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Table 1 Determination of predicted co-receptor usage in the HIV-1 isolate by 454 deep sequencing analyses

From: Defining the fitness of HIV-1 isolates with dual/mixed co-receptor usage

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
  1. Italics values indicate clones with different amino acids at the 11/25 positions
  2. 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 %.