Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection
- 21 March 2011
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 108 (14), 5661-5666
- https://doi.org/10.1073/pnas.1102036108
Abstract
HIV adaptation to a host in chronic infection is simulated by means of a Monte-Carlo algorithm that includes the evolutionary factors of mutation, positive selection with varying strength among sites, random genetic drift, linkage, and recombination. By comparing two sensitive measures of linkage disequilibrium (LD) and the number of diverse sites measured in simulation to patient data from one-time samples of pol gene obtained by single-genome sequencing from representative untreated patients, we estimate the effective recombination rate and the average selection coefficient to be on the order of 1% per genome per generation (10(-5) per base per generation) and 0.5%, respectively. The adaptation rate is twofold higher and fourfold lower than predicted in the absence of recombination and in the limit of very frequent recombination, respectively. The level of LD and the number of diverse sites observed in data also range between the values predicted in simulation for these two limiting cases. These results demonstrate the critical importance of finite population size, linkage, and recombination in HIV evolution.Keywords
This publication has 45 references indexed in Scilit:
- Multi-site adaptation in the presence of infrequent recombinationTheoretical Population Biology, 2010
- Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1Molecular Biology and Evolution, 2009
- Model with two types of CTL regulation and experiments on CTL dynamicsJournal of Theoretical Biology, 2009
- Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infectionThe Journal of Experimental Medicine, 2009
- The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infectionThe Journal of Experimental Medicine, 2009
- Human Immunodeficiency Virus Type 1 Population Genetics and Adaptation in Newly Infected IndividualsJournal of Virology, 2009
- Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infectionProceedings of the National Academy of Sciences of the United States of America, 2008
- The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptationTheoretical Population Biology, 2008
- Highly fit ancestors of a partly sexual haploid populationTheoretical Population Biology, 2007
- Rapid Viral Decay in Simian Immunodeficiency Virus-Infected Macaques Receiving Quadruple Antiretroviral TherapyJournal of Virology, 2006