Virology: Virus Structure and Characteristics

Characteristics of Viruses

• Viruses are not true cells
• Viruses lack ribosomes and cannot synthesize protein, making them metabolically inactive outside a host cell.
• Viruses are obligate intracellular parasites, replicating only inside host cells by utilizing the cell's metabolism to produce new virus copies.

Structure of a Virus

• Key components include:
  • Capsid: Protein coat
  • Genome: Genetic material
  • Envelope: Present in some viruses

Capsid

• The capsid is composed of protein subunits termed capsomeres that covers the viral genome
• The capsid functions to protect the viral genome from nucleases
• It also serves as an antigenic component and aids in the attachment to host cells
• The arrangement of capsomeres determines the shape of the virus

Viral Genome

• The viral genome codes for all viral structures and activities.
• The genome can be either DNA or RNA, but not both.
• DNA viruses are typically double-stranded, with the exception of Parvo virus ("SS DNA").
• RNA viruses are generally single-stranded, except for reovirus ("DS RNA").
• Most RNA viruses are not segmented, except for Rota, Bunaya, and influenza viruses ("Segmented RNA").

ssRNA

• +Ve sense acts like mRNA, initiating protein synthesis directly.
• -Ve sense requires transcription by RNA polymerase.

Envelope

• The envelope is a lipoprotein membrane surrounding some viruses.
• It is derived from the host cell membranes (cell or nuclear).
• Enveloped viruses acquire their envelope when budding from cytoplasmic or nuclear membranes.
• The protein part is coded by the viral genome by forcing the host cell synthesize it, and is virus-specific.
• The protein part aids in attachment to host cells by interacting with specific receptors and is antigenic.
• The lipid part can be disrupted by lipid solvents like alcohol, detergents, and ether.
• Enveloped viruses are thus sensitive and can be inactivated by lipid solvents.

Classification of Viruses

• Based on envelope and genome:
  • DNA viruses can be enveloped or naked.
  • RNA viruses can also be enveloped or naked.
• Based on host:
  • Human: Varicella-zoster virus (VZV)
  • Arthropods: Yellow fever virus
  • Animal: Rabies virus
  • Plants: Tobacco mosaic virus
• Based on the disease caused:
  • Respiratory viruses
  • Enteric viruses
  • Hepatitis viruses
• Based on families:
  • According to morphological features, genome, and replication strategies.

Viron

• The normal state of an intact virus.
• An enveloped virion comprises with an envelope, capsid, and genome.
• A naked virion consists of a capsid and genome.

Atypical Virus-Like Particles

• Defective virus: Cannot replicate without a helper virus.
• Pseudo virus: Contains host's DNA due to "error in assembly."
• Viroids: Circular RNA lacking a capsid or envelope, causing diseases in plants.
• Prions: Infectious misfolded proteins, the smallest infectious particles.

Pathogenesis of Viral Diseases

• Involves entry and primary replication, viral spread and cell tropism, effect on host cells, host immune response, fate of the virus, and virus shedding outside the host.

Entry and Primary Replication

• Entry: Virus enters the human body through the respiratory system, blood, broken epithelium, sexual contact, or vertical transmission (mother to baby).
• Replication: Occurs primarily at the entry site, potentially causing disease there (e.g., respiratory viruses) or spreading to cause disease at a distant site.

Viral Replication Cycle Inside Host Cells

• Attachment & Adhesion: Virus binds to the host cell.
• Entry: Occurs via fusion with the cell membrane, or endocytosis.
• Uncoating: Viral components release contents inside the cell via lysozymes.
• Synthesis of viral components: Transcription, translation, and genome production takes place inside cell.
• Assembly and release: Budding (enveloped viruses) or rupturing (naked viruses).
• Enveloped virus: Enters by fusion or endocytosis, releases by budding.
• Naked virus: Enters by endocytosis only, releases by rupturing.

Viral Spread and Cell Tropism

• After initial replication, viruses spread to distant locations through blood ("viremia"), lymphatics, or nerves.
• Cell tropism: Affinity of viruses to specific tissues/cells due to specific receptors on target cells (e.g., HIV virus and CD4 on T-helper cells), specific proteolytic enzymes, or favorable temperature, pH, and O2 tension.

Effect on Host Cells

• Cell death, direct injury due to viral replication (cytopathic effect), or immune response (CTLs and NKs killing infected cells).
• Malignant transformation by some oncogenic viruses.
• Oncogenic viruses cause malignant transformation through fusion/incorporation of viral genome with the host's, mutation of host regulatory genes, or insertion of viral oncogenes.
• Production of viral proteins inactivates host tumor suppressor genes.
  • Ex: E6 protein of Human Papilloma virus inactivates P53 ("Tumor suppressor gene").
• Chronic inflammation or chronic Hepatitis C virus infection can lead to hepatocellular carcinoma (HCC, "Liver Cancer").

Host Immune Response

• Immunity against viruses is primarily cell-mediated.
• Humoral immunity and interferons play a role.

Fate of the Virus

• Complete resolution: Most viruses are cleared after recovery.
• Persistent infection: Viral infection can either be chronic.
  • Virus is present with mild or without clinical signs (e.g., Hepatitis viruses HBV and HCV).
• Latent infection: Virus can hide ("remain dormant") inside the host with no activity
  • Reactivation can occur (e.g., Varicella zoster virus).
    • It can remain latent in sensory ganglia.
• Slow infection: Very long incubation period, slow progression (e.g., John Cunningham virus "JCV" causing PML "Progressive Multifocal Leuko-encephalopathy").

Virus Shedding Outside the Host

• Virus particles are released from the host to infect others.
• Usually occurs from the same site of entry.
• Humans are a dead-end host for some viruses (e.g., Rabies virus).

Types of Viral Diseases

• Localized disease:

  • Virus invades tissues next to the site of entry.
  • Short incubation period, no viremia, and transient immunity.

• Systemic disease:

  • Virus spreads widely, invading many tissues.
  • Long incubation period, viremia occurs, and long-lasting immunity.

Laboratory Diagnosis of Viral Diseases

• I- Direct Examination of clinical specimens
• II- Isolation
• III-Serology

Direct Examination of clinical specimens

• Detection of virus particles by electron microscopy (E/M).
  • Immunoelectron microscopy: Uses antibodies specific to the virus to form complexes for enhanced visualization.
• Detection of viral inclusion bodies ("IBs") by light microscopy (L/M) using hematoxylin and eosin stain (H&E).
  • Viral inclusion bodies can be an aggregation of mature virus particles ("virons"), viral proteins, or degenerative changes in host cells.
• Detection of viral antigens by ELISA, immunofluorescence (IF), and radioimmunoassay (RIA) (e.g., Hepatitis B virus).
• Detection of viral genome by PCR or Hyperdization.

Examples of Inclusion bodies:

• Intracytoplasmic inclusion bodies:
  • "Negri bodies" of Rabies virus.
• Intranuclear inclusion bodies:
  • "Cowdry bodies" of Herpes virus.

Virus Isolation on Artificial Media

• Isolation on tissue culture.
  • Viruses cannot grow on ordinary media, as they are obligate intracellular parasites.
• Effect of the virus on cells of the tissue culture can be
  • Cytopathic effect "CPE".
  • Cell death and detachment, cell rounding.
  • Cell Fusion Syncytia formation "Multinucleated giant cells".
  • Hemadsorption: Virally infected cells express hemagglutinins on the cell membrane, causing red blood cells (RBCs) to adsorb/stick to the infected cells.
  • Malignant transformation: Cells grow uncontrollably.
  • Inclusion body formation.

• Inhibition of previous effects by specific antiviral serum "Antibodies" can be used for definitive diagnosis.

Isolation on Chick Embryo

• Virus is caused by inoculated yolk sac or amniotic sac.
• Death of embryo.
• Pocks formation.
• Used mainly for vaccines production.

Isolation on lab animals

• Some Viruses cannot grow in vitro and have to be inoculated inside Lab animals like mice or monkeys.

Indirect methods "Serology"

• Used to detect Antibodies produced by the patient "most widely used method".
• Detection of IgM: First antibody to appear in the infection, used in diagnosis of Recent acute infection
• Detection of IgG: rise in the IgG titer is diagnostic for acute infection.
• Seroconversion: Detection of Antibodies in patient's serum when he previously didn't have any antibodies " Conversion from seronegative to seropositive".

Reaction to Chemical and Physical Agents

• Physical Agents:
  • Heat:
    • Heat destroys viral infectivity at 50-60°C for 30 minutes.
      • Except Hepatitis B virus.
  • Cold:
    • Viruses are stable at low temperatures.
      • Most Can be stored at -40 C till -70 C.
    • Some are inactivated by freezing and thawing.
    • Lyophilization (drying from frozen state under vacuum) can preserve viruses at 4 °C for years.
  • Radiation:
    • Ultraviolet rays, X-rays, and gamma-rays inactivate viruses.
• Chemical Agents
  • pH:
    • Viruses are sensitive to acidic and alkaline pH.
      • Enteroviruses survive acidic pH as in stomach.
  • Ether, alcohols, and Detergents:
    • Dissolve the viral envelope causing inactivation of enveloped viruses.
  • Oxidizing Agent:
    • Viruses are inactivated by chlorine, iodine, & H2O2.
  • Formaldehyde:
    • Formaldehyde destroys viral infectivity without affecting viral antigenicity.
      • Therefore, it's used in the production of inactivated viral vaccines.
  • Salts:
    • Some viruses (Picornaviruses and Reoviruses) can be stabilized by salt MgCl2 (1 mol/L) used in stabilization of live attenuated vaccine of poliomyelitis to be maintained potent for weeks at high temperature.
  • Phenole:
    • Most viruses are resistant to phenolic compounds.
  • Glycerol:
    • Glycerol (50%) destroys bacteria but preserves viruses.
  • Antibiotics:
    • They have no effect on viruses.

Mechanisms of Action of Antiviral Drugs

• Inhibition of Attachment and Uncoating of the Virus:
  • Fusion Inhibitor:
    • Blocks the virus envelope and cell membrane fusion step.
  • Inhibitors of Uncoating:
    • Administered prophylactically to have a significant protective effect.
• Inhibition of Nucleic Acid Synthesis:
  • DNA polymerase inhibitors:
    • Prevent building viral DNA.
  • RNA polymerase inhibitors:
    • Prevent building viral RNA.
  • Reverse. Transcriptase Inhibitors:
    • Blocking reverse transcriptase prevents HIV from replication.
• Inhibition of integrase enzyme:
  • Prevents the integration of viral DNA into the host DNA.
• Inhibition of protein synthesis:
  • Interferons:
    • Induce the production of enzymes (as protein kinase) = inhibition of protein synthesis.
      • Alpha interferon is used in chronic hepatitis B and C infections.
• Inhibition of Cleavage:
  • Inhibition of the protease = non-infectious viral particles.
• Inhibition of protein synthesis:
  • Neuraminidase Inhibitors:
    • Limits the infection by reducing the spread of the virus from one cell to another by inhibiting the release of viruses from infected cells.