Table 1.
Determination of predicted co-receptor usage in the HIV-1 isolate by 454 deep sequencing analyses
| Culture | N | Plasmid | N | Plasma | N | Genotype | PSSM results | Geno2Pheno (5 %) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 11/25 | Prediction | % X4 | % R5 | Prediction | FPR (%) | Prediction | ||||||
| Predicted co-receptor usage for B19 clonesa | ||||||||||||
| B19 C1 | 4,070 | B19 P1 | 4,102 | B19 R1 | 2,237 | S/E | CCR5 | 0.11 | 0.62 | CCR5 only | 33.90 | CCR5 |
| B19 C2 | 25 | S/E | CCR5 | 0.11 | 0.59 | CCR5 only | 10.90 | CCR5 | ||||
| B19 C3 | 5 | S/E | CCR5 | 0 | 0.1 | CCR5 only | 55 | CCR5 | ||||
| B19 C4 | 3 | S/E | CCR5 | 0.22 | 0.82 | CCR5 only | 41.20 | CCR5 | ||||
| B19 P2 | 3 | S/E | CCR5 | 0.22 | 0.89 | CCR5 only | 50.50 | CCR5 | ||||
| B19 R2 | 51 | S/K | CXCR4 | 0.24 | 0.92 | CCR5 only | 7.80 | CCR5 | ||||
| B19 R3 | 13 | S/E | CCR5 | 0.22 | 0.86 | CCR5 only | 26.90 | CCR5 | ||||
| B19 R4 | 11 | S/E | CCR5 | 0.11 | 0.42 | CCR5 only | 72 | CCR5 | ||||
| B19 R5 | 7 | S/E | CCR5 | 0.11 | 0.46 | CCR5 only | 47.70 | CCR5 | ||||
| B19 R6 | 7 | S/E | CCR5 | 0.11 | 0.46 | CCR5 only | 47.70 | CCR5 | ||||
| B19 R7 | 6 | S/E | CCR5 | 0.11 | 0.46 | CCR5 only | 47.70 | CCR5 | ||||
| B19 R8 | 6 | S/E | CCR5 | 0.11 | 0.46 | CCR5 only | 47.70 | CCR5 | ||||
| B19 R9 | 6 | S/E | CCR5 | 0.11 | 0.46 | CCR5 only | 47.70 | CCR5 | ||||
| B19 R10 | 5 | S/E | CCR5 | 0.11 | 0.6 | CCR5 only | 42.30 | CCR5 | ||||
| B19 R11 | 4 | S/E | CCR5 | 0.11 | 0.47 | CCR5 only | 18.20 | CCR5 | ||||
| B19 R12 | 4 | S/E | CCR5 | 0.09 | 0.39 | CCR5 only | 59.80 | CCR5 | ||||
| B19 R13 | 3 | S/E | CCR5 | 0.11 | 0.46 | CCR5 only | 47.70 | CCR5 | ||||
| B19 R14 | 3 | S/K | CXCR4 | 0.29 | 0.95 | CXCR4 capable | 3.20 | CXCR4 | ||||
| Plasmid | N | Culture | N | Genotype | PSSM Results | Geno2Pheno (5 %) | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| 11/25 | Prediction | % X4 | % R5 | Prediction | FPR (%) | Prediction | ||||
| Predicted co-receptor usage for B12 clonesa | ||||||||||
| B12_P1 | 3,611 | B12_C1 | 1,405 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 20.40 | CCR5 |
| B12_P2 | 55 | B12_C2 | 19 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 20.40 | CCR5 |
| B12_P3 | 24 | B12_C3 | 10 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 20.4 | CCR5 |
| B12_P4 | 21 | B12_C4 | 6 | S/Q | CCR5 | 0.27 | 0.95 | CCR5 only | 18.80 | CCR5 |
| B12_C5 | 6 | S/Q | CCR5 | 0.33 | 0.96 | CCR5 only | 22.60 | CCR5 | ||
| B12_C6 | 6 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 20.40 | CCR5 | ||
| B12_C7 | 5 | S/Q | CCR5 | 0.36 | 0.98 | CCR5 only | 10.50 | CCR5 | ||
| B12_C8 | 5 | S/Q | CCR5 | 0.36 | 0.98 | CCR5 only | 17.10 | CCR5 | ||
| B12_P10 | 3 | B12_C9 | 5 | S/Q | CCR5 | 0.33 | 0.96 | CCR5 only | 20.20 | CCR5 |
| B12_P17 | 3 | B12_C10 | 4 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 20.40 | CCR5 |
| B12_C11 | 4 | S/Q | CCR5 | 0.47 | 0.98 | CCR5 only | 36.90 | CCR5 | ||
| B12_P15 | 3 | B12_C12 | 3 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 20.40 | CCR5 |
| B12_C13 | 3 | S/Q | CCR5 | 0.51 | 0.98 | CCR5 only | 35.60 | CCR5 | ||
| B12_P8 | 4 | B12_C14 | 3 | S/Q | CCR5 | 0.33 | 0.96 | CCR5 only | 49.70 | CCR5 |
| B12_C5 | 3 | S/Q | CCR5 | 0.33 | 0.98 | CCR5 only | 14.40 | CCR5 | ||
| B12_P5 | 7 | B12_C1 | 1,405 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 20.40 | CCR5 |
| B12_P6 | 6 | B12_C2 | 19 | S/K | CXCR4 | 0.53 | 0.99 | CXCR4 capable | 4.80 | CXCR4 |
| B12_P7 | 4 | B12_C3 | 10 | S/E | CCR5 | 0.36 | 0.98 | CCR5 only | 1.70 | CXCR4 |
| B12_P9 | 3 | B12_C4 | 6 | S/Q | CCR5 | 0.29 | 0.95 | CCR5 only | 13.10 | CCR5 |
| B12_P11 | 3 | B12_C5 | 6 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 20.40 | CCR5 |
| B12_P12 | 3 | B12_C6 | 6 | S/Q | CCR5 | 0.42 | 0.98 | CCR5 only | 6.80 | CCR5 |
| B12_P13 | 3 | B12_C7 | 5 | S/Q | CCR5 | 0.31 | 0.96 | CCR5 only | 17.80 | CCR5 |
| B12_P14 | 3 | B12_C8 | 5 | S/Q | CCR5 | 0.33 | 0.96 | CCR5 only | 7.90 | CCR5 |
| B12_P16 | 3 | B12_C9 | 5 | S/Q | CCR5 | 0.29 | 0.95 | CCR5 only | 8.20 | CCR5 |
| B12_P18 | 3 | B12_C10 | 4 | S/Q | CCR5 | 0.51 | 0.98 | CCR5 only | 6.80 | CCR5 |
Italics values indicate clones with different amino acids at the 11/25 positions
aThe C2-V3 coding regions was RT-PCR amplified with barcoded 454 primers from the plasma RNA (only for B12), from the plasmid population following yeast recombination (no RT step), and from RNA of culture supernatant. Amino acid alignments grouped identical clones. Predictive co-receptor algorithms, 11/25, PSSM, and Geno2Pheno were run on the V3 loop amino acid sequences. FPR false positive rate for Geno2Pheno at 5 %.