Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1–6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance
Abstract
:1. Introduction
2. Results
2.1. HCV Genome-Wide Sequence Diversity
2.2. Frequency of Consensus Nucleotides and Amino Acids
Proportion of Total Positions | Core | E1 | E2 | p7 | NS2 | NS3 | NS4A | NS4B | NS5A | NS5B | Full-Genome |
---|---|---|---|---|---|---|---|---|---|---|---|
Pan-genotypic consensus positions | 80.6 | 38.5 | 60.3 | 25.4 | 39.6 | 70.4 | 53.7 | 55.6 | 46.4 | 55.3 | 56.5 |
Pan-genotypic conserved (95% ≤ x < 99%) | 33.0 | 14.1 | 20.7 | 4.8 | 15.2 | 31.4 | 20.4 | 27.2 | 20.4 | 24.8 | 23.9 |
Pan-genotypic highly conserved (x ≥ 99%) | 31.4 | 12.5 | 15.2 | 6.3 | 11.1 | 22.0 | 14.8 | 12.3 | 7.4 | 12.1 | 15.0 |
2.3. Positions under Positive Selective Pressure
2.4. Large-Scale Analysis of Amino Acid Variability at Positions Important for DAA Therapy
NS3 | 36 | 41 | 42 | 43 | 54 | 55 | 56 | 57 | 80 | 81 | 107 | 117 | 122 | 132 | 136 | 137 | 138 | 139 | 155 | 156 | 157 | 158 | 159 | 168 | 170 | 174 | 175 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
H77 | V | Q | T | F | T | V | Y | H | Q | D | V | R | S | I | K | G | S | S | R | A | A | V | C | D | I | S | L |
HCV1 | V97.9 | Q98.7 | T60.7 | F99.2 | T97.3 | V97.6 | Y92.4 | H99.3 | Q72.1 | D99.2 | V99.3 | R97.5 | S88.5 | I70.2 | K99.1 | G99.3 | S100 | S100 | R98.7 | A100 | A99.3 | V99.3 | C99.3 | D98.7 | I72.3 | S59.8 | L61 |
L1.0 | T0.7 | S38.3 | L0.7 | S1.9 | F6.8 | L0.7 | T0.7 | C1.6 | G7.6 | V28.8 | G0.7 | S0.7 | A0.7 | V0.7 | C0.7 | F0.7 | V27.1 | N36.3 | M38.3 | ||||||||
S0.7 | H0.6 | F0.7 | S0.1 | V0.7 | I1.2 | H0.7 | G0.7 | K24.2 | Q0.1 | H0.8 | T1.8 | L3.8 | R0.2 | K0.4 | T0.7 | E0.5 | P0.7 | G2.0 | E0.7 | ||||||||
M0.3 | A0.3 | X0.1 | A0.5 | X0.1 | L1.9 | Q0.1 | N1.3 | S0.7 | P 0.2 | G0.1 | A0.8 | X0.1 | |||||||||||||||
I0.1 | Y0.7 | D0.8 | R0.7 | L0.7 | |||||||||||||||||||||||
N0.6 | X0.1 | T0.2 | |||||||||||||||||||||||||
R0.3 | D0.1 | ||||||||||||||||||||||||||
M0.1 | F0.1 | ||||||||||||||||||||||||||
H0.1 | |||||||||||||||||||||||||||
HCV2 | L99.4 | Q100 | S92.6 | F100 | T98.2 | V99.4 | Y77.8 | H100 | G100 | D100 | V100 | R100 | R77.2 | L91.4 | K100 | G99.4 | S100 | S100 | R100 | A100 | A100 | V95.1 | C100 | D100 | I95.7 | S72.2 | L98.1 |
M0.6 | T7.4 | X1.2 | G0.6 | F22.2 | K21 | I7.4 | R0.6 | I3.1 | V3.1 | T17.9 | I1.9 | ||||||||||||||||
A0.6 | T1.2 | V0.7 | M1.2 | X1.2 | A9.3 | ||||||||||||||||||||||
X0.7 | X0.7 | A0.6 | M0.6 | ||||||||||||||||||||||||
HCV3 | L100 | Q100 | T100 | F100 | T98.1 | V100 | Y100 | H100 | Q100 | D100 | V94.2 | R100 | S100 | L82.7 | K100 | G100 | S100 | S100 | R100 | A100 | A100 | V98.1 | C96.1 | Q100 | I92.3 | T88.5 | L100 |
S1.9 | I5.8 | I15.4 | I1.9 | V7.7 | A5.8 | ||||||||||||||||||||||
V1.9 | V3.9 | S3.8 | |||||||||||||||||||||||||
X1.9 | |||||||||||||||||||||||||||
HCV4 | L100 | Q100 | S71.4 | F100 | T96.4 | V100 | Y98.2 | H100 | Q100 | D100 | V89.3 | R100 | T87.5 | I94.6 | K100 | G100 | S98.2 | S100 | R100 | A100 | A100 | V98.2 | C100 | D100 | V96.4 | S87.5 | L100 |
T28.6 | X3.6 | X1.8 | I7.1 | S10.7 | L3.6 | F1.8 | L1.8 | I3.6 | A7.1 | ||||||||||||||||||
X3.6 | X1.8 | V1.8 | N3.6 | ||||||||||||||||||||||||
X1.8 | |||||||||||||||||||||||||||
HCV5 | L100 | Q100 | T100 | F100 | T100 | V66.7 | F100 | H100 | K100 | D100 | V100 | R100 | T100 | I100 | K100 | G100 | S100 | S100 | R100 | A100 | A100 | V100 | C100 | E66.7 | I66.7 | N100 | L100 |
L33.3 | D33.3 | V33.3 | |||||||||||||||||||||||||
HCV6 | V83.9 | Q100 | S56.8 | F100 | T100 | V98.8 | Y90.1 | H97.5 | Q71.6 | D100 | R100 | N44.4 | I82.7 | K98.8 | G98.8 | S97.5 | S100 | R100 | A100 | A100 | V95.1 | C100 | D96.3 | V58 | N60.5 | M100 | |
L16.1 | T43.2 | X1.2 | F9.9 | K25.9 | T30.9 | L17.3 | R1.2 | A1.2 | F2.5 | I4.9 | E3.7 | I39.5 | S32.1 | ||||||||||||||
Y2.5 | L2.5 | S24.7 | A2.5 | A4.9 | |||||||||||||||||||||||
G2.5 |
NS5A Inhibitors | 23 | 28 | 29 | 30 | 31 | 32 | 35 | 36 | 37 | 54 | 56 | 58 | 62 | 92 | 93 | 95 | 97 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Reference H77 | L | M | P | Q | L | P | P | F | V | H | R | P | E | A | Y | T | P |
HCV1 | L99.1 | M58.5 | P99.3 | Q62.5 | L97.2 | P99.3 | P99.3 | F94.4 | V57.9 | H71.5 | R60.6 | H57.8 | E60.3 | A98 | Y97.2 | T99.0 | P98.4 |
K0.7 | L37.5 | Q0.7 | R35.4 | M2.0 | G0.7 | F0.6 | L4.8 | L21.8 | Q24.7 | T36.7 | P37.9 | Q37.2 | Y0.7 | H1.8 | G0.6 | S0.8 | |
I0.1 | V2.7 | L0.9 | P0.7 | L0.1 | V0.7 | F15.7 | Y1.6 | I1.2 | S1.3 | D1.2 | T0.5 | T0.7 | A0.2 | C0.7 | |||
M0.1 | P0.7 | H0.8 | I0.1 | I0.1 | I2.3 | N0.9 | C0.7 | C1 | I0.6 | V0.3 | C0.3 | V0.2 | H0.1 | ||||
T0.3 | K0.3 | M1.3 | T0.7 | V0.3 | T0.7 | K0.3 | P0.3 | ||||||||||
I0.2 | M0.1 | S0.7 | L0.4 | N0.2 | Q0.3 | R0.2 | G0.2 | ||||||||||
F0.1 | Y0.3 | C0.2 | A0.1 | L0.3 | A0.1 | S0.1 | |||||||||||
S0.1 | N0.2 | S0.1 | |||||||||||||||
L0.1 | Y0.2 | ||||||||||||||||
D0.2 | |||||||||||||||||
A0.1 | |||||||||||||||||
HCV2 | L100 | L61.1 | P99.4 | K97.5 | M72.8 | P100 | P100 | F96.3 | I84.5 | T98.8 | R96.3 | P95.7 | N85.8 | C93.8 | Y100 | E98.2 | P58.7 |
F35.2 | L0.6 | R2.5 | L27.2 | L3.1 | V12.4 | V1.2 | K2.5 | S3.7 | A3.7 | S4.9 | D0.6 | Q37.7 | |||||
C1.9 | S0.6 | L3.1 | Q1.2 | H0.6 | S3.1 | A1.2 | G0.6 | H1.8 | |||||||||
I1.2 | T3.1 | V0.6 | S1.2 | ||||||||||||||
S0.6 | V1.2 | A0.6 | |||||||||||||||
D0.6 | |||||||||||||||||
E0.6 | |||||||||||||||||
H0.6 | |||||||||||||||||
L0.6 | |||||||||||||||||
Y0.6 | |||||||||||||||||
HCV3 | L100 | M96.2 | P100 | A76.9 | L88.5 | P100 | P100 | F100 | I71.2 | S80.8 | R100 | P98.1 | S46.1 | E98.1 | Y100 | T96.1 | P100 |
L1.9 | K17.4 | M7.7 | L25 | T19.2 | R1.9 | T28.8 | G1.9 | V3.9 | |||||||||
I1.9 | L1.9 | V3.8 | F3.8 | M7.7 | |||||||||||||
S1.9 | A3.8 | ||||||||||||||||
V1.9 | D3.9 | ||||||||||||||||
E3.9 | |||||||||||||||||
L3.9 | |||||||||||||||||
P1.9 | |||||||||||||||||
HCV4 | L98.2 | L83.9 | P100 | R68.1 | M83.9 | P100 | P100 | F100 | L69.8 | H100 | T62.5 | P85.7 | E64.4 | A92.9 | Y89.2 | T89.3 | P92.8 |
X1.8 | M10.7 | L10.7 | L16.1 | F19.6 | V16.1 | T10.7 | N8.9 | X5.4 | H5.4 | S10.7 | X3.6 | ||||||
I3.6 | S10.7 | Y8.9 | I10.7 | R1.8 | S8.9 | T1.8 | R1.8 | S1.8 | |||||||||
V1.8 | Q5.4 | I1.8 | K7.1 | X1.8 | Q7.1 | S1.8 | A1.8 | ||||||||||
T3.4 | Q1.8 | R7.1 | T1.8 | ||||||||||||||
A1.7 | R1.8 | D3.6 | |||||||||||||||
HCV5 | L100 | L100 | P100 | Q100 | L100 | P100 | P100 | F100 | L55.6 | S88.9 | K100 | P100 | T88.9 | A100 | T100 | T100 | P100 |
F44.4 | Y11.1 | A11.1 | |||||||||||||||
HCV6 | L100 | V54.5 | P100 | S42.0 | L97.5 | P100 | P100 | F100 | L58.0 | H81.5 | T95.0 | T49.4 | V37.0 | A100 | T69.2 | T98.8 | P100 |
F22.9 | R32.1 | I2.5 | F23.5 | T9.9 | K2.5 | P45.7 | D16.1 | S29.6 | A1.2 | ||||||||
L20.7 | A23.5 | I11.1 | N4.9 | S2.5 | S2.5 | Q12.4 | I1.2 | ||||||||||
M1.9 | N2.4 | Y7.4 | R3.7 | X2.5 | N9.9 | ||||||||||||
E7.4 | |||||||||||||||||
S4.9 | |||||||||||||||||
M4.9 | |||||||||||||||||
K3.7 | |||||||||||||||||
A2.5 | |||||||||||||||||
T1.2 |
NS5B | 48 | 96 | 149 | 159 | 160 | 162 | 168 | 172 | 220 | 225 | 282 | 291 | 316 | 319 | 321 | 367 | 368 | 386 | 394 | 411 | 414 | 421 | 448 | 495 | 553 | 554 | 556 | 559 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
H77 | R | S | P | L | I | F | R | K | D | D | S | N | C | D | V | S | S | R | R | N | M | A | Y | P | A | G | S | D |
HCV1 | R99.3 | S99.3 | P99.2 | L97.3 | I99.2 | F93.3 | R99.3 | K99.3 | D99.2 | D99.2 | S99.1 | N99.3 | C86.8 | D99.3 | V99.7 | S99.8 | S99,1 | R99.0 | R99.1 | N99.1 | M99.0 | A88.2 | Y99.0 | P99.1 | A93.4 | G93.5 | S89.0 | D93.1 |
S0.7 | A0.6 | E0.7 | F2.0 | V0.7 | Y5.9 | V0.7 | M0.7 | T0.7 | S0.7 | G0.7 | N12.2 | L0.7 | I0.3 | - 0.2 | N0.7 | A0.7 | I0.7 | F0.7 | V10.0 | G0.7 | -0.1 | -6.1 | -6.1 | -6.1 | -6.5 | |||
T0.1 | A0.1 | I0.7 | F0.1 | P0.7 | C0.1 | E0.1 | R0.1 | T0.7 | G0.7 | -0.2 | D0.6 | −0.2 | -0.2 | -0.2 | -0.8 | -0.2 | G0.4 | Y0.3 | G3.9 | I0.3 | ||||||||
S0.1 | T0.1 | H0.1 | P0.1 | I0.1 | R0.7 | C0.1 | V0.1 | X0.1 | N0.7 | N0.1 | ||||||||||||||||||
R0.1 | −0.2 | V0.1 | T0.2 | H0.1 | ||||||||||||||||||||||||
Y0.1 | H0.1 | M0.1 | D0.3 | |||||||||||||||||||||||||
X0.1 | S0.1 | X0.1 | ||||||||||||||||||||||||||
Y0.1 | ||||||||||||||||||||||||||||
HCV2 | R100 | S100 | P100 | L100 | I100 | Y90.7 | R100 | K100 | D100 | D100 | S100 | N100 | C99.4 | D100 | V98.1 | S99.4 | S99.4 | R98.8 | R99.4 | N97.5 | Q94.4 | V81.5 | Y98.8 | P98.1 | -100 | -100 | -100 | -100 |
F9.3 | W0.6 | F0.6 | - 0.6 | -0.6 | −0.6 | T1.2 | L4.3 | A17.3 | X0.6 | -2.0 | ||||||||||||||||||
I0.6 | K0.6 | -0.6 | S0.6 | -0.6 | -0.6 | |||||||||||||||||||||||
X0.6 | -0.6 | D0.6 | -0.6 | X0.6 | ||||||||||||||||||||||||
HCV3 | R100 | S100 | P100 | L100 | I100 | Y96.1 | R100 | K100 | D100 | D100 | S98.1 | N100 | C100 | D100 | V100 | S98.1 | S100 | R100 | R100 | N96.2 | M100 | V100 | Y100 | P94.2 | V71.2 | G69.2 | G69.2 | D71.2 |
F3.9 | R1.9 | A1.9 | S3.8 | -5.8 | -28.8 | -28.8S1.9 | -28.8 | -28.8 | ||||||||||||||||||||
S1.9 | ||||||||||||||||||||||||||||
HCV4 | R100 | S100 | P100 | L98.2 | I100 | Y89.3 | R98.2 | K100 | D100 | D100 | S100 | N100 | C75 | D100 | V94.6 | S100 | S100 | R100 | R100 | N100 | L48.2 | V89.3 | Y100 | P100 | V87.5 | G89.3 | G80.4 | D87.5 |
X1.8 | F10.7 | V1.8 | N17.9 | I5.4 | I25 | A10.7 | -10.7 | -10.7 | ||||||||||||||||||||
H5.4 | V23.2 | X1.8 | -10.7 | -12.5 | ||||||||||||||||||||||||
X1.8 | Q3.6 | N7.1 | ||||||||||||||||||||||||||
A1.8 | ||||||||||||||||||||||||||||
HCV5 | R100 | S100 | P100 | L100 | I100 | Y100 | R100 | K100 | D100 | D100 | S100 | N100 | C100 | D100 | V100 | S100 | S100 | R100 | R66.7 | N100 | M100 | A55.6 | Y100 | P66.7 | V66.7 | G66.7 | G66.7 | D66.7 |
K33.3 | V44.4 | -22.2 | -33.3 | -33.3 | ||||||||||||||||||||||||
X11.1 | -33.3 | -33.3 | ||||||||||||||||||||||||||
HCV6 | R90.1 | S100 | P65.4 | L100 | I100 | Y85.2 | R100 | K100 | D100 | D100 | S97.5 | N100 | C100 | D100 | V100 | S100 | S92.6 | R100 | R100 | N100 | M100 | V100 | Y100 | P97.5 | A64.2 | G100 | S60.5 | D100 |
T11.1 | F14.8 | C2.5 | A7.4 | L2.5 | S33.3 | D30.9 | ||||||||||||||||||||||
K9.9 | V8.6 | V2.5 | ||||||||||||||||||||||||||
S7.4 | R6.2 | |||||||||||||||||||||||||||
M4.9 | G2.5 | |||||||||||||||||||||||||||
A2.6 |
Variants | HCV1 | HCV1a | HCV1b | HCV2 | HCV3 | HCV4 | HCV5 | HCV6 | DAA |
---|---|---|---|---|---|---|---|---|---|
NS3 | |||||||||
V36L | 1% | 1.2% | 0.5% | 99.4% | 100% | 100% | 100% | 83.9% | Telaprevir |
1% | 1.2% | 0.5% | 99.4% | 100% | 100% | 100% | 83.9% | Asunaprevir | |
1% | 1.2% | 0.5% | 99.4% | 100% | 100% | 100% | 83.9% | Boceprevir | |
Q80K | 24.2% | 39.3% | 0.25% | 0% | 0% | 0% | 0% | 0% | Simeprevir |
24.2% | 39.3% | 0.25% | 0% | 0% | 0% | 0% | 0% | Asunaprevir | |
S122T | 1.8% | 0% | 4.7% | 1.2% | 0% | 87.5% | 100% | 30.9% | Simeprevir/Asunaprevir |
S122R | 0.7% | 1.1% | 0% | 77.2% | 0% | 0% | 0% | 0% | Simeprevir |
S122N | 1.3% | 0% | 3.4% | 0% | 0% | 0% | 0% | 44.4% | Asunaprevir |
D168Q | 0% | 0% | 0% | 0% | 100% | 0% | 0% | 0% | Simeprevir |
D168E | 0.5% | 0.2% | 1% | 0% | 0% | 0% | 66.7% | 3.7% | Simeprevir/Asunaprevir/Paritaprevir |
I170V | 27.1% | 2.8% | 65.6% | 3.1% | 7.7% | 96.4% | 33.3% | 58% | Boceprevir |
M175L | 61% | 98% | 1% | 98.1% | 100% | 100% | 100% | 0% | Boceprevir |
NS5A | |||||||||
L28M | 58.5% | 94% | 2.5% | 0% | 96.2% | 10.7% | 0% | 1.9% | Daclatasvir |
M28V | 2.7% | 4.2% | 0.25% | 0% | 0% | 1.8% | 0% | 54.5% | Daclatasvir/Ombitasvir |
R30Q | 62.5% | 97.5% | 7% | 0% | 0% | 5.4% | 100% | 0% | Daclatasvir |
Q30K | 0.3% | 0% | 1% | 97.5% | 17.4% | 0% | 0% | 0% | Daclatasvir |
Q30R | 35.4% | 0.3% | 91% | 2.5% | 0% | 68.1% | 0% | 32.1% | Daclatasvir/Ledipasvir/Ombitasvir |
L30S | 0% | 0% | 0% | 0% | 1.9% | 10.7% | 0% | 0% | Daclatasvir |
L31M | 2% | 1.1% | 3.4% | 72.8% | 7.7% | 83.9% | 0% | 0% | Daclatasvir/Ledipasvir |
NS5B | |||||||||
A421V | 10% | 12.7% | 5.7% | 81.5% | 100% | 89.3% | 44.4% | 100% | Beclabuvir |
S556G | 3.9% | 1.1% | 8.4% | 0% | 69.2% | 80.4% | 66.7% | 2.5% | Dasabuvir |
3. Discussion
3.1. The Highly Diverse Nature of the HCV Genome
3.2. Implications for the Development of DAAs
3.3. Implications for Drug Resistance Testing
3.4. Implications for the Development of Genotyping Assays and Epidemiological Surveys
3.5. Limitations
4. Materials and Methods
4.1. Full-Length Genome Sequence Dataset
4.2. Diversity and Consensus Residues
4.3. Positive Selective Pressure
4.4. Drug Susceptibility-Related Positions
5. Conclusions
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
References
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Cuypers, L.; Li, G.; Libin, P.; Piampongsant, S.; Vandamme, A.-M.; Theys, K. Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1–6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance. Viruses 2015, 7, 5018-5039. https://doi.org/10.3390/v7092857
Cuypers L, Li G, Libin P, Piampongsant S, Vandamme A-M, Theys K. Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1–6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance. Viruses. 2015; 7(9):5018-5039. https://doi.org/10.3390/v7092857
Chicago/Turabian StyleCuypers, Lize, Guangdi Li, Pieter Libin, Supinya Piampongsant, Anne-Mieke Vandamme, and Kristof Theys. 2015. "Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1–6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance" Viruses 7, no. 9: 5018-5039. https://doi.org/10.3390/v7092857