Virology Chapter Overview

General Characteristics of Viruses

• Viruses are obligate intracellular parasites
• They lack the ability to generate energy, or synthesize proteins and replicate independently of the host cell
• They are small, less than 300 nanometers in size

Viral Structure

• A virion (viral particle) consists of:
  • Nucleic acid (either DNA or RNA, but not both). The genome.
  • A protein shell, the capsid.
  • An envelope (in some viruses).
  • Enzymes or other proteins essential for replication.

Viral Structure (capsid)

• The capsid is a rigid protein structure

• Individual proteins form successively larger units: protomers, capsomers and finally the complete capsid

• Some capsids are:

  • symmetric (helical or polyhedral), and are built stepwise
  • nonsymmetric (complex). These structures are associated with bacteriophages.

• An envelope is an external coating to the capsid composed of lipids and glycoproteins

  • The lipid portion of the envelope is derived from the host cell membrane. Specifically the infected cell.
  • Viral proteins are inserted into the lipid layer
  • The tegument/ matrix is situated between the inner face of the envelope and the nucleocapsid. It is composed of viral proteins

Viral Replication

• The replication cycle depends on the host cell; the host cell functions as a factory
  • The cell provides substrates, energy and machinery needed for viral protein synthesis and genome replication
• Viral infections occur with susceptible and permissive cells
  • Susceptible cells have specific receptors for a given virus, not necessarily permissive
  • Permissive cells have the capacity to replicate the virus, not necessarily susceptible
• Infections can be:
  • Productive (both susceptible and permissive)
  • Abortive (susceptible but non-permissive)
  • Restrictive (susceptible but semi-permissive - inefficient replication)
  • Latent (susceptible and permissive, but the viral genome is silent in the host cell- with possible reactivation)

Diagram of the Infectious Cycle

• The major steps in viral replication are the same for all viruses
  • Attachment
  • Penetration
  • Uncoating
  • Replication
  • Assembly
  • Release

Steps in Viral Replication

• Recognition of a target cell
• Attachment
• Penetration (non-enveloped, enveloped)
• Uncoating
• Macromolecular synthesis (Early mRNA, replication of genome, Later mRNA, and protein synthesis),
• Assembly
• Release (Budding, lysis)

Viral Replication (Steps 1-2)

• Initial contact is a random collision
• Efficient attack requires anti-receptor on the virion and its corresponding receptor (and co-receptor) on the host cell membrane
• Receptor binding determines host range and tissue tropism (the specific cells that the virus can infect)
  • Anti-receptors are capsid proteins in naked viruses, glycoproteins in enveloped

HIV Entry in the Host Cell

• HIV attaches to either CD4 or CCR5 (or CXCR4 ) on the host cell

Viral Replication (Step 3: Penetration)

• Non-enveloped viruses may penetrate the plasma membrane directly
• Enveloped viruses fuse their membranes to cell membranes, delivering the nucleocapsid directly into the cytoplasm or through receptor-mediated endocytosis, and fusion in the endosome.

Viral Replication (Step 4: Uncoating)

• Uncoating is a stepwise process to release the genome from the capsid.
• The specifics of uncoating vary per virus and are not fully understood.

Viral Replication (Step 5: Macromolecular Synthesis)

• The replication phase of the genome (by cellular or viral enzymes). There are many strategies
• Transcription to mRNA and virus protein synthesis (structural and non-structural). Viral proteins are synthesized

Viral Replicative Strategies (Baltimore system)

• Viruses have different genome configurations (ss (+) RNA or ss (-) RNA, Double Stranded RNA, etc etc) which affect replication. The diagram shows a classification of viruses by the replication mechanisms.

Viral Replication (Step 6: Assembly)

• New viral particles are assembled from genome copies and viral proteins
• Capsomers interact to create the full capsid. (helical, icosahedral)
• Some viruses assemble the capsid around their genome. Other virus first assemble an empty capsid.

Viral Replication (Step 7: Exit/Release)

• Cytolysis, the virions accumulate, forming clusters and are released by the bursting of the host cell - Budding— Enveloped virions escape through cellular membranes (plasma membranes, nuclear, or endoplasmic reticulum membranes). Their envelopes are derived from host membranes.

Release of a Virus by Budding

• The diagram illustrates the process of budding.

Viral Cytopathgenesis

• Different mechanisms are used by viruses
• Examples of mechanisms of cytopathic effects, e.g, inhibition of cellular proteins, inclusion bodies, syncytia formation, and effects on the cell structure, disruption of cytoskeleton.

Viral Infection Causes Cytopathic Effect (CPE)

• Any changes in a host cell due to viral infection is CPE
• CPE may include cell rounding, swelling, shrinking, detachment, cytoplasmic/nuclear inclusions, or syncytium formation.

Viral Cultures

• Viruses are obligate intracellular parasites reliant on host cells
• Viral cultures can use:
  • Embryonated eggs (still used for vaccines)
  • Experimental animals (rarely used in clinical labs)
  • Tissue culture cells (primary, continuous)

Tissue Culture Cells

• Primary cells — Isolated from specific organs, grown as monolayers and suspension, limited lifespan
  • Secondary cells— Derived from primary cultures, more homogeneous
  • Continuous cell lines— Derived from transformed cells or tumors, grow indefinitely (immortal).
    • Normal cells form a monolayer, stop dividing
    • Cancer cells do not exhibit density-dependent inhibition

Diagnosis of Viral Infection

• Culture-based systems (slow, labor-intensive, poorly sensitive)
  • Electron microscopy (expensive, not sensitive enough)
• Molecular methods - detection of viral nucleic acid by PCR.
• Serology— detection of virus-specific antibodies

Antiviral Drugs

• Viruses rely on host machinery for replication, making it hard to develop effective drugs
• Antivirals primarily target viral enzymes or structures critical to replication.
  • Some stimulants of host innate immune responses. (i.e., interferon)
  • Antiviral drugs usually have a narrow spectrum of activity (specific for certain types of viruses), have resistance issues (like bacterial resistance) due to high mutation rates in viruses and long term treatment

Antiviral Drugs

• Examples include inhibitors of:
  • Entry/fusion
  • Uncoating
  • Viral protein/nuclei acid synthesis
  • Viral release
  • Viral assembly
    • Examples like nucleoside analogs, protease inhibitors, neuraminidase inhibitors, and others

Antiviral Drugs: Examples

• Docosanol— inhibits herpes simplex virus entry into cells; used topically. - Amantadine/ rimantadine— Inhibits influenza A virus uncoating

Host Defenses Against Viral Infection

• Initial response is innate immunity (nonspecific), follow it by adaptive immunity. Innate immune mechanisms (nonspecific), and adaptive immune mechanisms (highly specific). - Type I IFNs.

Interferons (IFNs)

• A group of signaling proteins produced by the body's cells in response to viruses. Important modulators of innate immunity
• They have an antiviral role.
• Type I IFNs — generated by infected cells in response to viruses.
• IFN-A — generated by lymphocytes, and other cells
• IFN-B — generated by fibroblasts and other cells
  • IFN-γ produced by NK cells and CD8+ cells

Type I Interferons

• Viruses induce type I interferons
• They activate an "antiviral state"
• Interferons bind to receptors on the cells
• Activates protein kinase R and RNAse L. This inhibits viral protein synthesis, destroying viral particles, by degrading the viral mRNA

Type I Interferons

• Induce protection of cells for a short time
• Stimulate immune responses to control viral infections