Discovery of Several Thousand Highly Diverse Circular DNA Viruses

Overview

Journal Elife

Specialty Biology

Date 2020 Feb 5

PMID 32014111

Citations 90

Authors

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 Taala

Olga Pletnikova

Juan C Troncoso

Susan M Resnick

Ben Bolduc

Matthew B Sullivan

Arvind Varsani

Anca M Segall

Christopher B Buck

Affiliations

Soon will be listed here.

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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