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Background  RNA viruses have been isolated that infect marine organisms ranging from bacteria to whales, but little is known about the composition and population structure of the  in situ  marine RNA virus community. In a recent study, the majority of three genomes of previously unknown positive-sense single-stranded (ss) RNA viruses were assembled from reverse-transcribed whole-genome shotgun libraries. The present contribution comparatively analyzes these genomes with respect to representative viruses from established viral taxa.    Results  Two of the genomes (JP-A and JP-B), appear to be polycistronic viruses in the proposed order  Picornavirales  that fall into a well-supported clade of marine picorna-like viruses, the characterized members of which all infect marine protists. A temporal and geographic survey indicates that the JP genomes are persistent and widespread in British Columbia waters. The third genome, SOG, encodes a putative RNA-dependent RNA polymerase (RdRp) that is related to the RdRp of viruses in the family  Tombusviridae , but the remaining SOG sequence has no significant similarity to any sequences in the NCBI database.    Conclusion  The complete genomes of these viruses permitted analyses that resulted in a more comprehensive comparison of these pathogens with established taxa. For example, in concordance with phylogenies based on the RdRp, our results support a close homology between JP-A and JP-B and RsRNAV. In contrast, although classification of the SOG genome based on the RdRp places SOG within the  Tombusviridae , SOG lacks a capsid and movement protein conserved within this family and SOG is thus likely more distantly related to the  Tombusivridae  than the RdRp phylogeney indicates.

The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities