Known phyla dominate the Tara Oceans RNA virome

• Published in: Virus Evolution
• Main Author: Edgar, Robert
• Format: Article in Journal/Newspaper
• Language: English
• Published: Oxford University Press (OUP) 2023
• Subjects: Arctic; Arctic Ocean
• Online Access: http://dx.doi.org/10.1093/ve/vead063; https://academic.oup.com/ve/advance-article-pdf/doi/10.1093/ve/vead063/53048787/vead063.pdf; https://academic.oup.com/ve/article-pdf/9/2/vead063/53420572/vead063.pdf

Abstract A recent study proposed five new RNA virus phyla, two of which, ‘Taraviricota’ and ‘Arctiviricota’, were stated to be ‘dominant in the oceans’. However, the study’s assignments classify 28,353 putative RdRp-containing contigs to known phyla but only 886 (2.8%) to the five proposed new phyla combined. I re-mapped the reads to the contigs, finding that known phyla also account for a large majority (93.8%) of reads according to the study’s classifications, and that contigs originally assigned to ‘Arctiviricota’ accounted for only a tiny fraction (0.01%) of reads from Arctic Ocean samples. Performing my own virus identification and classifications, I found that 99.95 per cent of reads could be assigned to known phyla. The most abundant species was Beihai picorna-like virus 34 (15% of reads), and the most abundant order-like cluster was classified as Picornavirales (45% of reads). Sequences in the claimed new phylum ‘Pomiviricota’ were placed inside a phylogenetic tree for established order Durnavirales with 100 per cent confidence. Moreover, two contigs assigned to the proposed phylum ‘Taraviricota’ were found to have high-identity alignments to dinoflagellate proteins, tentatively identifying this group of RdRp-like sequences as deriving from non-viral transcripts. Together, these results comprehensively contradict the claim that new phyla dominate the data.