Bioinformatics of Recent Aqua- and Orthoreovirus Isolates from Fish: Evolutionary Gain or Loss of FAST and Fiber Proteins and Taxonomic Implications

• Published in: PloS one Vol. 8; no. 7; p. e68607
• Main Authors: Nibert, Max L., Duncan, Roy
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04.07.2013; Public Library of Science (PLoS)
• Subjects: Amino Acid Sequence; Analysis; Animals; Aquareovirus; Bioinformatics; Biological Evolution; Biology; Birds; Carp; Carps - virology; Computational Biology; Ctenopharyngodon idella; Double-stranded RNA; Electronic mail systems; FAST protein; Fish; Fish Diseases - virology; Genera; Genome, Viral; Genomes; Genomics; Homology; Mammals; Molecular Sequence Data; Nonstructural proteins; Orthoreovirus; Orthoreovirus - classification; Orthoreovirus - genetics; Phylogeny; Protein Structure, Secondary; Proteins; Reoviridae; Reoviridae - classification; Reoviridae - genetics; Reptiles; RNA polymerase; RNA, Double-Stranded; RNA, Viral - classification; RNA, Viral - genetics; Segments; Sequence Alignment; Sequence Homology, Amino Acid; Taxa; Taxonomy; Viral Nonstructural Proteins - classification; Viral Nonstructural Proteins - genetics; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0068607

Family Reoviridae, subfamily Spinareovirinae, includes nine current genera. Two of these genera, Aquareovirus and Orthoreovirus, comprise members that are closely related and consistently share nine homologous proteins. Orthoreoviruses have 10 dsRNA genome segments and infect reptiles, birds, and mammals, whereas aquareoviruses have 11 dsRNA genome segments and infect fish. Recently, the first 10-segmented fish reovirus, piscine reovirus (PRV), has been identified and shown to be phylogenetically divergent from the 11-segmented viruses constituting genus Aquareovirus. We have recently extended results for PRV by showing that it does not encode a fusion-associated small transmembrane (FAST) protein, but does encode an outer-fiber protein containing a long N-terminal region of predicted α-helical coiled coil. Three recently characterized 11-segmented fish reoviruses, obtained from grass carp in China and sequenced in full, are also divergent from the viruses now constituting genus Aquareovirus, though not to the same extent as PRV. In the current study, we reexamined the sequences of these three recent isolates of grass carp reovirus (GCRV)-HZ08, GD108, and 104-for further clues to their evolution relative to other aqua- and orthoreoviruses. Structure-based fiber motifs in their encoded outer-fiber proteins were characterized, and other bioinformatics analyses provided evidence against the presence of a FAST protein among their encoded nonstructural proteins. Phylogenetic comparisons showed the combination of more distally branching, approved Aquareovirus and Orthoreovirus members, plus more basally branching isolates GCRV104, GCRV-HZ08/GD108, and PRV, constituting a larger, monophyletic taxon not suitably recognized by the current taxonomic hierarchy. Phylogenetics also suggested that the last common ancestor of all these viruses was a fiber-encoding, nonfusogenic virus and that the FAST protein family arose from at least two separate gain-of-function events. In addition, an apparent evolutionary correlation was found between the gain or loss of NS-FAST and outer-fiber proteins among more distally branching members of this taxon.