{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-07T11:57:52Z", "providers": [ "Codex", "Grok" ], "missingProviders": [], "pass": 2, "cost": { "grok": { "usd": 0.01519426, "turns": 1, "seconds": 203.7, "error": null }, "codex": { "seconds": 95.2, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.3\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a07bb5-edbf-72f0-b47f-abfff50d069d\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: Zika virus\nRegistry id: vr.tr.zika-virus\nPlane / domain: ACT / ACT.ACT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\nA V" } } }, "metaModel": { "id": "THING-Q202864", "registryId": "vr.tr.zika-virus", "name": "Zika virus", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.ACT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q202864/", "model": { "registry_id": "vr.tr.zika-virus", "name": "Zika virus", "purpose": "Enable an AI agent to identify Zika virus, assess evidence of its presence and transmission relevance, and determine which handling, prevention or expert-review actions are justified.", "definition": "Zika virus (ZIKV) is a mosquito-borne orthoflavivirus (species Orthoflavivirus zikaense, family Flaviviridae) transmitted mainly by Aedes aegypti, capable of sexual and transplacental spread, that usually causes a mild self-limited infection in humans and is an established cause of congenital Zika syndrome and Guillain-Barré syndrome.", "scope_statement": "This model owns the identity and evidence-qualified properties of Zika virus under vr.tr.zika-virus, including links to variants, specimens, hosts, transmission events and applicable action constraints; ACT / ACT.ACT is its registry placement, not an assertion of intentional agency.", "in_scope": [ "Zika virus identity, aliases and relationships to reference sequences and named variants", "Evidence distinguishing Zika from dengue, other flaviviruses and clinically similar infections", "Specimen-specific observations of viral material and separately assessed infectiousness", "Host, vector and transmission-route relationships with temporal and geographic limits", "Links to congenital and neurological consequences that affect assessment priorities", "Evidence and authority required for handling, prevention and escalation decisions" ], "out_of_scope": [ "Patient records, individual diagnoses and treatment plans", "Congenital Zika syndrome and Guillain-Barré syndrome as independently modeled conditions", "Mosquito taxonomy, life cycles and vector-control programme operations", "Outbreak management, population surveillance systems and travel itineraries", "Laboratory assay implementation, specimen inventory and experimental protocols", "Independent models of dengue virus, chikungunya virus and other pathogens" ], "distinguishing_features": [ "Require Zika-specific laboratory attribution rather than identifying the virus from fever, rash or travel history, which overlap with other infections. [WHO Zika fact sheet](https://www.who.int/news-room/fact-sheets/detail/zika-virus)", "Test whether a serological identification remains ambiguous because of other flavivirus exposures; even neutralization testing may not separate Zika from related viruses. [CDC diagnostic guidance](https://www.cdc.gov/zika/hcp/diagnosis-testing/)", "Check that the referent is the virus itself rather than Zika virus disease, an infected person, a specimen or congenital Zika syndrome.", "Use mosquito, sexual and maternal-fetal transmission relationships as contextual checks, never as stand-alone identity tests. [WHO Zika fact sheet](https://www.who.int/news-room/fact-sheets/detail/zika-virus)" ], "characteristics": [ { "name": "Identity resolution", "kind": "state", "unit_or_values": "Zika-supported; unresolved flavivirus; conflicting evidence; unassessed", "why_it_matters": "Prevents an ambiguous observation from becoming a definite Zika identification." }, { "name": "Reference and variant assignment", "kind": "relation", "unit_or_values": "Named reference or sequence accession with version, assignment method and uncertainty", "why_it_matters": "Makes variant labels traceable without creating separate registry things unnecessarily." }, { "name": "Observed material", "kind": "category", "unit_or_values": "Viral RNA; virus-containing material; host antibody response; unspecified", "why_it_matters": "Separates the virus from molecular traces and indirect evidence of exposure." }, { "name": "Zika detection result", "kind": "state", "unit_or_values": "Detected; not detected; equivocal; invalid; not tested, qualified by method and specimen", "why_it_matters": "Keeps laboratory observations distinct from conclusions about infection." }, { "name": "Measured RNA abundance", "kind": "measurement", "unit_or_values": "Assay-reported copies/mL or other validated unit; include detection limit and specimen matrix", "why_it_matters": "Supports qualified comparisons without equating RNA abundance with infectiousness." }, { "name": "Infectiousness evidence", "kind": "state", "unit_or_values": "Demonstrated; suspected; not demonstrated under stated conditions; unknown", "why_it_matters": "Requires a separate basis for conclusions about transmission-capable material." }, { "name": "Observation timing", "kind": "measurement", "unit_or_values": "Collection date and days relative to exposure, symptom onset or birth, with uncertainty", "why_it_matters": "Makes time-dependent interpretation possible without assuming an exact infection date." }, { "name": "Host and specimen context", "kind": "relation", "unit_or_values": "Linked host or vector, specimen type and anatomical compartment", "why_it_matters": "Prevents evidence from one host or compartment from being generalized to all others." }, { "name": "Transmission attribution", "kind": "category", "unit_or_values": "Mosquito-borne; sexual; maternal-fetal; blood-associated; laboratory-associated; other proposed; unknown, each evidence-qualified", "why_it_matters": "Supports route-specific review while preserving alternative explanations." }, { "name": "Action authority", "kind": "relation", "unit_or_values": "Applicable guidance or institutional decision with jurisdiction, version, effective date and responsible role", "why_it_matters": "Connects an action to its actual authority rather than deriving permission from virus identity alone." } ], "affordances": [ "Resolve a Zika-labelled observation against reference identity and differential evidence.", "Attach and compare specimen-qualified observations while preserving conflicting interpretations.", "Assess whether available evidence supports presence, exposure or infectiousness as separate conclusions.", "Link suspected transmission to host, route, place and time without asserting an unproven chain.", "Flag pregnancy-related or neurological contexts for appropriate expert review.", "Determine whether a proposed handling or prevention action has applicable guidance and sufficient authorization." ], "what_it_is_for": [ "Zika virus is encountered in infectious disease surveillance, mosquito monitoring and laboratory research on mosquito-borne infections.", "Its identification supports assessment of transmission, pregnancy-related risks and the need for specialist public health review." ], "standards_and_regulation": [ "The International Committee on Taxonomy of Viruses classifies Zika virus within the species Orthoflavivirus zikaense in the family Flaviviridae." ], "visual_identification": [ "Electron microscopy can reveal small, roughly spherical enveloped particles, but this appearance is shared with other flaviviruses.", "Neither particle appearance nor the appearance of an infected person or mosquito reliably distinguishes Zika virus, so identification requires validated laboratory evidence." ], "failure_modes_and_hazards": [ "Infection during pregnancy can cause congenital Zika syndrome and serious developmental impairment.", "Infection can be associated with Guillain-Barre syndrome and other neurological complications.", "Unrecognised infection can contribute to mosquito-borne, sexual or transplacental transmission.", "Misidentification or false reassurance from incomplete testing can delay appropriate clinical and public health assessment." ] }, "sources": [ { "id": "who-zika-fact-sheet", "title": "Zika virus (fact sheet) - World Health Organization", "url": "https://www.who.int/news-room/fact-sheets/detail/zika-virus", "what_it_supports": "Clinical picture, incubation (3-14 days), Aedes transmission, sexual and congenital transmission, Guillain-Barré syndrome, and the 2016 PHEIC.", "url_status": "live" }, { "id": "cdc-zika", "title": "Zika virus - U.S. Centers for Disease Control and Prevention", "url": "", "what_it_supports": "U.S. case definitions, diagnostic algorithm versus dengue, pregnancy outcomes, notifiable-disease practice, and biosafety/clinical guidance." }, { "id": "ictv-orthoflavivirus-zikaense", "title": "Virus Taxonomy: Orthoflavivirus zikaense - International Committee on Taxonomy of Viruses", "url": "", "what_it_supports": "Current species name Orthoflavivirus zikaense and placement in genus Orthoflavivirus, family Flaviviridae (virus name remains Zika virus)." }, { "id": "dick-1952", "title": "Zika virus. I. Isolations and serological specificity - Transactions of the Royal Society of Tropical Medicine and Hygiene (Dick, Kitchen & Haddow, 1952)", "url": "", "what_it_supports": "Original isolation from a rhesus macaque in the Zika Forest, Uganda (1947), and early serological identity of the agent." }, { "id": "duffy-2009-nejm", "title": "Zika virus outbreak on Yap Island, Federated States of Micronesia - New England Journal of Medicine (Duffy et al., 2009)", "url": "", "what_it_supports": "First well-documented large human outbreak and the widely cited estimate that most infections are asymptomatic." }, { "id": "musso-gubler-2016", "title": "Zika Virus - Clinical Microbiology Reviews (Musso & Gubler, 2016)", "url": "", "what_it_supports": "Virology, African versus Asian lineages, diagnostics, and distinction from related flaviviruses and chikungunya." }, { "id": "wikidata", "title": "Wikidata item Q202864: Zika virus", "url": "https://www.wikidata.org/wiki/Q202864", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Zika virus", "url": "https://en.wikipedia.org/wiki/Zika_virus", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "zika-identity-and-boundaries", "name": "Zika identity and boundaries", "description": "Establish what a Zika reference denotes and how its identity is supported.", "rationale": "An agent must distinguish the registered virus from disease labels, specimens and uncertain pathogen identifications.", "layers": [ { "id": "virus-referent", "name": "Virus referent", "description": "Keep the registered thing distinct from entities that contain it or result from infection.", "findings": [ { "id": "zika-reference-resolution", "name": "Zika reference resolution", "description": "Record whether a name denotes Zika virus, a particular viral variant or a neighbouring clinical or material entity.", "questions": [ { "text": "Does this use of 'Zika' denote the virus, an infection, a disease outcome or a specimen?", "kind": "definition", "id": "zika-reference-resolution-q01" }, { "text": "Which existing registry or world-model reference owns any neighbouring concept mentioned here?", "kind": "boundary", "id": "zika-reference-resolution-q02" } ] } ] }, { "id": "reference-and-variant-evidence", "name": "Reference and variant evidence", "description": "Anchor taxonomic and variant labels to inspectable references.", "findings": [ { "id": "traceable-zika-assignment", "name": "Traceable Zika assignment", "description": "Retain the reference version, assignment basis and limits of any lineage or isolate designation.", "questions": [ { "text": "Which authoritative reference or sequence accession supports this Zika assignment?", "kind": "provenance", "id": "traceable-zika-assignment-q01" }, { "text": "What evidence supports the stated variant resolution, and what remains unresolved?", "kind": "boundary", "id": "traceable-zika-assignment-q02" } ] } ] } ] }, { "id": "zika-detection-and-differential", "name": "Zika detection and differential", "description": "Represent direct and indirect evidence without collapsing uncertainty into a positive or negative diagnosis.", "rationale": "Zika assessment requires attention to specimen timing and flavivirus ambiguity.", "layers": [ { "id": "molecular-observations", "name": "Molecular observations", "description": "Qualify Zika RNA results by specimen, timing and assay interpretation.", "findings": [ { "id": "time-qualified-rna-result", "name": "Time-qualified RNA result", "description": "A negative NAAT does not exclude recent infection; record timing and test limitations alongside the result. [CDC diagnostic guidance](https://www.cdc.gov/zika/hcp/diagnosis-testing/)", "questions": [ { "text": "What specimen and collection interval does this Zika RNA result describe?", "kind": "measurement", "id": "time-qualified-rna-result-q01" }, { "text": "Which assay limitations or conflicting observations constrain the result's interpretation?", "kind": "boundary", "id": "time-qualified-rna-result-q02" } ] } ] }, { "id": "serological-attribution", "name": "Serological attribution", "description": "Separate evidence of a flavivirus immune response from attribution specifically to Zika.", "findings": [ { "id": "cross-reactivity-resolution", "name": "Cross-reactivity resolution", "description": "Record relevant prior exposures, vaccination history and differential-test interpretations rather than treating a reactive antibody result as self-explanatory.", "questions": [ { "text": "Which prior flavivirus infections or vaccinations could affect this Zika antibody interpretation?", "kind": "provenance", "id": "cross-reactivity-resolution-q01" }, { "text": "Does the reviewed evidence resolve Zika specifically, or must attribution remain an unspecified flavivirus response?", "kind": "boundary", "id": "cross-reactivity-resolution-q02" } ] } ] } ] }, { "id": "zika-material-and-transmission", "name": "Zika material and transmission", "description": "Connect observed viral material to carefully bounded assessments of infectiousness and transmission.", "rationale": "Presence in a specimen and a supported transmission route answer different questions.", "layers": [ { "id": "compartment-specific-state", "name": "Compartment-specific state", "description": "Assess observations within their host, specimen and anatomical context.", "findings": [ { "id": "presence-versus-infectiousness", "name": "Presence versus infectiousness", "description": "Require explicit evidence before translating a molecular observation into a claim that material can transmit Zika.", "questions": [ { "text": "Is this observation of Zika RNA, indirect exposure evidence or material with separately supported infectiousness?", "kind": "definition", "id": "presence-versus-infectiousness-q01" }, { "text": "What evidence supports the infectiousness assessment for this compartment and observation time?", "kind": "provenance", "id": "presence-versus-infectiousness-q02" } ] } ] }, { "id": "route-and-exposure-context", "name": "Route and exposure context", "description": "Represent candidate transmission routes and the evidence for each.", "findings": [ { "id": "supported-transmission-attribution", "name": "Supported transmission attribution", "description": "Record source and recipient links, route, place and exposure interval without treating vector presence or travel alone as proof of transmission.", "questions": [ { "text": "What evidence supports mosquito-borne, sexual, maternal-fetal or another proposed route in this event?", "kind": "provenance", "id": "supported-transmission-attribution-q01" }, { "text": "Which alternative routes or uncertain exposure dates prevent a definite transmission attribution?", "kind": "boundary", "id": "supported-transmission-attribution-q02" } ] } ] } ] }, { "id": "zika-consequence-relevance", "name": "Zika consequence relevance", "description": "Capture consequence relationships that change review priorities while leaving clinical management to neighbouring models.", "rationale": "Zika can cause congenital harm and is linked to neurological complications. [WHO Zika fact sheet](https://www.who.int/news-room/fact-sheets/detail/zika-virus)", "layers": [ { "id": "pregnancy-and-fetal-links", "name": "Pregnancy and fetal links", "description": "Keep maternal exposure, maternal infection, fetal infection and observed outcomes distinct.", "findings": [ { "id": "maternal-fetal-evidence-separation", "name": "Maternal-fetal evidence separation", "description": "Represent each supported relationship separately and preserve uncertainty in exposure timing and outcome attribution.", "questions": [ { "text": "Which evidence supports maternal exposure, maternal infection, fetal infection or a congenital outcome, respectively?", "kind": "provenance", "id": "maternal-fetal-evidence-separation-q01" }, { "text": "What pregnancy timing information and uncertainty must accompany referral to the pregnancy or congenital-condition model?", "kind": "action", "id": "maternal-fetal-evidence-separation-q02" } ] } ] }, { "id": "neurological-outcome-links", "name": "Neurological outcome links", "description": "Qualify links between Zika evidence and separately assessed neurological conditions.", "findings": [ { "id": "neurological-attribution-limit", "name": "Neurological attribution limit", "description": "Distinguish a general consequence relationship from evidence attributing a particular person's neurological condition to Zika.", "questions": [ { "text": "What supports the proposed relationship between this Zika observation and the linked neurological condition?", "kind": "provenance", "id": "neurological-attribution-limit-q01" }, { "text": "Which conclusions require clinical assessment rather than inference from the virus model?", "kind": "boundary", "id": "neurological-attribution-limit-q02" } ] } ] } ] }, { "id": "zika-action-eligibility", "name": "Zika action eligibility", "description": "Determine which evidence, guidance and responsible authority govern a proposed action involving Zika.", "rationale": "Handling decisions and exposure-prevention decisions depend on different contexts and cannot be granted by a pathogen label alone.", "layers": [ { "id": "material-handling-authority", "name": "Material handling authority", "description": "Link Zika-containing or suspected material to institutionally applicable handling requirements.", "findings": [ { "id": "authorized-material-disposition", "name": "Authorized material disposition", "description": "Record material state, requested operation, applicable requirements and responsible approval without embedding experimental procedures.", "questions": [ { "text": "Which current institutional requirements apply to the proposed storage, transfer, analysis or disposal of this material?", "kind": "provenance", "id": "authorized-material-disposition-q01" }, { "text": "Does the responsible role have sufficient evidence and authorization to proceed, or is specialist review required?", "kind": "action", "id": "authorized-material-disposition-q02" } ] } ] }, { "id": "exposure-prevention-guidance", "name": "Exposure prevention guidance", "description": "Bind prevention and public-health referrals to the relevant route, location, date and affected context.", "findings": [ { "id": "contextual-zika-guidance", "name": "Contextual Zika guidance", "description": "Record the guidance version and its applicability instead of hard-coding changing travel classifications, prevention intervals or testing eligibility.", "questions": [ { "text": "Which dated authority covers this exposure route, jurisdiction and pregnancy or reproductive context?", "kind": "provenance", "id": "contextual-zika-guidance-q01" }, { "text": "What evidence or contextual change would require updating the guidance link or escalating to a qualified professional?", "kind": "action", "id": "contextual-zika-guidance-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "African lineage", "Asian lineage", "Pacific/American epidemic clade (Asian-lineage expansion, 2007-2016)", "Prototype strain MR 766 (Uganda 1947, mouse-brain adapted)", "Contemporary clinical reference isolates (e.g. PRVABC59, H/PF/2013)" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of Zika virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "scheme": "Wikidata", "value_or_pattern": "Q202864", "note": "Item for Zika virus (the virus, not the disease)." }, { "scheme": "NCBI Taxonomy", "value_or_pattern": "64320", "note": "Taxon Zika virus." }, { "scheme": "ICTV species", "value_or_pattern": "Orthoflavivirus zikaense", "note": "Current species; historical genus/species names were Flavivirus / Zika virus. The virus name remains Zika virus (ZIKV)." }, { "scheme": "NCBI RefSeq", "value_or_pattern": "NC_012532", "note": "Complete genome reference sequence." }, { "scheme": "ICD-10 / ICD-10-CM", "value_or_pattern": "A92.5", "note": "Codes Zika virus disease, not the virus as a taxon." }, { "scheme": "ICD-11", "value_or_pattern": "1D49", "note": "Zika virus disease." }, { "scheme": "MeSH", "value_or_pattern": "D000071243", "note": "Zika Virus (D000071244 is Zika Virus Infection)." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of Zika virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "International Health Regulations (2005): Zika virus disease was a WHO Public Health Emergency of International Concern, 1 February-18 November 2016 - World Health Organization", "Surveillance case definitions for Zika virus disease and congenital Zika virus infection - World Health Organization; PAHO in the Americas", "Nationally notifiable Zika virus disease and congenital infection case definitions - CDC / Council of State and Territorial Epidemiologists (United States)", "Laboratory testing for Zika virus infection (interim guidance) and the CDC Trioplex rRT-PCR / IgM-plus-PRNT diagnostic algorithm - WHO and CDC", "Blood and tissue donor screening and travel-related deferral during and after the Americas outbreak - U.S. Food and Drug Administration", "Biosafety in Microbiological and Biomedical Laboratories: routine diagnostic work typically at BSL-2 - CDC / NIH", "IATA Dangerous Goods Regulations for shipping diagnostic specimens (typically UN 3373, Category B) - International Air Transport Association" ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of Zika virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Public-health arbovirus surveillance: human case reporting, pregnancy registries, and Aedes mosquito pool testing in endemic and outbreak settings.", "Travel medicine: advising pregnant people and other travellers during and after outbreaks, historically including delayed conception guidance.", "Prenatal and neonatal work-up when maternal infection is suspected (ultrasound, neonatal head circumference, neuroimaging, ophthalmology).", "Front-line differential diagnosis of acute fever, rash, and arthralgia alongside dengue and chikungunya, using rRT-PCR on serum/urine and flavivirus serology.", "Blood-product and tissue-donation risk management during epidemic transmission.", "Countermeasure research: inactivated, live-attenuated, and nucleic-acid vaccine candidates and diagnostic EUA-style assays after 2015-16." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of Zika virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "quantity": "Genome length", "typical_range": "10.7-10.8 (often ~10794 nt)", "unit": "kb" }, { "quantity": "Virion diameter", "typical_range": "40-50", "unit": "nm" }, { "quantity": "Incubation period", "typical_range": "3-14", "unit": "days" }, { "quantity": "Duration of acute illness", "typical_range": "2-7", "unit": "days" }, { "quantity": "Asymptomatic infections", "typical_range": "~80 (Yap Island outbreak estimate)", "unit": "%" }, { "quantity": "Serum RNA detection window after symptom onset", "typical_range": "typically 0-7 (urine often a few days longer)", "unit": "days" }, { "quantity": "Zika-associated birth defects among completed pregnancies with confirmed infection", "typical_range": "about 5-10 overall; higher with first-trimester infection in U.S. pregnancy-registry analyses", "unit": "%" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of Zika virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Congenital Zika syndrome: microcephaly, intracranial calcifications, ocular lesions, arthrogryposis, and fetal loss after infection in pregnancy.", "Guillain-Barré syndrome after infection, first strongly linked in French Polynesia (2013-14) and later in the Americas.", "Sexual transmission and prolonged RNA shedding in semen, which vector-control programmes do not stop.", "Transfusion and laboratory exposure risk during high-incidence outbreaks.", "False-positive or uninterpretable IgM because of cross-reaction with dengue, yellow fever vaccine, and other flaviviruses.", "Silent spread: most infections are asymptomatic, so case-based control undercounts transmission.", "Co-circulation with dengue and chikungunya, which confounds both clinical recognition and serosurveys." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of Zika virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ "Africa: African lineage, sylvatic Aedes cycles (e.g. Aedes africanus), historically little documented congenital syndrome - whether from lineage, immunity, or under-ascertainment is unsettled.", "Yap (2007) and French Polynesia (2013-14): first large Asian-lineage outbreaks; French Polynesia made the Guillain-Barré association clinically obvious.", "Brazil and the wider Americas (2015-16): urban Aedes aegypti epidemic, Asian-lineage American clade, and the recognition of congenital microcephaly (Brazilian clinical discourse often used 'microcefalia' and 'vírus Zika').", "Continental United States: almost entirely travel-associated cases plus limited local Aedes transmission in southern Florida and Texas, versus intense transmission in Puerto Rico and other territories.", "South and Southeast Asia: Asian lineage with endemic/sporadic detection and less explosive reported congenital clusters than in the naive Americas." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of Zika virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Reported by the breadth pass; each item needs checking against its source before it becomes normative.", "evidence": [ { "name": "Dengue virus", "difference": "Virus-specific rRT-PCR (or a multiplex such as CDC Trioplex) in the first week; IgM is unreliable. Plaque-reduction neutralization with a ≥4-fold higher titer to one virus supports identification; comparable titers are reported as unspecified flavivirus. Dengue NS1 antigen positivity points to dengue, not Zika." }, { "name": "Chikungunya virus", "difference": "CHIKV is an alphavirus (Togaviridae), not a flavivirus; multiplex RT-PCR separates them. Clinically, chikungunya more often causes severe, prolonged arthralgia; serology does not cross-react as flaviviruses do." }, { "name": "Spondweni virus", "difference": "Closest known orthoflavivirus relative and historically the same serogroup; IgM/PRNT can misclassify. Nucleotide sequencing or a well-validated virus-specific RT-PCR is the discriminator." }, { "name": "Yellow fever virus", "difference": "YF is typically a viscerotropic, jaundicing illness; Zika is not. Separate by YFV-specific RT-PCR, vaccination history, and PRNT interpreted against the full flavivirus panel." }, { "name": "Congenital cytomegalovirus (and other TORCH agents)", "difference": "For neonatal microcephaly, CMV is confirmed by CMV PCR of saliva or urine in the first 21 days of life. CZS more often shows a fetal brain-disruption pattern with calcifications at the grey-white junction; maternal/infant Zika rRT-PCR or IgM plus neuroimaging separate the two." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of Zika virus this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which current taxonomic authority, reference accessions and variant vocabulary should anchor Zika identity, and does an existing world model already own this concept?", "Which assay- and specimen-specific evidence rules should govern Zika attribution across differing prior flavivirus exposures?", "What evidence supports the duration of infectiousness in each relevant compartment, and where are only RNA-persistence observations available?", "How precisely can congenital and neurological risks be qualified by infection timing, population and study uncertainty?", "Which maintained jurisdictional and institutional sources should govern transmission classifications, prevention guidance and material-handling decisions?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 28 } }