Mining viruses in public databases unveils the diversity within the Deltaflexiviridae family

Cloud computing platforms aided the scalability and applicability of viral mining in genomic databases. The Serratus project reported SRA accessions that may contain viral sequences. This study analyzed SRA accessions containing sequences similar to Tymovirales members to verify the presence of sequence data derived from viral genomes. All steps in the genome mining analysis were performed by a pipeline running on virtual machines hosted on the Google Cloud Platform. Manual curation of the pipeline output discovered 111 putative genomes in the analyzed SRAs. Among the genomes identified, four were classified as isolates within the Betaflexiviridae family, and two were putative new members of the Alphaflexiviridae family. Another four sequences were likely classified in a family not yet accepted by the ICTV. The phylogenetic reconstruction of the Deltaflexiviridae family revealed three distinct clades, one of them containing 81 genomes (34 putative new species), a second clade with 18 novel genomes (7 putative new species), and a third with one putative new species. Given the high divergence between these three groups, we suggest the establishment of a new family, "Epsilonflexiviridae", and the split of the Deltaflexiviridae family into two by establishing the family "Zetaflexiviridae". The results of this work provide insight into important aspects of the evolutionary history of the order Tymovirales and offer new ways for virus-mining projects in genomic databases.