Loss and Recovery of Genetic Diversity in Adapting Populations of HIV

TL;DR

This study analyzes HIV's genetic diversity loss and recovery during drug resistance evolution, revealing the roles of hard and soft sweeps and estimating the effective population size within patients.

Contribution

It provides new insights into HIV population genetics by quantifying effective population size and characterizing the dynamics of genetic diversity during resistance development.

Findings

HIV resistance evolves mainly through single mutations at a time

Genetic diversity decreases around resistance mutations due to hitchhiking

Effective population size of HIV in patients is estimated at ~150,000

Abstract

The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence data, we make four observations that shed a light on the underlying processes and allow us infer the short-term effective population size of the viral population in a patient. Our first observation is that the evolution of drug resistance usually occurs by the fixation of one drug-resistance mutation at a time, as opposed to several changes simultaneously. Second, we find that these fixation events are accompanied by a reduction in genetic diversity in the region surrounding the fixed drug-resistance mutation, due to the hitchhiking effect. Third, we observe that the fixation of drug-resistance mutations involves both hard and soft selective sweeps. In a hard sweep, a resistance mutation arises in a single viral particle and drives all linked mutations with it when it spreads in the viral population, which dramatically reduces genetic diversity. On the other hand, in a soft sweep, a resistance mutation occurs multiple times on different genetic backgrounds, and the reduction of diversity is weak. Using the frequency of occurrence of hard and soft sweeps we estimate the effective population size of HIV to be 1.5 * 10^5 (95% confidence interval 0.8 * 10^5, 4.8 * 10^5). This number is much lower than the actual number of infected cells, but much larger than previous population size estimates based on synonymous diversity. We propose several explanations for the observed discrepancies. Finally, our fourth observation is that genetic diversity at non-synonymous sites recovers to its pre-fixation value within 18 months, whereas diversity at synonymous sites remains depressed after this time period.