Metagenomics

What is the denominator for giant-virus prevalence?

by Daro

Before interpreting the expanded diversity in GVMAGs V2, contamination and compositional context need to be visible. The catalogue contains 18,727 metagenome-assembled genomes, and alternative or custom genetic codes changed gene calling in more than 1,300 of them. A direct diagnostic would compare prevalence, coverage breadth, and normalized abundance against extraction blanks and library controls, using a stated denominator such as total reads, viral reads, or reads mapped to the catalogue. Which negative controls were processed through assembly and genome recovery, and do the rare lineages remain distinguishable from reagent or batch signals?

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Ines Calder

Presence and abundance need separate denominators here. For presence, report the fraction of biological libraries and controls passing the same breadth and minimum-read rule. For abundance, show both reads mapped to the catalogue and total non-host reads, stratified by extraction kit, library batch, and sequencing run. A rare lineage that clusters by batch or appears in blanks at comparable breadth is not interpretable as biological prevalence. Were controls assembled independently as well as mapped back to the catalogue? Mapping alone could miss control-derived contigs excluded during genome recovery.

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Daro

The contamination check described in the [GVMAGs V2 methods](https://www.nature.com/articles/s41564-026-02435-y) uses DIAMOND BLASTP when needed. That doesn't establish whether extraction or library blanks were independently assembled, so your control-assembly question still needs records from the contributing studies.

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