Appendix D — Glossary
Concise, one-line definitions of the terms used throughout this book. Terms are listed alphabetically so you can scan quickly.
| Term | Meaning |
|---|---|
| Alpha diversity | within-sample diversity (richness and evenness of viruses in one sample) |
| AMG (auxiliary metabolic gene) | host-derived metabolic gene carried by a virus that can reprogram host metabolism during infection |
| ANI (average nucleotide identity) | average identity between two genomes over aligned regions; species-level vOTUs use 95% ANI over an 85% alignment fraction (MIUViG) |
| CheckV contamination | in CheckV, host DNA flanking an integrated provirus (not cross-sample contamination); it is trimmed off and is not used to lower the quality tier |
| Baltimore classification | grouping of viruses (I–VII) by how their genome produces mRNA |
| Bacteriophage | virus that infects bacteria |
| Beta diversity | between-sample difference in viral community composition |
| Capsid | protein shell that encloses and protects a viral genome |
| CheckV completeness | estimated fraction of a viral genome recovered in a contig |
| Contig | a contiguous sequence assembled from overlapping reads |
| Coverage / depth | number of reads aligned across a position or contig; reflects abundance |
| CRISPR spacer | short host-derived sequence in a CRISPR array that can match and identify a virus’s host |
| Dark matter (viral) | viral sequences with no close match in current reference databases |
| Decoy / negative control | a known non-target or blank sample used to detect contamination and false positives |
| Dereplication | collapsing near-identical sequences into representative clusters (e.g. vOTUs) |
| Hallmark gene | gene strongly diagnostic of viral identity (e.g. capsid, terminase, portal) |
| Host prediction | computational inference of the likely host of a viral sequence |
| ICTV taxonomy | the official virus taxonomy framework maintained by the ICTV |
| Integrase | enzyme that integrates a temperate phage genome into the host chromosome and excises it again during induction |
| Lysogeny | temperate lifestyle in which a phage genome persists as a prophage |
| Lytic cycle | infection in which a phage replicates, assembles, and lyses the host to release progeny |
| MAG (metagenome-assembled genome) | a genome reconstructed by binning contigs from a metagenome |
| N50 | length at which 50% of assembled bases lie in contigs of that length or longer |
| Provirus / prophage | a viral genome integrated into, or persisting alongside, a host genome |
| RdRp (RNA-dependent RNA polymerase) | enzyme that replicates RNA virus genomes; a key marker for RNA viruses |
| Realm | the highest rank in ICTV virus taxonomy (e.g. Duplodnaviria) |
| Terminase | phage enzyme that packages DNA into the capsid; a common hallmark gene |
| TPM (transcripts per million) | length- and depth-normalized abundance value for cross-sample comparison |
| Viral metagenomics | metagenomic analysis focused on recovering viral sequences |
| Virome | the collection of viruses in a sample or ecosystem |
| Viromics | the sequencing-based study of viral communities |
| VirSorter2 / geNomad | tools that flag candidate viral sequences in assemblies |
| vOTU (viral operational taxonomic unit) | a species-level viral cluster, typically defined at 95% ANI over 85% alignment fraction (MIUViG) |
| Baltimore group | one of the seven classes (I–VII) in the Baltimore system |
| att site | attachment site where a prophage integrates into or excises from a host genome |
| Enrichment (VLP) | wet-lab step (filtration, nuclease treatment) that concentrates virus-like particles before sequencing |