A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

The argument that viruses do not replicate or evolve independently of cells and hence should not be deemed worthy of living status (84) has been toned down because each species replicates and evolves in nature and requires coexistence with other life forms (87) . In short, there is a need to broaden our definitions of "life" and to abandon viewing virions as viruses [sensu (86) ]. In light of these arguments, we contend that it is legitimate to study viral origins and evolution on a scale comparable to that of Archaea, Bacteria, and Eukarya and to ask fun-damental questions related to the evolutionary history of cells and viruses. Here, we propose that the encoded genetic makeup and its ancient history define the functionalities of virions, capsids, and replicons that are necessary to complete the reproduction cycle of a virus. We therefore study the proteomic composition of viral replicons to infer viral evolutionary trajectories (similar to how phylogenetic analysis of cellular genes tells us about their history), presenting a hypothesis of virus origin and evolution that is more compatible with virus biology and large-scale molecular data.