Ribovirus classification by a polymerase barcode sequence

Abstract

RNA viruses encoding a polymerase gene (riboviruses) dominate the known eukaryotic virome. High-throughput sequencing is revealing a wealth of new riboviruses known only from sequence, precluding classification by traditional taxonomic methods. Sequence classification is often based on polymerase sequences, but standardised methods to support this approach are currently lacking. To address this need, we describe the polymerase palmprint, a segment of the palm sub-domain robustly delineated by well-conserved catalytic motifs. We present an algorithm, Palmscan, which identifies palmprints in nucleotide and amino acid sequences; PALMdb, a collection of palmprints derived from public sequence databases; and palmID, a public website implementing palmprint identification, search, and annotation. Together, these methods demonstrate a proof-of-concept workflow for high-throughput characterisation of RNA viruses, paving the path for the continued rapid growth in RNA virus discovery anticipated in the coming decade.

Transcriptome mining extends the host range of theFlaviviridaeto non-bilaterians

“…While CnidFV and the EVE are relatively closely related to each other, there is a large amount of divergence between these sequences. This has been previously observed with crocidura pestivirus and a Crocidura EVE and may reflect divergent evolution since the historic endogenization event (Li et al 2022).…”

“…The clear relatedness between GmebHV and rodent hepacivirus (QLM02863), combined with evidence from our co-evolutionary analyses, suggests that this sequence might represent a cross-species transmission event between bats and rodents. Similarly, ancestral state reconstructions have previously shown that cross-species transmission from rodents is likely the source of the sloth and ringtail hepaciviruses (Jo et al 2022; Moreira-Soto et al 2020). In this case, we cannot resolve the direction of virus transmission with any certainty or whether intermediate species are involved.…”

“…Transcriptome mining is a proven method of virus discovery that leverages previous investment in metagenomics (Dheilly et al 2022; Edgar et al 2022; Greninger 2018; Grimwood et al 2021; Iwamoto et al 2021; Mifsud et al 2022; Miller et al 2021; Olendraite et al 2022; Paraskevopoulou et al 2021; Parry et al 2019). To understand the host range of flaviviral sequences throughout the Metazoa and hence more accurately determine the age of the Flaviviridae , we used the Serratus RNA-dependent RNA polymerase (RdRp) search (https://www.serratus.io/explorer/rdrp) to mine the Sequence Read Archive (SRA) database for novel flaviviral sequences.…”

An Unwanted Association: The Threat to Papaya Crops by a Novel Potexvirus in Northwest Argentina

“…To investigate whether the detected virus might be present in other datasets, we employed the Serratus palmID tool [ 41 ] which extracts Palmprint sequences using as query the predicted RdRp of this virus with standard parameters. Palmprints are a ~100 aa sub-sequence of the polymerase gene containing A, B, and C conserved RdRp motifs [ 42 ]. The related SRA datasets were processed as described elsewhere [ 43 ].…”

Known phyla dominate the RNA virome in Tara Oceans data, not new phyla as claimed

“…Examples of endogenous host insertions. The figure shows PSSM alignments of the A, B and C motifs in the RdRp palm domain by palmscan Babaian and Edgar (2021). WP_185168479.1 is an RdRp-like protein from Proteus mirabilis .…”