Viral evolution is characterized by high rates of horizontal gene transfer and fast sequence divergence. Furthermore, there are no universal genes shared by all viruses. As a result, distant relationships among viruses are better represented by a network than by a tree. Here we discuss 3 network representations of the virus world with decreasing levels of complexity, from a multilayer network that integrates sequence conservation and patterns of gene sharing to a classic genome similarity network. As new tools for network analysis are developed, we expect that novel insights into virus evolution will result from the study of more complex representations of the virus world.
Keywords: bipartite network; gene sharing network; multilayer network; phylogenomics; viral evolution; viral taxonomy.