A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses.This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages.This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.While viruses are known to be the most abundant organisms on earth, their collective evolutionary history, biodiversity and functional capacity is poorly understood [1-3]. Despite many inherent obstacles, viral metagenomics is enabling a more detailed evaluation of environmental viral diversity, and is burgeoning as an important tool for studying virus evolution [4-7]. Perhaps the greatest impediment to the evolutionary study of viruses is that there is no single phylogenetic marker in common amongst all viruses. Instead, “virus hallmark genes” [8] that are present in sub-groups of viruses are often used as the basis for taxonomic classification and evolutionary studies. However, lateral gene transfer between viruses complicates these analyses and virus classification schemes are likewise intens