Virology

• What is a virus?

  Obligate intracellular parasite

  Needs a host cell to survive

  Lacks organelles – no nucleus, mitochondria, ribosomes etc

  Extremely small filterable agents − Range from 18 – 230 nm

  Need electron microscope to visualise

  Some viruses can remain viable in the environment for a long time e.g. months but they cannot replicate outside of the cell

  Viruses are much smaller than bacteria and parasites/protozoa

   
• Virus Nomenclature:

  Family name= End in –viridae

  Genus name= Ends in –virus

  Virus species = A group of viruses sharing the same genetic information and ecological niche

  Can be further divided into types and subtypes

  E.g. Rhabdoviridae, Lyssavirus, Rabies Lyssavirus
• Some ds and ss RNA can be segmented

  more than 1 molecule of genomic material, so rather than having all the RNA encoded onto one molecule, it’s on multiple.

  Allows the virus to increase its genetic capacity as RNA is typically fragile.

  As size of RNA gets bigger it may become more susceptible to degradation but If the genetic information is then on several smaller segments, the chances of the virus keeping those smaller segments intact is greater. It allows viruses to increase their genome size so they can code for more proteins without the risk of their genomic information becoming degraded.
• Some ds DNA viruses can be circular. Even those that are linear have mechanisms to make them adopt a circular configuration as this is important for replication.
• All DNA viruses are monopartite (all viral genes on a single segment)
• DNA viruses are all mostly DS
• there's little diversity in structure with the DNA viruses
• most RNA viruses are SS
• SS RNA viruses can either have a positive or negative sense
• all DS RNA viruses are segmented
• Segmentation of RNA viruses

  Allows virus to increase its diversity very rapidly (reassortment)
• all viruses have a capsid
• Icosahedral Capsid (Parvoviridae and Adenoviridae)

  Twelve vertices

  20 triangular sides (facets)

  Composed of capsomers (basic structural building block of the capsid)

  penton capsomers (5)

  hexon capsomers (6)
• Penton capsomers (5)

  • Found at the vertex (pointy bits/corners?) of the capsid
  • 12 present – one at each vertex
  • Has 5 neighbouring capsomers

  Hexon capsomers (6)

  • Has 6 neighbouring capsomers
  • Number present in capsid varies depending on size
  • Found in spaces between the penton capsomers

  
• most viruses with a Icosahedral Capsid structure do not have an envelope
• Biological Properties of Viruses:

  Can vary depending on

  Whether the virus has an envelope

  Structure and composition of its genomic material (RNA viruses are more variable than DNA)
• Genome composition of a virus affects its biological properties

  DNA viruses are more stable, show very little variation

  RNA viruses are more variable

  RNA polymerase is error prone and has no proof reading

  Can adapt easily to new environments (jump species/zoonotic)

  Some RNA viruses are segmented and so can reassort or swap genes (cover this in more detail in the sessions on influenza viruses)
• Virus Envelope proteins

  Contain receptors that allows the virus to attach and then enter the host cell

  Are targets of the humoral and cellular immune response

  Antibodies will recognise these surface exposed viral proteins

  Interact with the capsid during virus assembly
• Non-Structural Viral Proteins

  Are not structural components of the virus particle

  Made in the virus-infected cell following infection:

  Often enzymes involved in viral replication

  Proteases

  Helicases

  Polymerase (can be a structural protein!)

  Protein primers for nucleic acid replication

  Can be proteins that help the virus avoid the host immune response

  Targets of the host cellular response (T cell epitopes)
• Naked viruses can be transmitted inside vesicles (so sometimes have an envelope!):

  • Some RNA viruses can be transmitted as virus clusters inside vesicles
  • Rotavirus and noroviruses are transmitted as clusters
  • Vesicles remain intact (?) and they pass through the GI tract to the intestines
  • vesicles are used to transmit the naked viruses from one one host to another
• Entry of Herpes Simplex Virus - Cell membrane fusion

  • An enveloped virus
  • Initial binding glycoprotein B or glycoprotein C to heparin sulphate (a complex carbohydrate expressed on the surface of many cell types)
  • Attachment of glycoprotein D to
  • HveA (lymphocytes, epithelial cells, fibroblasts)
  • Nectin 1 & 2 (neurons, epithelial cells, fibroblasts)
  • Fusion of the viral envelope with cell membrane
  • Uses multiple types of spike glycoproteins to bind and enter different types of cells

  
• Entry of Human Immunodeficiency Virus - Cell membrane fusion

  • Binding of HIV gp120 (HIV Spike protein) to CD4+ T cells
  • Induces conformational change in gp120
  • Enables binding of gp120 to CCR5 or CXCR4
  • Causes the gp120 trimer to break apart
  • Allows gp41 to be pulled towards the cell membrane
  • Fusion of gp41 with cell membrane
  • Releases nucleocapsid into the cytoplasm
  • Nucleocapsids are targeted to nucleus

  
• Entry of influenza virus - Receptor mediated endocytosis

  • Binding of haemagglutinin (HA) to sialic acid receptor
  • Internalisation in clathrin coated pit
  • Movement into endocytotic vacuole which fuse with lysosomes
  • Low pH triggers conformational change in HA trimer
  • Exposes fusion domain which allows fusion of viral membrane and endosome membrane
  • Release of nucleocapsids into cytoplasm

  
• Uncoating

  • Release of viral nucleic acid from viral capsid
  • Process is variable: For some viruses
  • nucleic acids may still be in a nucleoprotein complex
  • the capsid is only partially disintegrated

  
• Routes of Virus Entry and Mechanisms of Spread:

  Must overcome innate defences to enter body

  Both physical & immunological

  Many viruses enter via mucosal surfaces

  Different viruses adopt different strategies

  Some viruses may use several entry routes

  e.g. Foot and Mouth Disease Virus inhaled (most common) or ingested

  Entry route may differ in different host species

  e.g. Influenza: Faecal-oral in wild birds and respiratory in humans
• How do viruses enter the body & initiate infections?

  Skin

  Respiratory tract

  Alimentary tract (GI tract)

  Urogenital tract

  Eye

  Viruses attach to cells at these locations by attaching to receptor molecules on certain cells
• Mechanisms of Spread

  Some viruses remain localised at the site of infection

  Influenza virus in the respiratory tract

  Rotavirus in the alimentary tract

  Replication occurs in epithelium at initial infection site.

  Cell-to-cell spread occurs, but virus does not disseminate to other tissues

  Usually acute (short incubation period, short duration)

  Site of shedding = site of entry
• Respiratory Tract - Defences

  • Specialised ciliated epithelium & mucus: MUCOCILIARY ESCALATOR (in Upper Respiratory Tract (URT) and bronchi)
  • Filters out large particles (particles <5uM can enter terminal airways and alveolar)
  • Sneezing & coughing
  • Innate immunological defences (e.g. alveolar macrophages, complement, cytokines, natural killer cells)
• Respiratory Tract - Virus entry

  Via aerosolized droplets expelled by an infected individual

  Spread by coughing or sneezing

  Contact with saliva from an infected individual
• Examples of viruses entering via respiratory route

  Influenza

  Foot and Mouth Disease Virus

  Rhinovirus (common cold)
• Gastrointestinal (GI) Tract - Defences

  Low pH in stomach (Denatures protein and kills most microorganisms)

  Bile and proteolytic enzymes in intestines

  High pH in the duodenum (rapid change)

  Mucous
• Gastrointestinal (GI) Tract - Virus Entry + examples

  Oral route (ingestion)

  Examples of viruses entering via the GI tract

  Rotavirus

  Norovirus
• Spread via blood stream (Viraemia) to other tissues

  Some viruses can spread to distant sites

  Virus reaches blood via lymphatic system

  Primary viraemia (clinically silent – increases virus levels allowing infection of distant organs)

  Secondary viraemia (virus replication in other organs leads to high concentrations of virus in circulation)

  Infection spreads to more sites

  Allows entry and exit routes from host to differ

  Usually have longer incubation period (more severe pathology)

  Greater involvement of adaptive immune responses and IgG
• Spread via the Central Nervous System (CNS)

  Entry: Bite of a rabid animal or contamination of scratch wounds by virus-infected saliva.

  Rabies replicate in peripheral tissues (striated or connective tissue) at site of infection

  Can remain at site of infection for days/weeks or longer

  Virus enters peripheral nerves. (Infects unmyelinated nerve endings in muscle)

  Spreads to CNS and enters brain (causes behaviour changes)

  Migrates to salivary glands (replicates) and excreted in saliva

  No viraemia

  Also allows rabies to evade immune system
• Virus Tropism

  Specificity of a virus for a particular host, tissue or cell

  Determines the host range of virus

  For virus infection to occur, the cell must be:

  Susceptible

  Appropriate cell surface receptors for entry (susceptibility)

  Permissive

  Able to support replication of the virus

  May need particular cellular proteins to complete infection

  May need to be in a particular cell type

  E.g. Canine parvovirus needs rapidly dividing cells
• Virus Tropism

  
• Factors affecting Tropism

  Not just receptors that determine tropism

  Cells need to be susceptible (able to support replication of the virus)

  Other factors that can determine tropism:

  Cellular protease can activate fusion

  Protease cleavage by digestive enzymes

  Temperature of replication

  pH Lability of viruses

  Anatomical Barriers
• Cellular protease can activate fusion

  • Some enveloped viruses require proteolytic cleavage of envelope glycoprotein for activation of fusion domain
  • Fusion of the two membranes (which is needed for cell entry) is dependent on cleavage by specific proteases, if the cell in the endosome doesn't have those proteases, then we're not going to get a effective infection, as without the proteases, the virus gets trapped in the endosome and will be degraded within that cell
• Protease cleavage by digestive enzymes

  Reoviruses are activated into infectious virions by cleavage with digestive enzymes

  Cleavage of VP4 spike to form VP8 and VP5

  Conformational change permitting virus to bind to M cells in the gut

  retroviruses need this proteolytic cleavage to generate their receptors
• Temperature of replication

  Some viruses are temperature sensitive, even if they can get into the cells, if the temperature is not right for them, they're not going to replicate

  Most human viruses replicate at 37°C

  Upper respiratory tract has a lower temp – about 33°C

  Rhinoviruses replicate efficiently at 33°C but poorly at 37°C

  This limits their ability to spread beyond the upper respiratory tract