Origins and Evolution of the Global RNA Virome

Yuri I. Wolf; Darius Kazlauskas; Jaime Iranzo; Adriana LucÍa-Sanz; Jens H. Kuhn; Mart Krupovic; Valerian V. Dolja; Eugene V. Koonin

For example, it appears that all dsRNA viruses in the two major clades within Branches 2 and 4 715 share homologous structural modules that combine with distinct RdRps. At least in the case of 716 partiti-picobirnaviruses in Branch 2, the dsRNA virus ("toti-like virus") CP apparently displaced 717 the ancestral SJR-CP. However, this particular protein structure does not seem to be essential to 718 encapsidate a dsRNA genome: birnaviruses, whose provenance is uncertain due to the 719 permutation in their RdRps, retain SJR-CP, which is most closely related to SJR-CP of 720 nodaviruses and tetraviruses (19). An even more striking example of module shuffling is 721 presented by amalgaviruses, dsRNA viruses that group with partitiviruses in the RdRp tree but 722 encode a distant homolog of the nucleocapsid protein of -RNA bunyaviruses (111-114). More 723 generally, structural and replication modules have been repeatedly shuffled during the evolution 724 of +RNA viruses. Examples include displacement of the ancestral SJR-CP by a filamentous CP 725 in potyviruses and by a helical nucleocapsid protein in nidoviruses, and multiple cases of 726 displacement with rod-shaped-like CP and unique nucleocapsid proteins in Branch 3. Thus, 727