Table 2. Diversity parameters of HVR1 HCV variants in seven hospitalized patients infected with HCV 1b.
| Patient ID | Number of NGS reads before filtering | Number of HVR1 nucleotide variantsa | Number of HVR1 amino acid variantsa | Number of nucleotide substitutionsa, b | Nucleotide diversity (per site)a, b |
|---|---|---|---|---|---|
| 2 | 3363 | 2 | 2 | 4 | 0.01515 |
| 3 | 3588 | 3 | 2 | 6 | 0.01705 |
| 4 | 4149 | 7 | 3 | 12 | 0.01705 |
| 5 | 4185 | 5 | 3 | 5 | 0.01061 |
| 6 | 5987 | 3 | 3 | 3 | 0.00852 |
| 7 | 6481 | 1 | 1 | 0 | 0.00000 |
| 8 | 3789 | 3 | 3 | 50 | 0.15333 |
| MEAN (median) | 4506 (4149) | 3.4 (3.0) | 2.4 (3.0) | 11.4 (5.0) | 0.03167 (0.01515) |
a >0.5% frequency cutoff
b With respect to consensus sequence (the most frequent sequence in all patients)