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. TroncosoSusan M. Resnick, Ben Bolduc, Matthew B. Sullivan, Arvind Varsani, Anca M. Segall, Christopher B. Buck

Research output: Contribution to journalArticle

5 Scopus citations

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.

Original languageEnglish (US)
Article numbere51971
JournaleLife
Volume9
DOIs
StatePublished - Feb 2020

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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    Tisza, M. J., Pastrana, D. V., Welch, N. L., Stewart, B., Peretti, A., Starrett, G. J., Pang, Y. Y. S., Krishnamurthy, S. R., Pesavento, P. A., McDermott, D. H., Murphy, P. M., Whited, J. L., Miller, B., Brenchley, J., Rosshart, S. P., Rehermann, B., Doorbar, J., Ta’ala, B. A., Pletnikova, O., ... Buck, C. B. (2020). Discovery of several thousand highly diverse circular DNA viruses. eLife, 9, [e51971]. https://doi.org/10.7554/eLife.51971