Models of RNA virus evolution and their roles in vaccine design

Ojosnegros, Samuel; Beerenwinkel, Niko

The usefulness of phylogenetic trees is limited in the presence of reticulate evolutionary events, such as hybridization, horizontal gene transfer, or recombination, which cannot be represented by a tree. For this situation, phylogenetic network models have been developed [111] . They generalize phylogenetic tree models and include reticulate networks and split networks [112] . In most RNA viruses, homologous recombination can occur when a cell is coinfected with two different strains. In HIV, multiple infections are common [113] and the recombination rate is on the order of 2 to 3 times per genome per replication cycle [114] . Several epidemiological circulating recombinant forms provide evidence for recombination in HIV. Intra-host evolutionary dynamics are also shaped by recombination affecting the generation of multidrug-resistant strains in treated patients [115, 116] and the development of immune escape variants. Efficient parsimony algorithms have been developed for computing recombination networks [117, 118] .