5 | K70 | Tag-CCA GTA TTT GCC ATA AAG ARG AAR GAY AGT ACT AA | 18 | 2724→2758 |
| 6 | 70R | Tag-CCA GTA TTT GCC ATA AAG ARG AAR GAY AGT ACT AG | 21 | 2724→2758 |
| 7 | L74 | Tag-CAT AAA AAA GAA RGA CAG TAC HAR RTG GAG AAA AT | 67 | 2735→2769 |
| 8 | 74V | Tag-CAT AAA AAA GAA RGA CAG TAC HAR RTG GAG AAA AG | 90 | 2735→2769 |
| 9 | Y115 | Tag-AGT RCT RGA YGT GGG RGA TGC ATA | 73 | 2870→2893 |
| 10 | 115F | Tag-AGT RCT RGA YGT GGG RGA TGC ATT | 62 | 2870→2893 |
| 11 | Q151 | Tag-GGA TTA GRT ATC AAT ATA ATG TRY TNC CAC | 29 | 2971→3000 |
| 12 | 151M | Tag-GGA TTA GRT ATC AAT ATA ATG TRY TNC CAA | 36 | 2971→3000 |
| 13 | M184 | Tag-AGR GCA AAA AAT CCA GAM RTR GTY ATC TRY CAA TAY A | 37 | 3063→3099 |
| 14 | 184V | Tag-AGR GCA AAA AAT CCA GAM RTR GTY ATC TRY CAA TAY G | 22 | 3063→3099 |
| 15 | K219 | Tag-AAR TGG GGR TTT ACY ACA CCA GAC A | 53 | 3180→3204 |
| 16 | 219Q | Tag-AAR TGG GGR TTT ACY ACA CCA GAC C | 44 | 3180→3204 |
| 17 | 219E | Tag-AAR TGG GGR TTT ACY ACA CCA GAK G | 96 | 3180→3204 |
| 18 | L100 | Tag-CAA TTA GGR ATA CCA CAC CCA KCA GGR T | 42 | 2820→2847 |
| 19 | 100I | Tag-CAA TTA GGR ATA CCA CAC CCA KCA GGR A | 58 | 2820→2847 |
| 20 | K101 | Tag-AAT TAG GRA TAC CAC ACC CAK CAG GRW TRA | 55 | 2821→2850 |
| 21 | 101P | Tag-AAT TAG GRA TAC CAC ACC CAK CAG GRW TRC C | 89 | 2821→2851 |
| 22 | 101E | Tag-AAT TAG GRA TAC CAC ACC CAK CAG GRW TRG | 65 | 2821→2850 |
| 23 | K103 | Tag-GAA TAC CAC ACC CAK CAG GGT TRA ARA AGA AA | 19 | 2827→2858 |
| 24 | 103N | Tag-GAA TAC CAC ACC CAK CAG GGT TRA ARA AGA AY | 66 | 2827→2858 |
| 25 | 103R | Tag-GAA TAC CAC ACC CAK CAG GGT TRA ARA AGA GA | 63 | 2827→2858 |
| 26 | V106 | Tag-ACA CCC AKC AGG GTT AAA RAA GAA HAA RTC WGT | 20 | 2834→2866 |
| 27 | 106A | Tag-ACA CCC AKC AGG GTT AAA RAA GAA HAA RTC WGC | 39 | 2834→2866 |
| 28 | 106M | Tag-CAC ACC CAK CAG GGT TAA ARA AGA AHA ART CWA | 75 | 2833→2865 |
| 29 | Y181 | Tag-GCC CTT TAG RRC AMA AAA TCC AGA MVT RGT YAT CTA | 9 | 3056→3091 |
| 30 | 181C | Tag-GCC CTT TAG RRC AMA AAA TCC AGA MVT RGT YAT CTG | 82 | 3056→3091 |
| 31 | Y188 | Tag-CAG AAA TRG TYA TCT RTC AAT AYR TRG ATG AYT TRT A | 83 | 3076→3112 |
| 32 | 188L | Tag-CAG AAA TRG TYA TCT RTC AAT AYR TRG ATG AYT TRC T | 93 | 3076→3112 |
| 33 | G190 | Tag-ATA GTY ATC TRT CAA TAT RTG GAT GAC TTR TAT GTR GG | 97 | 3081→3118 |
| 34 | 190A | Tag-ATA GTY ATC TRT CAA TAT RTG GAT GAC TTR TAT GTR GC | 76 | 3081→3118 |
| 35 | V32 | Tag-CTC TYT TAG AYA CAG GAG CAG ATG AYA CAG | 14 | 2317→2346 |
| 36 | 32I | Tag-CTC TYT TAG AYA CAG GAG CAG ATG AYA CAA | 48 | 2317→2346 |
| 37 | I47 | Tag-TGC CAG GRA RAT GGA AAC CAA RAA TRA | 30 | 2365→2391 |
| 38 | 47V | Tag-GCC AGG RAR ATG GAA ACC AAR AAT RGT | 43 | 2366→2392 |
| 39 | 47A | Tag-GCC AGG RAR ATG GAA ACC AAR AAT RGC | 78 | 2366→2392 |
| 40 | L76 | Tag-AAA TTT GTG GRA AAA ARG CTR TAG GTA CAG TRT | 28 | 2446→2478 |
| 41 | 76V | Tag-AAA TTT GTG GRA AAA ARG CTR TAG GTA CAG TRG | 70 | 2446→2478 |
| 42 | I84 | Tag-AGT ATT ART RGG RCC TAC ACC TGT CAA YA | 35 | 2474→2502 |
| 43 | 84V | Tag-AGT ATT ART RGG RCC TAC ACC TGT CAA YG | 77 | 2474→2502 |
| 44 | L90 | Tag-CCT ACA CCT GTC AAC ATA ATT GGR AGR AAY HTR T | 95 | 2487→2520 |
| 45 | 90 M | Tag-CCT ACA CCT GTC AAC ATA ATT GGR AGR AAY HTR A | 57 | 2487→2520 |
a
One primer was designed for each wild-type and mutant allele at 20 drug resistance mutation loci, and five loci have two types of mutant allele, so a total of 45 ASPE primers were designed.
b
Each Tag matches with one of the MagPlex-TAG microspheres (Luminex Corp., Austin, TX, USA). ID, identification.
c
Positions based on HXB2 sequence positions from 5′ to 3′.