identifier: traitmech:000263 label: Viperin system definition: A phage defense system in which an organism possesses a prokaryotic viperin locus represented by a pVip profile that can produce antiviral modified ribonucleotides and protect against phage infection. definition_source: DOI:10.1038/s41586-020-2762-2 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Viperin synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: pVip synonym_type: RELATED_SYNONYM source: DOI:10.1038/s41586-020-2762-2 evidence: - reference: DOI:10.1038/s41586-020-2762-2 snippet: Here we show that eukaryotic viperin originated from a clade of bacterial and archaeal proteins that protect against phage infection notes: Bernheim et al. support treating prokaryotic viperins as bacterial and archaeal phage-protective proteins rather than only as an animal antiviral factor. - reference: DOI:10.1038/s41586-020-2762-2 snippet: Prokaryotic viperins produce a set of modified ribonucleotides notes: Bernheim et al. support modified ribonucleotide synthesis as a recurring output of prokaryotic viperin proteins. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Viperin | 10\.1038/s41586-020-2762-2 | Prokaryotic viperins produce diverse antiviral molecules notes: The DefenseFinder model registry maps the named Viperin system to the Bernheim et al. prokaryotic viperin paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Viperin\tViperin\t1\t1\tViperin__pVip" notes: The DefenseFinder rules table models Viperin with a pVip profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: Viperin__pVip | Viperin__pVip | Viperin notes: The DefenseFinder HMM inventory records pVip in the Viperin model namespace. causal_graphs: - graph_id: viperin_modified_ribonucleotides_restrict_phage title: Prokaryotic viperins produce antiviral ribonucleotides description: Conservative system-level sketch linking possession of a prokaryotic viperin locus to modified ribonucleotide production and inhibited phage transcription. scope_status: NONMECHANISTIC scope_notes: The graph captures characterized pVip-mediated modified ribonucleotide production and T7 transcription inhibition without asserting one universal nucleotide product, viral polymerase target, accessory-gene architecture, or phage range across all Viperin loci. nodes: - node_id: viperin_locus label: Viperin locus node_type: GENETIC_ELEMENT description: A prokaryotic viperin phage-defense locus satisfying a DefenseFinder rule over the pVip profile. - node_id: modified_ribonucleotide_production label: modified ribonucleotide production node_type: BIOLOGICAL_PROCESS description: Production of modified ribonucleotides by prokaryotic viperin enzymes. - node_id: t7_phage_transcription_inhibition label: T7 phage transcription inhibition node_type: BIOLOGICAL_PROCESS description: Inhibition of T7 phage polymerase-dependent transcription. - node_id: viperin_system_trait label: Viperin system node_type: TRAIT grounding: traitmech:000263 description: Possession of a genome-encoded prokaryotic viperin phage-defense locus. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: viperin_locus predicate: contributes to predicate_id: RO:0002326 object: modified_ribonucleotide_production description: The Viperin locus encodes a pVip-class radical-SAM enzyme that produces modified ribonucleotides. evidence: - reference: DOI:10.1038/s41586-020-2762-2 snippet: Prokaryotic viperins produce a set of modified ribonucleotides notes: Bernheim et al. support modified ribonucleotide production as a pVip output. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Viperin\tViperin\t1\t1\tViperin__pVip" notes: The DefenseFinder rules table supports pVip as the required Viperin system profile. - subject: modified_ribonucleotide_production predicate: enables predicate_id: RO:0002327 object: t7_phage_transcription_inhibition description: Prokaryotic viperin products can inhibit T7 phage polymerase-dependent transcription. evidence: - reference: DOI:10.1038/s41586-020-2762-2 snippet: prokaryotic viperins protect against T7 phage infection by inhibiting viral polymerase-dependent transcription notes: Bernheim et al. connect prokaryotic viperin activity to inhibition of T7 transcription. - subject: t7_phage_transcription_inhibition predicate: confers predicate_id: METPO:2007700 object: viperin_system_trait description: Inhibition of phage transcription is a source-backed antiviral output that realizes the Viperin system trait. evidence: - reference: DOI:10.1038/s41586-020-2762-2 snippet: prokaryotic viperins protect against T7 phage infection by inhibiting viral polymerase-dependent transcription notes: Bernheim et al. support pVip-mediated protection from T7 phage infection. - subject: viperin_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Viperin system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1038/s41586-020-2762-2 snippet: Here we show that eukaryotic viperin originated from a clade of bacterial and archaeal proteins that protect against phage infection notes: Bernheim et al. support Viperin as a prokaryotic phage-defense system. discussions: - discussion_id: viperin-product-and-subtype-gap prompt: Resolve Viperin nucleotide products, accessory genes, and phage-target breadth before minting narrower Viperin mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Bernheim et al. support prokaryotic viperins as phage-protective producers of modified ribonucleotides, and DefenseFinder models Viperin through the pVip profile, but Viperin-family loci need separate review before TraitMech asserts one universal antiviral nucleotide, polymerase target, or accessory-gene architecture. attaches_to: - causal_graphs#viperin_modified_ribonucleotides_restrict_phage posed_by: codex posed_date: '2026-09-19' curation_history: - timestamp: '2026-09-19T03:43:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Viperin system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v140. llm_assisted: true - timestamp: '2026-09-19T03:58:00Z' curator: codex action: EDIT changes: 'Replaced the Viperin phage-defense-system subclass edge snippet with a Bernheim et al. phage-protection abstract span found by local adversarial review in issue #1037.' llm_assisted: true - timestamp: '2026-09-19T04:06:03Z' curator: codex action: EDIT changes: 'Aligned the Viperin definition with the bacterial and archaeal prokaryotic scope identified in Claude review issue #1038.' llm_assisted: true