Table 2.
List of mutations found in each gene using Geno2pheno for both Sanger and Next-Generation Sequencing (NGS) sequences.
| Cluster HCV | Pt | HCV Infection | HCV-RNA (IU/mL) | IL 28 | RAS | Other Mutations | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NS3 Sanger |
NS5B Sanger |
NS5A Sanger |
NS5A NGS |
% NGS |
NS3 Sanger |
NS5A Sanger |
NS5A NGS 1% |
NS5B Sanger |
|||||
| TC1 | Pt1 | Acute | 3270 | CT | None | None | Y93H | Y93H | 99.7% | V48I, V51A, A66G, T72I, P86Q, K87A, V132I, F147S, V170I, S174T (5–180aa) |
K6R, S17T, K26R, L34V, L37F, K78R, R123QR, V164AE, V174T, Q176M (1–184aa) |
K6R, S17T, K26R, L34V, L37F, K78R, V164E, V174T, Q176M (1–205 aa) |
T181N, S210A, C213S (153–337aa) |
| Pt2 | Chronic | 2820000 | CC | None | None | Y93H | Y93HY | 97.8% | V48I, V51A, A66G, T72I, P86Q, K87A, V132I, F147LS, V170I, S174T (1–180aa) |
K6R, S17ST, K26R, L34V, L37F, G49EG, K78R, V164A, V174T, Q176M (1–211aa) | K6R, V8IV, S17ST, K26KR, L34V, L37FL, G49EG, I63IL, K78R, C98CS, N105NS, R108KR, A114AS, N137NS, V138IMV, A146AT, V164AE, V174T, Q176MT (1–205aa) | S19NS, M57L, K81R, Q90K, R98K, N110NS, V116I, N117KN, K124E, Q127L, T181N, S210A, C213RS, S231NS, T377S, C451H, A513S, R531K (1–540aa) | |
| TC2 | Pt3 | Chronic | 2340000 | CT | None | None | Y93HY | Y93HY | 32.9% | S7A, V48I, Y56F, A66G, P86Q, K87S, S122N, V132I, F147S, A150V (2–180aa) |
S3T, K6R, S17T, L34V, K44R, Q54H, T56IT, T64A, H85R, T122V, M133MV, V138LV, R157QR, V164A, V174T (1–213aa) | S3T, K6R, S17T, L34V, K44R, D50DE, I52IDNV, Q54H, T56IT, T64A, H85R, A92AT, T122AV, V124GV, M133MV, V138LIV, R157QR, V164A, V174T (1–205aa) |
M57L, V85IV, Q90K, Q127L, N206K, K209A, A252AV, T377S, A513S, T520I, K523MR (1–548aa) |
| Pt4 | Acute | 2090 | CT | None | None | None | None | None | V48I, Y56F, A66G, P86Q, K87S, S122N, V132I, F147S, V170I (15–180aa) | S3T, K6R, S17T, L34V, K44R, Q54H, T64A, H85R, T122V, V138L, R157Q, V164A, V174T (1–187aa) | S3T, K6R, S17T, L34V, K44R, Q54H, T64A, H85R, T122V, V124GV, V138L, R157Q, V164A, V174T (1–205aa) | N206K, K209A, A252V, T377S, I424V, M426T, A513S, T520I, K523R (151–538aa) |
|
| Pt5 | Acute | 165 | CC | None | None | None | None | None | V48I, Y56F, A66G, P86Q, K87S, S122N, V132I, F147S, V170I (15–180aa) | S3T, K6R, S17T, L34V, K44R, Q54H, T64A, H85R, T122V, V138L, R157Q, V164A, V174T, C190CG (1–196aa) |
S3T, K6R, V15AV, S17T, P32PS, L34V, K44R, Q54H, A61AV, T64A, T83MT, H85R, T122MV, V124GV, G132AG, V138L, R157Q, V164A, V174T, L199I (1–205aa) | N206K, K209A, A252V, R254KR, E258EQ, T377S, A513S, T520I, K523R, S549G, V552A (151–562aa) | |
| TC3 | Pt6 | Chronic | 1800000 | CT | None | None | None | None | None | S7A, C16CW, V48I, S61A, A66G, P86Q, K87AS, F147S (1–180aa) |
K6R, S17T, L34V, L37F, T56I, K78R, T79A, V164A, V174T, L183V, S201ST, M202MR, T213AT (1–213 aa) |
K6R, S17AT, L34V, L37FL, Y43FY, Q54HQ, T56IT, I63FL, K78R, T79A, T83MT, N105NS, R108KR, V164AT, V174T, L183V, A197AT (1–205aa) |
A15S, M57L, Q90K, N117R, R120N, Q127L, T130N, F162Y, G198K, N206NS, C213S, R254K, T377S, V405I, Q464E, V499T, A513S, R531K, S549G (1–565a aa) |
| Pt7 | Chronic | 577000 | CC | None | None | Y93H | Y93H | 99.65% | S7A, V48I, V51A, S61A, A66G, T72I, P86Q, K87A, S122G, F147S, V170I (1–181aa) |
K6R, S17T, L34V, L37F, K44R, G49EG, Q54H, K78R, H85N, V138I, V164A, V174T, Q176L, L183V (1–194 aa) |
K6R, S17T, L34V, F36FL, L37F, K44R, G49EG, Q54H, T56IT, T64AT, V75AV, K78R, H85NS, V124GV, F127FS, V138I, K139KR, V164A, V174T, Q176L, Q181HQ, L183V (1–205aa) | A15S, M57L, Q90K, V116I, N117R, R120N, Q127L, T130N, V147IV, F162Y, S189PS, G198KR, C213S, R254K, T377S, V405IV, A421V, I424V, T427P, Q464E, V499T, A513S, T520MT, Q544R, S549G, L564V, S565P (1–569 aa) |
|
| Pt9 | Chronic | 94600 | CC | None | None | None | None | None | S7A, L14F, V48I, V51A, S61A, A66G, P86Q, K87A, F147S, S174A (1–180aa) |
K6R, S17T, L34V, L37F, Q54H, V75A, K78R, T83M, Y161H, V164A, V174T (1–185aa) |
K6R, I12IL, S17T, K26KR, L34V, P35LP, L37F, Q54H, V75A, K78R, C80CR, T83M, H85HCRY, A92AS, T99AT, P102LP, R108KR, Y161H, V164A, V174T, A197AT (1–205aa) | A15S, M57L, Q90K, N110S, V116I, N117R, R120N, Q127L, F162Y, K270R, T312S, L314S, V315A, A333AV, S335N, T377S, V405I, K441Q, Q464E, V499T, A513S, K535R, S549G (1–568aa) | |
| TC4 | Pt8 | Chronic | 219000 | CT | None | None | R30Q L31M Y93H |
R30Q L31M Y93H |
98.8% 98.8% 99.1% |
V48I, A66G, P86Q, K87A, F147S, A150V, I153V (1–180aa) |
K6R, S17T, L34V, L37F, Q54H, K78R, R123Q, V124I, M133V, V164A, E171Q, V174T, Q176L, T204TP (1–210aa) |
K6R, S17T, L34V, L37F, Q54H, N69NT, K78R, T95MT, R108KR, R123Q, V124I, M133MV, K139KR, V164A, E171Q, V174T, Q176L, A197T, L199V (1–205aa) | A39S, M57L, R65Q, Q90K, K106KR, S113G, Q127L, E131N, I134L, F162Y, S231N, I262V, T377S, A513S, R531K (1–568aa) |
| Pt10 | Acute | 163 | CC | None | None | R30Q L31M Y93H. |
R30Q L31M Y93H |
99.4% 99.4% 97.6% |
V48I, A66G, P86Q, K87A, F147S, A150V, I153V (16–180aa) |
K6R, S17T, L34V, L37F, Q54H, K78R, R123Q, V124I, M133V, V164A, E171Q, V174T, Q176LQ (1–177aa) | K6R, S17T, L23LP, L34V, L37F, Q54H, K78R, R123Q, V124I, M133V, G155EG, V164A, E171Q, V174T, Q176L, A197T, L199V (1–205aa) | F162Y, S231N, I262V, T377S, T403AT, A513S, R531K (153–550aa) |
|
| TC5 | Pt11 | Acute | 334000 | CC | None | None | None | None | None | S7A, L14F, S61A, T72TI, D103ND, R118RW, S122T (181aa) |
K6R, S17T, L34V, L37F, T83M, V138I, V164A, V174T, A197T (1–213aa) |
K6R, S17T, L34V, L37F, V46IV, V75FV, T83M, H85HFLY, V138I, V164A, V174T, A197T (1–205aa) |
T19S, L31IV, L36M, L47Q, N117R, R120N, T130N, T132S, F162Y, G198K, E202D, A207T, A210S, A218S, N231S, A300S, V321I E333A, K355Q, Q464E, V499T, R510K, S549G (1–570aa) |
| Pt12 | Acute | 16100 | CC | None | None | Y93HY | Y93H | 99.2% | S7A, L14F, S61A, S122T (181aa) |
K6R, S17T, L34V, L37F, T55AT, T83M, P89LP, H128HY, V138I, V164A, V174T, A197T (1–206aa) | K6R, S17AT, L34V, L37F, M53MV, T83M, V138I, V164A, V174T, A197T (1–205aa) | T19S, L36M, L47Q, N117R, R120N, T130N, T132S, G198K, E202D, A207T, A210S, A218S, N231S, A300T, V321I, E333A, K355Q, E437KE, Q464E, V499T, R510K, Q514R, S549G (1–580aa) |
|
| Pt13 | Acute | 19690 | CT | None | None | None | None | None | S7A, V48I, S61A, S122T (1–140aa) |
K6R, S17T, L34V, L37F, T56IT, T83M, A92T, T135A, V138I, V164A, V174T (1–186aa) |
K6R, S17T, L34V, L37F, T83M, A92T, T135A, V138I, V164A, V174T, A197AT, T200AT (1–205aa) |
A16TA, T19S, L36M, L47Q, R98K, N117R, R120N, , T130N, E131EG, T132S, F162Y, G198K, E202D, A207T, A210S, A218S, N231S, C242S, A300S, V321I, E333A, K355Q, K441Q, Q464E, V499T, R510K, S549G (1–570aa) |
|
| Pt15 | Acute | 1620000 | NA | None | None | None | None | None | S7A, L13LF, L14F, S42SF, S61A, S122T, S93SF, S133SF (181aa) |
K6R, S17T, L34V, L37F, T83M, V138I, V174T, A197T (1–213aa) |
K6R, S17T, L34V, L37F, Q54HQ, T83M, A92AT, N105NS, V124GV, T135AT, V138I, R157LR, V164AV, V174T, P192PS, A197T, D205DE (1–205aa) |
A16T, T19S, L36M, L47Q, R98K, N117R, R120N, T130N, T132S, F162Y, T181N, G189K, E202D, A207T, A210S, A218S, N231S, A300S, V321I, G328EG, E333A, K335Q, K441Q, Q464E, V499T, R510K, S549G, W574L, L588S (1–589aa) | |
Abbreviations: TC, transmission cluster; Pt, patient; RAS, resistance associated substitution; NGS, next-generation-sequencing. Genotype 1b sequences were used as a reference. NS5A ultra-deep consensus sequences were reported as 1% cutoff.