Table 4.
Polymorphisms and RASs identified in GT1a-infected patients.
| HCV-infected patients | HCV/HIV-coinfected patients | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Clade I | Clade II | Clade I | Clade II | |||||||||
| A.A position | Mutation | N = 38 patients | % | Mutation | N = 262 patients | % | Mutation | N = 66 patients | % | Mutation | N = 222 patients | % |
| 24 | K24Q | 1 | 0.1 | K24Q/R | 3 | 0.1 | – | – | – | K24R | 2 | 0.0 |
| 28 | M28V | 1 | 0.1 | M28V | 10 | 0.2 | M28L/T | 2 | 0.1 | M28A/T/V | 10 | 0.2 |
| 30 | – | – | – | Q30H/R | 7 | 0.1 | – | – | – | Q30E/R | 5 | 0.1 |
| 31 | – | – | – | L31M | 1 | 0.0 | L31M | 2 | 0.1 | L31M | 1 | 0.0 |
| 48 | R48K/Q | 4 | 0.5 | R48H/K/Q | 212 | 3.9 | R48K/Q | 8 | 0.5 | R48H/K/N/Q/S | 187 | 3.7 |
| 58 | H58P | 1 | 0.1 | H58L/P/Q | 13 | 0.2 | H58D/P | 4 | 0.3 | H58D/P/N/R | 22 | 0.4 |
| 64 | T64A/K/N | 20 | 2.3 | T64A/N/S | 78 | 1.4 | T64A/N/S | 33 | 2.1 | T64A/K/N/S | 83 | 1.6 |
| 92 | – | – | – | A92P | 1 | 0.0 | – | – | – | A92A/D/F/S/V | 3 | 0.1 |
| 93 | Y93C/F | 3 | 0.4 | Y93H/N | 5 | 0.1 | Y93C | 3 | 0.2 | Y93C/H | 4 | 0.1 |
| 107 | K107E/T | 20 | 2.3 | T107A/E/K/M | 16 | 0.3 | K107E/R/S/T | 38 | 2.4 | T107A/K/M | 11 | 0.2 |
| 123 | R123Q | 25 | 2.9 | Q123R | 226 | 4.2 | R123Q | 38 | 2.4 | Q123R | 201 | 4.0 |
| 131 | S131T | 38 | 4.4 | T131S | 1 | 0.0 | S131T | 65 | 4.1 | – | – | – |
| 144 | I144V | 38 | 4.4 | V144I | 1 | 0.0 | I144V | 64 | 4.0 | V144I | 1 | 0.0 |
| 171 | E171D | 7 | 0.8 | E171D | 198 | 3.6 | E171D | 15 | 0.9 | E171D | 179 | 3.5 |
| 213 | A213T | 6 | 0.7 | T213A | 235 | 4.3 | A213S/T | 14 | 0.9 | T213A | 207 | 4.1 |
| 226 | M226E/L/V | 34 | 4.0 | V226E/L/M | 132 | 2.4 | M226E/L/V | 51 | 3.2 | V226A/E/L/M | 153 | 3.0 |
| 293 | E293D | 1 | 0.1 | D293E/G | 219 | 4.0 | E293D/Q | 2 | 0.1 | D293E | 187 | 3.7 |
| 296 | V296I | 31 | 3.6 | V296I | 21 | 0.4 | V296I | 49 | 3.1 | V296I | 28 | 0.6 |
| 305 | K305R | 1 | 0.1 | R305K | 237 | 4.4 | K305R | 5 | 0.3 | R305K | 203 | 4.0 |
| 308 | R308G/K | 7 | 0.8 | K308N/R | 176 | 3.2 | R308K | 6 | 0.4 | K308R/S | 155 | 3.1 |
| 310 | A310P/T | 12 | 1.4 | T310A/G/N/P/V | 140 | 2.6 | A310E/P/T/V | 26 | 1.6 | T310A/G/P/S/V | 126 | 2.5 |
| 311 | R311A/H/P/Q/S | 35 | 4.1 | P311A/Q/R/S/T | 16 | 0.3 | R311A/H/K/P/Q/T | 60 | 3.8 | P311A/Q | 3 | 0.1 |
| 315 | V315I | 18 | 2.1 | I315C/V | 23 | 0.4 | V315F/I | 33 | 2.1 | I315F/L/V | 34 | 0.7 |
| 326 | V326I/L | 28 | 3.3 | L326I/M/V | 9 | 0.2 | V326I/L | 53 | 3.3 | L326I/M/V | 14 | 0.3 |
| 348 | R348K/Q | 22 | 2.6 | R348K/Q | 165 | 3.0 | R348K/Q/S/T | 44 | 2.8 | R348K/Q | 157 | 3.1 |
| 357 | – | – | – | R357K | 200 | 3.7 | K357R | 6 | 0.4 | R357K | 193 | 3.8 |
| 368 | L368I/V | 30 | 3.5 | V368I/L | 23 | 0.4 | L368I/V | 54 | 3.4 | V368A/I/L/M | 26 | 0.5 |
| 392 | N392A/D/S | 18 | 2.1 | N392A/D/G/H/S | 172 | 3.2 | N392D/G/S/T | 23 | 1.4 | N392D/G/H/I/S/T/V | 165 | 3.3 |
| 400 | A400P/S/T/V | 7 | 0.8 | S400A/C/D/G/N/P/T/V | 219 | 4.0 | A400P/S/T/V | 11 | 0.7 | S400A/D/G/P/T | 178 | 3.5 |
| 403 | G403D/V | 4 | 0.5 | A403D/G/I/P/S/T/V | 150 | 2.8 | G403A/D/S/V | 18 | 1.1 | A403D/G/I/P/T/V | 110 | 2.2 |
| 405 | P405L/S | 6 | 0.7 | P405C/F/H/L/Q/R/S | 168 | 3.1 | P405H/L/Q/S | 20 | 1.3 | P405C/D/F/H/L/R/S | 173 | 3.4 |
| 410 | V410A/D/N/T | 34 | 4.0 | A410G/V | 28 | 0.5 | V410A/D/N | 57 | 3.6 | A410T/V | 16 | 0.3 |
| 439 | G439E | 23 | 2.7 | R439D/E/G | 226 | 4.2 | G439E | 39 | 2.4 | R439E/G | 195 | 3.8 |
| 440 | A440D | 1 | 0.1 | D440A/E/G/T/V | 211 | 3.9 | A440D/G/S/T | 8 | 0.5 | D440A/G/S/V | 175 | 3.4 |
| 441 | D441G/S | 19 | 2.2 | D441G/N/S | 32 | 0.6 | D441G/S | 38 | 2.4 | D441E/G | 15 | 0.3 |
| 442 | T442A | 8 | 0.9 | K442A/P/S/T | 213 | 3.9 | T442A/K/P/Q | 18 | 1.1 | K442A/E/G/N/P/Q/R/S/T | 183 | 3.6 |
| Total | 855 | 100.0 | 5.430 | 100.0 | 1.595 | 100.0 | 5.074 | 100.0 | ||||
Only polymorphic sites whose frequency is above 2% and RASs are shown; see Table SI6 for the complete dataset of all polymorphisms and mutations. AA, amino acids; resistance-associated substitutions (RASs) are represented in bold and substitution on scored position are underscored.