Recombination rate and selection strength in HIV intra-patient evolution

TL;DR

This study estimates HIV's intra-patient recombination rate and selection strength using time-resolved sequence data, revealing key parameters that influence HIV evolution and drug resistance development.

Contribution

It introduces methods to infer recombination and selection coefficients from population data, accounting for selection effects often ignored in previous estimators.

Findings

Effective recombination rate estimated at 1.4e-5 per site per generation.

Selection coefficients for many non-synonymous polymorphisms exceed 0.8%.

Results enable more detailed future studies with higher-resolution data.

Abstract

The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the parameters governing genetic diversification and the strength of selection need to be known. While mutation rates can be measured in single replication cycles, the relevant effective recombination rate depends on the probability of coinfection of a cell with more than one virus and can only be inferred from population data. However, most population genetic estimators for recombination rates assume absence of selection and are hence of limited applicability to HIV, since positive and purifying selection are important in HIV evolution. Here, we estimate the rate of recombination and the distribution of selection coefficients from time-resolved sequence data tracking the evolution of HIV within single patients. By examining temporal changes in the genetic composition of the population, we estimate the effective recombination to be r=1.4e-5 recombinations per site and generation. Furthermore, we provide evidence that selection coefficients of at least 15% of the observed non-synonymous polymorphisms exceed 0.8% per generation. These results provide a basis for a more detailed understanding of the evolution of HIV. A particularly interesting case is evolution in response to drug treatment, where recombination can facilitate the rapid acquisition of multiple resistance mutations. With the methods developed here, more precise and more detailed studies will be possible, as soon as data with higher time resolution and greater sample sizes is available.