Transmission genetics of drug-resistant hepatitis C virus
- Stanford University School of Medicine, United States
- The Scripps Research Institute, United States
- Dalhousie University, Canada
Figures
Figure 1 with 3 supplements
Construction of codon altered JFH1.
(A) Cell cultures coinfected with two strains of HCV result in four populations: uninfected, two types of singly infected, and coinfected cells. (B) Three segments of the JFH1 genome, that were …
Figure 1—figure supplement 1
Alignment of codon-altered and wild-type JFH1 viral RNAs.
Sequence alignments were generated using ClustalW to highlight the nucleotide changes incorporated into the CA-1 viral RNA. Sequences highlighted with orange bars identify regions containing …
Figure 1—figure supplement 2
Alignment of codon-altered and wild-type JFH1 viral RNAs.
Sequence alignments were generated using ClustalW to highlight the nucleotide changes incorporated into the CA-2 viral RNA. Sequences highlighted with orange bars identify regions containing …
Figure 1—figure supplement 3
Alignment of codon-altered and wild-type JFH1 viral RNAs.
Sequence alignments were generated using ClustalW to highlight the nucleotide changes incorporated into the CA-3 viral RNA. No regions of covarying mutations were observed within this region.
Figure 2
Differentiation of codon-altered and wild-type JFH1 using confocal microscopy and flow cytometry.
(A) RNA in situ hybridization probes were designed to differentiate between wild-type (WT) and codon-altered (CA) viral RNAs. These probes utilize branched DNA technology to amplify the contiguous …
Figure 3 with 3 supplements
Flow cytometry to test dominance of viruses resistant to NS3 protease inhibitor.
(A) Structure of protease inhibitor BILN-2061. (B) Structure of NS3 protein. D168 (red) is located in the protease domain adjacent to the active site (lavender). D168A confers resistance to …
Figure 3—figure supplement 1
NS3-D168A confers resistance to BILN-2061 in both the wild-type and the codon-altered backgrounds.
D168A was cloned into both the WT (left) and CA (right) backgrounds and tested for resistance to BILN-2061. Huh7.5.1 cells were infected with WT, WT-D168A, CA or CA-D168A viruses at MOI = 0.1 …
Figure 3—figure supplement 2
Exogenously expressed drug-resistant NS3 and NS5A do not rescue drug-susceptible HCV in trans.
(A) Schematic of codon-altered HCV RNA, and non-structural protein expression plasmids (pTM-NS3-5B) that contain either no mutation, the D168A mutation that confers resistance to BILN-2061 or the …
Figure 3—figure supplement 3
Drug resistance to R1479 confers major fitness cost to JFH1.
(A) R1479 is a nucleotide analog inhibitor of the HCV NS5B polymerase. (B) WT virus was passaged every 72 hr ten times in the presence of 25 μM R1479. Extracted vRNA from each passage was quantified …
Figure 4
NS5A-resistant HCV is cis-dominant.
(A) Structures of SR2486 or Daclatasvir. (B) Structure of NS5A dimer with Y93 identified (orange). NS5A variants, Y93N and Y93H have previously been shown to confer drug resistance to multiple NS5A …
Figure 5
Complex formation between drug susceptible and drug-resistant NS5A in the absence of RNA replication.
(A) HCV NS3-5B constructs driven by T7 polymerase and encoding tandem tagged copies of NS5A (Berger et al., 2014) were created to co-express HA- and GFP-tagged NS5A alleles. Huh7-Lunet-T7 cells were …
Figure 6
Drug-susceptible and drug-resistant RNA replication complexes segregate in coinfected cells.
(A) Huh7.5.1 cells were coinfected with CA and WT-Y93N at a MOI of 1 FFU/cell for 24 hr. Cells were fixed and co-stained with WT and CA negative-strand or positive strand viral RNA probe sets and …
Additional files
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Transparent reporting form
- https://doi.org/10.7554/eLife.32579.015
