virus
(virology) ultramicroscopic infectious agent that replicates itself only within cells of living hosts; many are pathogenic; a piece of nucleic acid (DNA or RNA) wrapped in a thin coat of protein
Research draft, second pass
A second pass drafted this model: the structure a model of this thing needs, and what is known about it in the world. The line under this one says how the second half was obtained - researched against sources, or recalled without web access, in which case nothing here was read anywhere and every claim is a lead to verify. Unreviewed either way.
recalled by Codex without web access - no source was read
Researched by: Codex
Purpose and description
Enable an agent to recognise a virus, distinguish its biological identity from a particle or detection result, assess its evidenced state, and determine appropriate handling or referral.
A virus is an acellular infectious entity with a DNA or RNA genome that replicates through host-cell machinery and typically produces genome-containing particles called virions, whose protein capsid may be surrounded by a lipid envelope.
It can be Resolve a viral name or sequence assignment against a dated taxonomic authority.; Compare isolates using genome and particle evidence while preserving uncertainty.; Assess whether observations support exposure, infection or productive replication in a host.; Interpret detection and abundance results within the limits of their assays.; Track persistence or inactivation evidence under documented conditions.; Refer handling, transport or disposal decisions to applicable reviewed requirements..
Distinguishing features
Separate the biological virus from a computer virus by requiring a biological host and a nucleic-acid-based infection context.
Distinguish a virus from a cellular microorganism by examining cellular organisation and whether replication depends on infection of host cells.
Distinguish a virus from a prion by establishing a viral nucleic acid genome rather than protein-only propagation.
Distinguish a virus from a viroid by examining genome identity and encoded viral functions, including any particle-forming proteins; absence of an observed capsid alone does not settle the boundary.
Distinguish an infectious virus from an isolated genome fragment, antigen or virus-like particle by recording what evidence supports identity and what separately supports infectivity.
Scope
+ Distinction between viral taxon, lineage, isolate, population and individual virion
+ Genome organisation and relationships between genome, capsid and any envelope
+ Host range, cellular susceptibility and dependence on host replication machinery
+ Infection, replication, persistence and extracellular particle states
+ Evidence of viral presence, identity, infectivity and applicable handling constraints
- The host organism and its complete physiology
- The disease or syndrome associated with infection
- Viroids, prions and other neighbouring infectious entities as independent models
- Diagnostic instruments, assay products and laboratory procedures
- Vaccines, antiviral medicines and treatment decisions
- Computer viruses and other malicious software
Characteristics
- Entity level
- taxon | lineage | isolate | population | virion | unresolved Prevents properties of a taxon from being assigned automatically to a particular particle or sample.
- Taxonomic assignment
- taxon name and identifier, authority, release or date, assignment evidence and confidence Makes identity traceable when names and classifications change.
- Genome organisation
- DNA or RNA; strandedness; polarity where applicable; topology; segment count; unknown Supports identification and distinguishes genome organisation from the mechanism used to replicate it.
- Genome length
- nt for single-stranded sequence or bp for double-stranded genome; per-segment and total lengths with completeness Allows sequence comparisons without treating an incomplete assembly as a complete genome.
- Particle organisation
- capsid architecture, envelope status, particle form, absent where established, or unresolved Separates observed particle properties from assumptions based on the registry definition.
- Supported host and tissue range
- host taxon, tissue or cell type, exposure or infection evidence, productive replication evidence, conditions Detection in a host does not by itself establish that the host supports replication.
- Biological state
- extracellular particle | intracellular replication | persistent infection | latent state where applicable | inactivated | unresolved Identifies which actions and interpretations are relevant to the entity being assessed.
- Measured viral abundance
- genome copies, particle counts or assay-specific infectious units per stated quantity of material Keeps molecular abundance, particle abundance and infectious titre distinct.
- Infectivity assessment
- demonstrated | not detected under stated conditions | not assessed | indeterminate Prevents a positive molecular result or a negative infectivity assay from supporting an unrestricted conclusion.
Analytical facets
- substance
- living
- origin
- natural
- agency
- inert
- mobility
- not-applicable
- scale
- not-applicable
- affordances
- observable
Also called
+44
Where this came from
oewn:2024 · CC BY 4.0
Drafted structure
Bundle to layer to finding to question, as the second pass will find it: 6 bundles · 11 layers · 19 findings · 29 questions.
Viral identity and boundaries Establish what viral entity is being represented and how its identity is supported.
The same viral name can refer to a taxon, an isolate or a particle, each supporting different assertions.
Entity and taxonomy
Separate the represented entity from its classification.
Dated identity assignment
Record entity level, accepted assignment, aliases and the authority used without implying that every virus has a species-level identification.
- Does this record represent a taxon, lineage, isolate, population or individual virion? definition
- Which authority, release and underlying evidence support the name and taxonomic assignment? provenance
Neighbouring biological entities
Resolve boundaries with other infectious agents and virus-derived material.
Virus versus associated material
Require an explicit basis for distinguishing a virus from a viroid, prion, cellular organism, endogenous viral sequence or noninfectious particle.
- What evidence places this entity within the viral concept rather than a neighbouring infectious-agent category? boundary
- Is the observed material a virus, a viral component or a host-associated sequence whose relationship to an active virus remains unresolved? boundary
Genome and particle organisation Describe the viral genome and its relationship to any physical infectious particle.
Viral identity and state require distinctions between sequence, genome complement and particle architecture.
Genome architecture
Represent genome composition and completeness without substituting a sequence fragment for the entire genome.
Genome complement
Capture nucleic acid type, strandedness, polarity where relevant, topology, segments and uncertainty about completeness.
- What genome type, topology and segment organisation are supported for this virus? definition
- What lengths were measured, in which units, and does the evidence establish a complete genome complement? measurement
Particle architecture
Connect structural observations to the particles actually examined.
Observed virion structure
Record capsid, envelope, morphology and genome packaging as evidenced properties, allowing exceptional or unresolved cases.
- Which capsid, envelope and particle-form observations are directly supported, and by what methods? provenance
- Does a particle contain the complete required genome complement, only part of it, or no demonstrated viral genome? boundary
Host dependence and infection Represent the relationship between a virus, susceptible hosts and intracellular infection states.
Host association, cell entry and successful replication are distinct claims that must not be collapsed.
Host range and tropism
Qualify host and tissue associations by the kind of evidence available.
Supported host relationship
Distinguish exposure or detection from entry, infection and production of infectious progeny.
- Which host taxa and cell or tissue types support infection, and which are merely associated with detection? boundary
- What evidence supports these relationships in natural hosts versus experimental systems? provenance
Replication and persistence states
Represent supported infection states and dependencies without assuming one universal viral life cycle.
State and required dependencies
Identify the evidenced infection state and any established host, helper-virus or integration dependencies.
- What observations distinguish productive replication, abortive infection, persistence or latency in this case? measurement
- Which host functions or helper entities are required, and is integration part of this virus's supported biology? definition
Transmission and environmental fate Connect movement between hosts and environmental conditions to evidence of retained infectivity.
Viral material can persist or move without establishing an infectious transmission route.
Transmission relationships
Distinguish supported transmission pathways from incidental carriage or environmental detection.
Evidenced transmission route
Record source host, recipient host, route and any reservoir or vector role with separate supporting evidence.
- Which routes have evidence of transmission to a susceptible host rather than movement of viral material alone? provenance
- What establishes an associated organism as a reservoir or vector rather than an incidental carrier? boundary
Persistence and inactivation
Qualify survival and inactivation observations by material, conditions, duration and endpoint.
Condition-specific infectivity
Separate retained molecular detectability from retained infectivity under documented conditions.
- Under what matrix, environmental conditions and elapsed time was residual infectivity assessed? measurement
- Which reviewed evidence supports an inactivation decision for the relevant material and intended use? action
Detection evidence and decisions Define what measurements justify and which decisions require further evidence or specialist review.
Sequence detection, infectious titre and disease association answer different questions and support different actions.
Assay interpretation
Bind each result to its target, sample context, method and limitations.
Presence, abundance and infectivity
Keep genome copies, antigens, particle counts and infectious units distinct and preserve assay-specific uncertainty.
- What did the assay measure, in which sample and units, and with what detection limits and controls? measurement
- Does the result support viral presence, identity, infectivity or disease causation, and where does that inference stop? boundary
Handling and referral
Link decisions to identified material, intended activity and applicable requirements.
Evidence-bounded action
Record the basis for handling, transport, disposal or referral decisions without inferring requirements from the word virus alone.
- Which current institutional or jurisdictional requirements apply to this identified material and proposed activity? provenance
- What unresolved identity, infectivity or host-risk evidence requires specialist review before the proposed action? action
Evidence and external alignment What the world already says about this thing, gathered so the model can be checked against it.
A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.
Reported evidence
Findings from the breadth pass, kept separate from the structural claims.
Check these first
Recalled without web access and unsourced; every item is a lead to verify.
- Virus is a broad category, not a species: no single binomial, geographic range or conservation assessment applies, and its placement among living things is conceptually contested.
- The six kinds summarize genome and replication distinctions; the Baltimore classification separates reverse-transcribing viruses into two groups, giving seven groups overall.
- This is recalled knowledge, not source-verified research; verify current ICTV names and virus-specific measurements or regulatory requirements before publication.
- Which of these check these first hold for the sense of virus this model covers, and on what evidence? provenance
Kinds and varieties
Recalled without web access and unsourced; every item is a lead to verify.
- Double-stranded DNA viruses
- Single-stranded DNA viruses
- Double-stranded RNA viruses
- Positive-sense single-stranded RNA viruses
- Negative-sense single-stranded RNA viruses
- Reverse-transcribing viruses, including RNA-genome and DNA-genome groups
- Which of these kinds and varieties hold for the sense of virus this model covers, and on what evidence? provenance
Identifiers and schemes
Recalled without web access and unsourced; every item is a lead to verify.
- NCBI Taxonomy - 10239 - The broad Viruses node; individual viral taxa have their own taxonomy identifiers.
- ICTV taxon names - Species names are binomials consisting of a genus name and a species epithet. - Species names identify taxa, not individual virions, isolates or strains; common virus names are distinct from formal species names.
- INSDC sequence accession - Accession identifier with an optional sequence-version suffix - Identifies a deposited nucleotide sequence through GenBank, ENA or DDBJ, rather than a virus species.
- Which of these identifiers and schemes hold for the sense of virus this model covers, and on what evidence? provenance
Standards and regulation
Recalled without web access and unsourced; every item is a lead to verify.
- International Code of Virus Classification and Nomenclature, issued by the International Committee on Taxonomy of Viruses (ICTV).
- Which of these standards and regulation hold for the sense of virus this model covers, and on what evidence? provenance
Real-world use
Recalled without web access and unsourced; every item is a lead to verify.
- Viral vectors deliver genetic material in research and gene therapy.
- Bacteriophages are used in bacterial research and selected antibacterial applications.
- Modified or inactivated viruses serve as vaccine components.
- Oncolytic viruses are used in selected cancer treatments.
- Viruses provide experimental systems for studying replication, evolution and host defence.
- Which of these real-world use hold for the sense of virus this model covers, and on what evidence? provenance
Typical measurements
Recalled without web access and unsourced; every item is a lead to verify.
- Virion diameter - Approximately 20-300 for many viruses; giant and filamentous forms fall outside this range. - nm
- Infectious titre - Depends on the virus, sample, host cells and assay; no universal typical range. - plaque-forming units per mL
- Genome concentration - Sample-dependent; genome counts do not directly establish infectivity. - genome copies per mL
- Which of these typical measurements hold for the sense of virus this model covers, and on what evidence? provenance
Failure modes and hazards
Recalled without web access and unsourced; every item is a lead to verify.
- Some viruses cause disease in humans, other animals, plants or microorganisms; infection does not necessarily cause disease.
- Host switching and transmission can produce outbreaks when suitable biological and ecological conditions coincide.
- Mutation, recombination or reassortment can alter viral properties; reassortment requires compatible segmented genomes.
- Persistent or latent infections can evade clearance, and some can reactivate.
- Certain viruses contribute to cancer through persistent infection or disruption of cellular regulation.
- Which of these failure modes and hazards hold for the sense of virus this model covers, and on what evidence? provenance
Regional variation
Recalled without web access and unsourced; every item is a lead to verify.
- Distribution and transmission vary with host and vector ranges, climate, population immunity and contact patterns.
- Biosafety, transport and reporting requirements vary by jurisdiction and by the particular virus.
- Which of these regional variation hold for the sense of virus this model covers, and on what evidence? provenance
Neighbouring kinds and how to tell them apart
Recalled without web access and unsourced; every item is a lead to verify.
- virion - A virion is a virus particle; virus also refers to the biological entity across its intracellular replication cycle.
- bacterium - A bacterium is a cell with ribosomes and cellular organisation; a virus lacks its own ribosomes and depends on host-cell translation.
- viroid - A viroid is a small infectious RNA that does not encode proteins or form a virus-like protein capsid.
- prion - A prion propagates an infectious protein conformation without a nucleic-acid genome.
- viral disease - A viral disease is a pathological consequence of infection, not the infectious entity itself.
- virus species - A virus species is a taxonomic category encompassing related viruses, not an individual particle or infection.
- Which of these neighbouring kinds and how to tell them apart hold for the sense of virus this model covers, and on what evidence? provenance
What the second pass must settle
- How should the registry definition accommodate recognised viruses without a conventional extracellular protein-coated particle?
- Where should the model draw researched boundaries around satellite viruses, defective viral entities and endogenous viral elements?
- Which taxonomic authority and release should anchor classification, and how should unclassified sequence-based candidates be represented?
- What evidence thresholds should distinguish host association, productive infection, reservoir status and demonstrated transmission across different host groups?
- Which assay-specific and context-specific evidence is sufficient for an infectivity or inactivation decision without overstating a negative result?