Basics Flashcards
Characteristics virus (vs bacteria)
Intracellular parasite, needs cell to replicate.
Others: size, cellular machinery, plasma membrane.
Virus genome
Nucleic acid.
Variable size, haploid (except Retroviruses), DNA/RNA, +/-, ss/ds, linear/circular segmented
Capsid
Protects genome.
Helical/icosahedral/complex shape.
For naked (no envelope) viruses relevant for entry (eg Papilloma virus)
Envelope/membrane
Optional. Lipid bilayer derived from host cell > contains cellular and viral proteins (incl glycoproteins mediating binding and host cell entry)
Def. virion, surface protein, nucleocapsid, structural proteins.
Virion = virus particle
Surface proteins = glyco-/envelope/membrane protein
Neucleocapsid = capsid + genome (inside particle)
Strucutral proteins = viral proteins present within virions
(non-str.: expressed in infected cell, not contributing to particle structure
Virus replication
- Attachment and entry
- Uncoating (>release of genome)
- Gene expression and genome replication
- Assembly and release (from infected cel)
Classification
Viruses can be classified according to their components (classical approach).
Alternative approach: Baltimore system (focus on generation of mRNA).
Determinants of viral sensitivity to disinfectants
Presence of envelope is associated with increased sensitivity to disinfectants
Under which conditions will bacteria/virus replicate?
Virus: cells in culture
Bacteria: LB medium
2 Types of transmission
- Horizontal (between members of same species, not in parent-child relationship)
- Vertical (transmission from mother to child)
Types of horizontal transmission + ex
Parenteral (blood) - eg HIV Fecal oral (feces) - HepA Droplets - Influenza Vectors - FSME Organ transplantation - CMV
Types of vertical transmission
In utero
Intrapartum (perinatal)
Breast milk (postnatal)
eg HIV
Portals of entry
Mucosal tissue
Skin
Blood
Acute vs persistent infection
Acute: Immune system clears virus (or host dies) (eg Influenza)
Persistent: immune evasion, virus replication continues despite immune response (eg HIV)
Persistent vs latent
Persistent: viral replication can be detected at each time point (HIV)
Latent: phases without viral replication and phases of reactivation of viral replication (Herpes)
Primary vs permanent cell culture
Primary: generated directly from tissue, contain, several types, divide about 20 times
Permanent: cells are immortalized, divide continuously, generate from primary cultures by treatment with mutagenic agent/tumor viruses, adherent or suspension culture
Cytophathic effect (CPE), ex
Changes in cell morphology, to some degree virus-specific.
Smaller nucleus > Picorna
Syncytia > Corona
Rounding/detachment > Rhabdo
Neutralizing ab can block CPE development.
Plaque test
- seed adherent cells
- inoculate cell monolayers with diff dilution of viruses
- remove excess viruses, cover cells with agar
- Dye for visualization
Each hole (plaque) from one infectious unit (PFU)
PFU, MOI
PFU: plaque-forming units (PFU/ml)
MOI: multiplicity of infection (PFU/cell)
Diagnostics - options
Detection of viral material: PCR, ELISA, EM
Detection of ab: ELISA; Complement binding reaction, neutraliztation test, Western Blot
EM characteristics
Rapidly detect infectious agents. High particle conc required. Particle visualization with heavy metals
Neutralisation test
Neutralising ab bind GP > prevent entry.
Plaque assay: at which dilution is plasma able to prevent appearance of plaques?
Entry of non-enveloped viruses
Pore formation:
Receptor binding > conformational changes in coat protein, endocytosis > pore formation > genome release
(eg Polio)
Entry of enveloped viruses
Membrane fusion. Mediated by GPs.
Diff classes:
1 (Retrov.), 2 (Alphav.) 3 (Rhabdov.)
Porcesses: Priming, triggering
Priming
Membrane fusion proteins (GPs) must be primed: sythesis as inactive precursors > cleavage by host cell protease
eg Inluenza hemagglutinin
prevents premature triggering
Triggers of membrane fusion - ex
Receptor binding triggers membrane fusion (eg Avian retroviruses)
Internalization into endosome > low pH triggers fusion (eg Influenza)
Replication in DNA viruses
Transcription and replication interconnected. Early phase (E): enzymes for genome replication, negative autoregulation, synthesis of transactivators for L phase. Late phase (L): produciton of structural proteins
Replicaiton requires on origin and priming.
Modes of DNA replication initiation
RNA primin (Polyomav.) Protein priming (Adenov.) Hairpin priming (Parvov.)
RNA viruses - initiation of translation
Cap-dependent
Assembly of 40S ribosome + initiation factors
Scan for AUG (start codon)
Picronavirus RNA
Not capped. Ribosomes bind via IRES (internal ribosomal entry sites at 5’UTR).
Coding strategy of Picornaviridae
Encode for one bif precusor (poly)protein > processed by viral proteases
Rhabdoviridae transcription
RdRP (pol) binds to terminal leader sequence > transcription starts at intergenic regions > mRNA expression levels correlate with position in genome
Packaging of nucleic acids
Simple: condensation of protein shell around nucleic acid (+RNA v.)
Complex: preformatino of capsid eg via scaffold then packaging of nucleic acid (eg DNA v.)
Packaging signals required.
Virus release strategies
- Cell lysis (naked viruses)
2. Budding (enveloped viruses
Sites of budding
Viruses can use different cellular compartments: cell membrane, rER, Golgi, intermediate compartment
ESCRT proteins
Facilitate membrane fission and particle release.
Maturation
Transit of precursor proteins in their functional forms by proteolytic processing.
Required for infectivity.
