Recent data suggest a significant increase in the prevalence of recombinants in some countries [26▪▪,55,63▪▪] and several newly discovered CRFs/URFs in parts of Asia and Africa [49–52,58,59]. This suggests that coinfection or superinfection by divergent HIV-1 strains has become more common in regions where multiple subtypes cocirculate [26▪▪,42,49,52,64]. Viral sequences from recombinant forms have been shown to affect the accuracy of phylogenetic reconstructions [65,66]. This is due to the different regions of the aligned recombinant genome having distinct evolutionary relationships that affect tree topology and branch lengths . Furthermore, such sequences introduce errors in phylodynamic inferences  by biasing ancestral state reconstruction and estimations for the most recent common ancestor . As the prevalence of recombinant forms increases, these challenges are expected to become more important for molecular epidemiological-based investigations. The scale up of cheaper near full-length genome sequencing approaches is critical in improving the accuracy of viral classification. It is important to consider how the fast-increasing emergence of HIV recombinant forms will impact accurate diagnosis, phylogenetic reconstruction, antiretroviral treatment and future vaccine development.
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