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A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses
Published on: August 31, 2014
Recombination rate and selection strength in HIV intra-patient evolution
Richard A Neher1, Thomas Leitner
1Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California, United States of America. neher@kitp.ucsb.edu
Plos Computational Biology
|February 4, 2010
Summary
This study quantifies human immunodeficiency virus (HIV) evolution by estimating its recombination rate and selection coefficients from patient data. Findings reveal key parameters for understanding HIV genetic diversification and drug resistance.
Area of Science:
- Evolutionary biology
- Virology
- Population genetics
Background:
- HIV evolution during chronic infection is shaped by host immunity and drug treatment.
- Accurate modeling requires understanding genetic diversification and selection pressures.
- Existing recombination rate estimators often fail to account for selection, limiting their use for HIV.
Purpose of the Study:
- To estimate the effective recombination rate in HIV.
- To determine the distribution of selection coefficients for HIV variants.
- To provide quantitative parameters for modeling HIV evolution, including drug resistance.
Main Methods:
- Analysis of time-series sequence data from HIV-infected patients.
- Application of population genetic methods to infer recombination rates.
- Estimation of selection coefficients from temporal changes in viral genetic composition.
Main Results:
- The effective recombination rate was estimated at rho = 1.4+/-0.6 x 10(-5) recombinations per site per generation.
- At least 15% of observed non-synonymous polymorphisms have selection coefficients exceeding 0.8% per generation.
- These parameters offer a foundation for more detailed HIV evolution studies.
Conclusions:
- The study provides crucial quantitative estimates for HIV recombination and selection.
- Findings enhance understanding of HIV genetic diversification and fitness landscapes.
- Recombination's role in rapid acquisition of drug resistance mutations is highlighted.
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