eLife (Feb 2020)
Discovery of several thousand highly diverse circular DNA viruses
- Michael J Tisza,
- Diana V Pastrana,
- Nicole L Welch,
- Brittany Stewart,
- Alberto Peretti,
- Gabriel J Starrett,
- Yuk-Ying S Pang,
- Siddharth R Krishnamurthy,
- Patricia A Pesavento,
- David H McDermott,
- Philip M Murphy,
- Jessica L Whited,
- Bess Miller,
- Jason Brenchley,
- Stephan P Rosshart,
- Barbara Rehermann,
- John Doorbar,
- Blake A Ta'ala,
- Olga Pletnikova,
- Juan C Troncoso,
- Susan M Resnick,
- Ben Bolduc,
- Matthew B Sullivan,
- Arvind Varsani,
- Anca M Segall,
- Christopher B Buck
Affiliations
- Michael J Tisza
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
- Diana V Pastrana
- ORCiD
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
- Nicole L Welch
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
- Brittany Stewart
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
- Alberto Peretti
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
- Gabriel J Starrett
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
- Yuk-Ying S Pang
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
- Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
- Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, United States
- David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
- Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
- Jessica L Whited
- ORCiD
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States; Broad Institute of MIT and Harvard, Cambridge, United States; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
- Bess Miller
- ORCiD
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States; Broad Institute of MIT and Harvard, Cambridge, United States
- Jason Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Cambridge, United States
- Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
- Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
- John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Blake A Ta'ala
- Mililani Mauka Elementary, Mililani, United States
- Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
- Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
- Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, United States
- Ben Bolduc
- Department of Microbiology, Ohio State University, Columbus, United States
- Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, United States; Civil Environmental and Geodetic Engineering, Ohio State University, Columbus, United States
- Arvind Varsani
- ORCiD
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, United States; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, South Africa
- Anca M Segall
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, United States
- Christopher B Buck
- ORCiD
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
- DOI
- https://doi.org/10.7554/eLife.51971
- Journal volume & issue
-
Vol. 9
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.
Keywords
