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@ARTICLE{Lauber:289663,
      author       = {C. Lauber and X. Zhang and J. Vaas$^*$ and F. Klingler$^*$
                      and P. Mutz$^*$ and A. Dubin and T. Pietschmann and O. Roth
                      and B. W. Neuman and A. E. Gorbalenya and R.
                      Bartenschlager$^*$ and S. Seitz$^*$},
      title        = {{D}eep mining of the {S}equence {R}ead {A}rchive reveals
                      major genetic innovations in coronaviruses and other
                      nidoviruses of aquatic vertebrates.},
      journal      = {PLoS pathogens},
      volume       = {20},
      number       = {4},
      issn         = {1553-7366},
      address      = {Lawrence, Kan.},
      publisher    = {PLoS},
      reportid     = {DKFZ-2024-00845},
      pages        = {e1012163 -},
      year         = {2024},
      note         = {#LA:F170#LA:D430#},
      abstract     = {Virus discovery by genomics and metagenomics empowered
                      studies of viromes, facilitated characterization of pathogen
                      epidemiology, and redefined our understanding of the natural
                      genetic diversity of viruses with profound functional and
                      structural implications. Here we employed a data-driven
                      virus discovery approach that directly queries unprocessed
                      sequencing data in a highly parallelized way and involves a
                      targeted viral genome assembly strategy in a wide range of
                      sequence similarity. By screening more than 269,000 datasets
                      of numerous authors from the Sequence Read Archive and using
                      two metrics that quantitatively assess assembly quality, we
                      discovered 40 nidoviruses from six virus families whose
                      members infect vertebrate hosts. They form 13 and 32
                      putative viral subfamilies and genera, respectively, and
                      include 11 coronaviruses with bisegmented genomes from
                      fishes and amphibians, a giant 36.1 kilobase coronavirus
                      genome with a duplicated spike glycoprotein (S) gene, 11
                      tobaniviruses and 17 additional corona-, arteri-, cremega-,
                      nanhypo- and nangoshaviruses. Genome segmentation emerged in
                      a single evolutionary event in the monophyletic lineage
                      encompassing the subfamily Pitovirinae. We recovered the
                      bisegmented genome sequences of two coronaviruses from RNA
                      samples of 69 infected fishes and validated the presence of
                      poly(A) tails at both segments using 3'RACE PCR and
                      subsequent Sanger sequencing. We report a genetic linkage
                      between accessory and structural proteins whose phylogenetic
                      relationships and evolutionary distances are incongruent
                      with the phylogeny of replicase proteins. We rationalize
                      these observations in a model of inter-family S
                      recombination involving at least five ancestral corona- and
                      tobaniviruses of aquatic hosts. In support of this model, we
                      describe an individual fish co-infected with members from
                      the families Coronaviridae and Tobaniviridae. Our results
                      expand the scale of the known extraordinary evolutionary
                      plasticity in nidoviral genome architecture and call for
                      revisiting fundamentals of genome expression, virus particle
                      biology, host range and ecology of vertebrate nidoviruses.},
      cin          = {F170 / D430},
      ddc          = {610},
      cid          = {I:(DE-He78)F170-20160331 / I:(DE-He78)D430-20160331},
      pnm          = {314 - Immunologie und Krebs (POF4-314)},
      pid          = {G:(DE-HGF)POF4-314},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:38648214},
      doi          = {10.1371/journal.ppat.1012163},
      url          = {https://inrepo02.dkfz.de/record/289663},
}