A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

In summary, the virus-mediated infection of (ancient or modern) cells is an old process that has evolved gradually over billions of years but materialized fully once lineages of organisms diversified. After the proto-virocells reduced to completely lose their cellular nature and acquired types of folds to build viral capsids (jelly-roll and other forms), modern viruses were born. The cellular nature of viruses is restored when modern viruses infect and replicate inside modern cells or when they become integral parts of their genomes. Whether the infection is modern or ancient, it has two interesting consequences: (i) viruses gain complete access to and control of the cellular machinery to create genes and protein folds, thus explaining the large size of class I proteins and VSFs (Fig. 1, A and B) , and (ii) they can also pick old or newly created genes from cells, spreading them to other cellular lineages through virus-to-cell gene transfer (Fig. 2) , if it provides selective advantages to the evolving host. Thus, our model, which explains the evolution of virocells, is biphasic and identifies an early cell-like phase followed by the emergence of modern-day viral lineages.