A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity

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Qi, H., Olson, C.-A., Wu, N.-C., Ke, R., Loverdo, C., Chu, V., Truong, S., Remenyi, R., Chen, Z., Du, Y., Su, S.-Y., Al-Mawsawi, L.-Q., Wu, T.-T., Chen, S.-H., Lin, C.-Y., Zhong, W., Lloyd-Smith, J.-O., & Sun, R. (2014). A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity. PLoS Pathog., 10(4). https://doi.org/10.1371/journal.ppat.1004064

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@article{Qi2014_299,
  author = {Qi, Hangfei and Olson, C. Anders and Wu, Nicholas C. and Ke, Ruian and Loverdo, Claude and Chu, Virginia and Truong, Shawna and Remenyi, Roland and Chen, Zugen and Du, Yushen and Su, Sheng-Yao and Al-Mawsawi, Laith Q. and Wu, Ting-Ting and Chen, Shu-Hua and Lin, Chung-Yen and Zhong, Weidong and Lloyd-Smith, James O. and Sun, Ren},
  year = {2014},
  month = {4},
  title = {A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity},
  journal = {PLoS Pathog.},
  publisher = {PUBLIC LIBRARY SCIENCE},
  volume = {10},
  number = {4},
  address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
  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.},
  url = {http://www.dx.doi.org/10.1371/journal.ppat.1004064},
  doi = {10.1371/journal.ppat.1004064},
  issn = {1553-7366},
}

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TY  - JOUR
AU  - Qi, Hangfei
AU  - Olson, C. Anders
AU  - Wu, Nicholas C.
AU  - Ke, Ruian
AU  - Loverdo, Claude
AU  - Chu, Virginia
AU  - Truong, Shawna
AU  - Remenyi, Roland
AU  - Chen, Zugen
AU  - Du, Yushen
AU  - Su, Sheng-Yao
AU  - Al-Mawsawi, Laith Q.
AU  - Wu, Ting-Ting
AU  - Chen, Shu-Hua
AU  - Lin, Chung-Yen
AU  - Zhong, Weidong
AU  - Lloyd-Smith, James O.
AU  - Sun, Ren
PY  - 2014
DA  - 2014/04/01
TI  - A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity
JO  - PLoS Pathog.
VL  - 10
IS  - 4
PB  - PUBLIC LIBRARY SCIENCE
SN  - 1553-7366
AB  - 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.
DO  - 10.1371/journal.ppat.1004064
UR  - http://www.dx.doi.org/10.1371/journal.ppat.1004064
ER  -