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Updated: Jun 3, 2026

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase
Trevor Hinkley1, João Martins, Colombe Chappey
1ETH Zürich, Institute of Integrative Biology, Zürich, Switzerland.
Understanding human immunodeficiency virus type 1 (HIV-1) drug resistance evolution is complex. This study reveals that epistatic interactions, not just individual mutations, significantly shape HIV-1 fitness landscapes, impacting drug resistance.
Area of Science:
- Virology
- Evolutionary Biology
- Computational Biology
Background:
- Understanding viral evolution and the fitness landscape in human immunodeficiency virus type 1 (HIV-1) drug resistance is challenging due to numerous drugs and resistance mutations.
- HIV-1 drug resistance testing is crucial for guiding treatment decisions.
Purpose of the Study:
- To quantitatively analyze the fitness landscape of HIV-1 drug resistance.
- To investigate the role of epistatic interactions among single amino acid variants in HIV-1 protease and reverse transcriptase.
- To assess the predictive power of models incorporating epistasis for viral replicative capacity.
Main Methods:
- Analysis of 70,081 HIV-1 subtype B virus samples from individuals undergoing drug resistance testing.
- Assay of in vitro replicative capacity in the absence and presence of 15 individual drugs.
- Application of generalized kernel ridge regression to estimate fitness effects and epistasis of 1,859 single amino acid variants.
Main Results:
- Models incorporating epistatic interactions predicted 54.8% of the variance in replicative capacity across 16 environments.
- Models with epistasis substantially outperformed models based on main fitness effects alone.
- The fitness landscape of HIV-1 protease and reverse transcriptase is characterized by strong epistasis.
Conclusions:
- Epistatic interactions are a critical component of the HIV-1 fitness landscape.
- Accurate modeling of HIV-1 evolution and drug resistance requires consideration of these complex interactions.
- This quantitative understanding can inform future drug development and treatment strategies.
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