Discovery of several thousand highly diverse circular DNA viruses

Author:

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 M.,Rosshart Stephan P.,Rehermann Barbara,Doorbar John,Ta’ala Blake A.,Pletnikova Olga,Troncoso Juan,Resnick Susan M.,Bolduc Ben,Sullivan Matthew B.,Varsani Arvind,Segall Anca M.,Buck Christopher B.ORCID

Abstract

SummaryAlthough it is suspected that there are millions of distinct viral species, fewer than 9,000 are catalogued in GenBank’s RefSeq database. We selectively enriched for and amplified the genomes of circular DNA viruses in over 70 animal samples, ranging from cultured soil nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2,500 circular 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 viruses 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.

Publisher

Cold Spring Harbor Laboratory

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