A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.


Abstract

Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients.

Submission Details

ID: VUPsxLdA4

Submitter: Shu-Ching Ou

Submission Date: July 31, 2018, 4:43 p.m.

Version: 1

Publication Details
Qi H;Olson CA;Wu NC;Ke R;Loverdo C;Chu V;Truong S;Remenyi R;Chen Z;Du Y;Su SY;Al-Mawsawi LQ;Wu TT;Chen SH;Lin CY;Zhong W;Lloyd-Smith JO;Sun R,PLoS Pathog (2014) A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity. PMID:24722365
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1YUY 2005-02-14T00:00:00+0000 1.9 HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE GENOTYPE 2a
1YV2 2005-02-14T00:00:00+0000 2.5 Hepatitis C virus NS5B RNA-dependent RNA Polymerase genotype 2a
1YVX 2005-02-16T00:00:00+0000 2.0 Hepatitis C Virus RNA Polymerase Genotype 2a In Complex With Non- Nucleoside Analogue Inhibitor
1YVZ 2005-02-16T00:00:00+0000 2.2 Hepatitis C Virus RNA Polymerase Genotype 2a In Complex With Non- Nucleoside Analogue Inhibitor
2XWH 2010-11-03T00:00:00+0000 1.8 HCV-J6 NS5B polymerase structure at 1.8 Angstrom
4ADP 2012-01-02T00:00:00+0000 1.9 HCV-J6 NS5B POLYMERASE V405I MUTANT
2KZQ 2010-06-21T00:00:00+0000 0 s34r Structure
2LIF 2011-08-29T00:00:00+0000 0 Solution Structure of KKGF
2LVG 2012-07-05T00:00:00+0000 0 NMR structure of HCV Non-structural protein AB, NS4B(1-40)
2XXD 2010-11-10T00:00:00+0000 1.88 HCV-JFH1 NS5B polymerase structure at 1.9 angstrom

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.7 Genome polyprotein P27960 POLG_HCVJ5
91.0 Genome polyprotein P26660 POLG_HCVJ6
100.0 Genome polyprotein Q99IB8 POLG_HCVJF