Purpose of review: An improved understanding of how recombination affects the evolutionary history of HIV is crucial to understand its current and future evolution. The present review aims to disentangle the manifold effects of recombination on HIV by discussing its effects on the evolutionary history and the adaptive potential of HIV in the context of concepts from evolutionary genetics and genomics.
Recent findings: The increasing occurrence of secondary contacts between divergent subtype populations (during coinfection) results in increased observations of recombinants worldwide. Recombination is heterogeneous along the HIV genome. Consequences of recombination of HIV evolution are, in combination with other demographic processes, expected to either homogenize the genetic composition of HIV populations (homogenization) or provide the potential for novel adaptations (diversification). New methods in population genomics allow deep characterization of recombinant genome (the segment composition and origin) and their evolutionary trajectories.
Summary: HIV recombinants increase worldwide and invade geographical regions where pure subtypes were previously predominant. This trend is expected to continue in the future, as ease to travel worldwide increases opportunities for recombination between divergent HIV strains. While the effects of recombination in HIV are much researched, more effort is required to characterize current HIV recombinant composition and dynamics. This can be achieved with new population genetic and genomic methods.