A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

Although VSFs were detected in all seven viral subgroups, they were mostly specific for them ( (26, 27) . It is also present in the hemagglutinin glycoproteins of influenza viruses, helping recognize the cell surface receptor (28, 29) . Thus, it could be a unifying feature of most RNA viruses (read below). Extending the number of VSFs from 66 to 109 by considering the 43 potential VSFs as true VSFs did not change the overall picture (Table 1) . Only six additional VSFs were shared by more than one viral subgroup, including mainly viral attachment proteins and envelope glycoproteins [with the possible exception of "Bacterial enterotoxins" FSF (b. 40.2) ]. Some of these could be candidates of virus-to-virus HGT during coinfection of a common host or could be vertically inherited from a common ancestor. Most VSFs were restricted to a single viral subgroup, suggesting that each genome type has evolved different VSFs to successfully carry out its reproductive cycle and that VSFs have evolved rather recently in viral lineages during infection cycles in host cells (confirmed below).