Parallel evolution of picobirnaviruses from distinct ancestral origins

ABSTRACT Picobirnaviruses (PBVs) are small, bi-segmented, double-stranded RNA viruses frequently associated with gastrointestinal and recently linked to respiratory infections. Detected in hosts from distant biological kingdoms, debate swirls as to their age and origins and whether they are prokaryotic or eukaryotic viruses. Our evolutionary analysis revealed a contemporaneous emergence for PBV, as PBV-R1&3 species arose ~350 years ago with both segments, whereas the more ancient species, PBV-R2, initially lacked capsid. Integrated phylogenetic reconstruction defined two origins for PBV, determining PBV-R1&3 species descended from Reovirus and PBV-R2 branched with Partitivirus ancestors. These results, coupled with the heterogeneity of Shine-Dalgarno motifs, argue against a prokaryotic origin. Epistatic interactions identified in the RdRp of PBV-R1&3 evidenced the constraints imposed by vertebrate host immunity, whereas its absence in PBV-R2 concurs with its fungal origin. After acquisition of capsid, PBV-R2 increased its adaptive and functional divergences in RdRp domains and the compactness of its RNA structure to enable encapsidation. While their pathogenicity remains an open question, picobirnaviruses likely originated from both fungal and avian hosts: parallel evolution mechanisms have driven the genetic similarities shared among present-day PBV species. IMPORTANCE Picobirnaviruses (PBVs) are highly heterogeneous viruses encoding a capsid and RdRp. Detected in a wide variety of animals with and without disease, their association with gastrointestinal and respiratory infections, and consequently their public health importance, has rightly been questioned. Determining the “true” host of Picobirnavirus lies at the center of this debate, as evidence exists for them having both vertebrate and prokaryotic origins. Using integrated and time-stamped phylogenetic approaches, we show they are contemporaneous viruses descending from two different ancestors: avian Reovirus and fungal Partitivirus. The fungal PBV-R2 species emerged with a single segment (RdRp) until it acquired a capsid from vertebrate PBV-R1 and PBV-R3 species. Protein and RNA folding analyses revealed how the former came to resemble the latter over time. Thus, parallel evolution from disparate hosts has driven the adaptation and genetic diversification of the Picobirnaviridae family.