1. Volume 140, Issue 3, Pages 755-760.e12 (March 2011)
Sequence and Phenotypic Analysis for Resistance Monitoring in Hepatitis C Virus Drug Development: Recommendations From the HCV DRAG 
Ann D. Kwong, Isabel Najera, Jill Bechtel, Scott Bowden, Joseph Fitzgibbon, Patrick Harrington, Dale Kempf, Tara L. Kieffer, Diana Koletzki, George Kukolj, Sharlene Lim, Tami Pilot–Matias, Kai Lin, Nina Mani, Hongmei Mo, Jules O'Rear, Michael Otto, Neil Parkin, Jean–Michel Pawlotsky, Chris Petropoulos, Gaston Picchio, Robert Ralston, Jacqueline D. Reeves, Robert T. Schooley, Scott Seiwert, David Standring, Lieven Stuyver, James Sullivan, Veronica Miller 
Gastroenterology 
Volume 140, Issue 3, Pages e12 (March 2011)
DOI: /j.gastro
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2. Figure 1
Comparison of population and clonal sequencing of the same sample.
Figure courtesy of Robert Ralston and adapted from the Second International Workshop on Hepatitis C: Resistance and New Compounds.42
Gastroenterology  , e12DOI: ( /j.gastro )
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3. Supplementary Figure 1
Average frequency of variants in 2 representative samples with varying viral load.
Figure courtesy of Tara Kieffer and adapted from the First International Workshop on Hepatitis C: Resistance and New Compounds, October 25–26,
Gastroenterology  , e12DOI: ( /j.gastro )
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4. Supplementary Figure 2
Representative subgenomic replicons used for cassette cloning of patient-derived NS3 protease and NS5B polymerase. (A) Schematic of subgenomic replicon construct for cassette cloning of genotype 1 NS3 protease.17 A poliovirus IRES (pi) upstream of the firefly luciferase reporter (luc) increases reporter signal and RNA replication. Translation of HCV sequence is driven by an EMCV IRES (ei). Translation start codon is in bold letters. HCV sequences are derived from genotype 1b-Con1 (white). Cloning sites (ClaI and AscI) flanking the NS3 protease insert (black) are indicated. Adaptive mutations located at E1202G, T1280I, and K1846T are indicated (numbering relative to the amino acid position in the viral open reading frame). (B) Schematic of subgenomic replicon construct for cassette cloning of genotype 1a NS5B.21 Firefly luciferase (luc) is used as a reporter and translation of chimeric HCV sequence is driven by an EMCV IRES (ei). Chimeric sequences are derived from genotype 1a H77 (grey) and genotype 1b Con1 (white). Cloning sites (PacI and AscI) flanking the NS5B insert (black) are indicated. Adaptive mutations located at Q1067R, E1202G, S1222T, P1496L, and S2204I are indicated (numbering relative to the amino acid position in the viral open reading frame). (C) Schematic of subgenomic replicon construct for cassette cloning of genotype 1b NS5B.21 Firefly luciferase (luc) is used as a reporter and translation of chimeric HCV sequence is driven by an EMCV IRES (ei). HCV sequences are derived from genotype 1b-N (cross-hatch). Cloning sites (PacI and AscI) flanking the NS5B insert are indicated. Adaptive mutations located at A1098T, E1202G, and S2204I are indicated (numbering relative to the amino acid position in the viral open reading frame).
Gastroenterology  , e12DOI: ( /j.gastro )
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5. Supplementary Figure 3
Consensus files generated from 4875 HCV subtype 1a and 13,023 HCV subtype 1b nonstructural (NS3-NS5B) region sequences.
Gastroenterology  , e12DOI: ( /j.gastro )
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6. Supplementary Figure 3
Consensus files generated from 4875 HCV subtype 1a and 13,023 HCV subtype 1b nonstructural (NS3-NS5B) region sequences.
Gastroenterology  , e12DOI: ( /j.gastro )
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7. Supplementary Figure 3
Consensus files generated from 4875 HCV subtype 1a and 13,023 HCV subtype 1b nonstructural (NS3-NS5B) region sequences.
Gastroenterology  , e12DOI: ( /j.gastro )
Copyright © 2011 AGA Institute Terms and Conditions

8. Supplementary Figure 3
Consensus files generated from 4875 HCV subtype 1a and 13,023 HCV subtype 1b nonstructural (NS3-NS5B) region sequences.
Gastroenterology  , e12DOI: ( /j.gastro )
Copyright © 2011 AGA Institute Terms and Conditions

9. Supplementary Figure 4
Distribution of HCV viral loads in 2 sample populations of patients chronically infected with HCV. (A) HCV-positive strand RNA viral load determined by the Bayer Versant HCV RNA 3.0 bDNA test. The average viral load is approximately 500,000 IU/mL (≈2,500,000 copies/mL).
Figure courtesy of Scott Bowden. (B) Quantitative HCV viral load assays and their dynamic range. Adapted from Chevaliez et al.14
Gastroenterology  , e12DOI: ( /j.gastro )
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10. Supplementary Figure 5
Comparison of in vitro vs in vivo fitness measurements for variants resistant to a HCV protease inhibitor.
Gastroenterology  , e12DOI: ( /j.gastro )
Copyright © 2011 AGA Institute Terms and Conditions