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Discovery of several thousand highly diverse circular DNA viruses.
Tisza, Michael J; Pastrana, Diana V; Welch, Nicole L; Stewart, Brittany; Peretti, Alberto; Starrett, Gabriel J; Pang, Yuk-Ying S; Krishnamurthy, Siddharth R; Pesavento, Patricia A; McDermott, David H; Murphy, Philip M; Whited, Jessica L; Miller, Bess; Brenchley, Jason; Rosshart, Stephan P; Rehermann, Barbara; Doorbar, John; Ta'ala, Blake A; Pletnikova, Olga; Troncoso, Juan C; Resnick, Susan M; Bolduc, Ben; Sullivan, Matthew B; Varsani, Arvind; Segall, Anca M; Buck, Christopher B.
Affiliation
  • Tisza MJ; Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States.
  • Pastrana DV; Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States.
  • Welch NL; Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States.
  • Stewart B; Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States.
  • Peretti A; Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States.
  • Starrett GJ; Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States.
  • Pang YS; Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States.
  • Krishnamurthy SR; Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
  • Pesavento PA; Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, United States.
  • McDermott DH; Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
  • Murphy PM; Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
  • Whited JL; Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.
  • Miller B; Broad Institute of MIT and Harvard, Cambridge, United States.
  • Brenchley J; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States.
  • Rosshart SP; Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.
  • Rehermann B; Broad Institute of MIT and Harvard, Cambridge, United States.
  • Doorbar J; Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Cambridge, United States.
  • Ta'ala BA; Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.
  • Pletnikova O; Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.
  • Troncoso JC; Department of Pathology, University of Cambridge, Cambridge, United Kingdom.
  • Resnick SM; Mililani Mauka Elementary, Mililani, United States.
  • Bolduc B; Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States.
  • Sullivan MB; Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States.
  • Varsani A; Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, United States.
  • Segall AM; Department of Microbiology, Ohio State University, Columbus, United States.
  • Buck CB; Department of Microbiology, Ohio State University, Columbus, United States.
Elife ; 92020 02 04.
Article in En | MEDLINE | ID: mdl-32014111
ABSTRACT
Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these 'dark matter' sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.
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Full text: 1 Database: MEDLINE Main subject: DNA, Circular / DNA Viruses Limits: Animals / Humans Language: En Journal: Elife Year: 2020 Type: Article Affiliation country: United States
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Full text: 1 Database: MEDLINE Main subject: DNA, Circular / DNA Viruses Limits: Animals / Humans Language: En Journal: Elife Year: 2020 Type: Article Affiliation country: United States