Viruses and Prions: Structure, Replication, and Clinical Applications

Introduction to Viruses and Prions

Overview

Viruses are acellular, submicroscopic infectious agents that require a host cell for replication. Prions are infectious proteins lacking genetic material. Both play significant roles in infectious diseases and have unique structural and replication features.

Viral Structure and Classification

Basic Components of Viruses

• Virion: A single, infectious virus particle composed of a protein capsid and genetic material (DNA or RNA).

• Capsid: Protein shell made of capsomere subunits that protects the viral genome.

• Envelope: Lipid-based membrane derived from the host cell, present in enveloped viruses.

• Spikes (Peplomers): Glycoprotein extensions that facilitate attachment and entry into host cells.

Capsid Symmetry

• Helical: Hollow tube-like structure.

• Icosahedral: Three-dimensional polygon, often appearing spherical.

• Complex: Deviations from helical or icosahedral, seen in bacteriophages.

Enveloped vs. Naked Viruses

• Naked Viruses: Lack an envelope; released by lysing the host cell.

• Enveloped Viruses: Surrounded by a lipid envelope; released by budding from the host cell.

Viral Genome Types

• DNA or RNA

• Single-stranded (ss) or double-stranded (ds)

• Segmented or non-segmented

• Circular or linear

Classification Criteria (ICTV)

• Type of nucleic acid (DNA or RNA)

• Capsid symmetry (helical, icosahedral, complex)

• Presence or absence of envelope

• Genome architecture (e.g., ssDNA, dsRNA)

Note: Viruses are classified into Order, Family, Genus, and Species, but not into domains, kingdoms, phyla, or classes.

Viral Host Range and Tropism

Host Range

• Defines the collection of species a virus can infect.

• Some viruses infect only one species (e.g., measles virus infects only humans), while others infect multiple species.

• Approximately 70% of human-infecting viruses are harbored in other animals.

Tropism

• Refers to the specificity for certain tissues or cell types within a host.

• Determined by viral surface factors (e.g., spike proteins).

• Broad tropism: Infects a wide range of cells/tissues.

• Narrow tropism: Infects only specific cell/tissue types.

Viral Replication Pathways

Bacteriophage Replication

• Lytic Cycle: Virus immediately replicates, lyses host cell, and releases new virions.

• Lysogenic Cycle: Viral genome integrates into host DNA (prophage), replicates with host, can later enter lytic cycle.

Steps in the Lytic Cycle

1. Attachment (Adsorption): Phage binds to specific receptors on bacterial cell wall.

2. Penetration: Phage injects genome into host cell.

3. Replication: Synthesis of viral components; host DNA degraded.

4. Assembly: New phage particles assembled.

5. Release: Lysozyme breaks cell wall; cell lyses, releasing phages.

Lysogenic Cycle

• Phage genome integrates into host chromosome (prophage).

• Replicates with host cell division.

• Can excise and enter lytic cycle under stress.

Phage Conversion

• Prophages may provide new pathogenicity factors (e.g., toxins) to bacteria (e.g., Corynebacterium diphtheriae, Clostridium botulinum).

Animal Virus Replication

1. Attachment: Virus binds to host cell membrane (capsid proteins for naked viruses).

2. Penetration: Entry via endocytosis or membrane fusion.

3. Uncoating: Capsid is removed by host enzymes.

4. Replication (Synthesis): Genome and proteins are synthesized.

5. Assembly: New virions are formed.

6. Release: Enveloped viruses bud off; naked viruses lyse the cell.

Types of Infections

• Acute: Rapid production of new virions.

• Persistent: Virus remains in host, evading immune system (chronic or latent).

• Chronic: Continuous release of virions (e.g., HIV).

• Latent: Periods of dormancy with intermittent flare-ups (e.g., Herpesviridae family).

Oncogenic Viruses

• Viruses that can cause cancer (oncoviruses), e.g., Human papillomaviruses (HPVs).

• Responsible for 10-15% of human cancers.

Viral Genomes and Mutation

Genome Diversity

• Viruses may have ssRNA, dsRNA, ssDNA, or dsDNA genomes.

• Genome can be segmented or non-segmented.

RNA Virus Replication Strategies

• ssRNA(+): Functions as mRNA; directly translated by host ribosomes.

• ssRNA(-): Complementary to mRNA; transcribed into mRNA by RNA-dependent RNA polymerase (RdRP).

• dsRNA: Transcribed to make mRNA; requires RdRP.

• Retroviruses: Use reverse transcriptase to make DNA from RNA, which integrates into host genome (e.g., HIV).

Mutation and Evolution

• RNA viruses mutate rapidly due to lack of proofreading by RNA polymerases.

• DNA polymerases have proofreading ability, leading to lower mutation rates.

• Mutations can lead to antigenic drift (minor changes in viral proteins, e.g., influenza HA and NA spikes).

• Reassortment (antigenic shift) occurs when two different viral strains coinfect a cell, producing new strains.

Laboratory Cultivation and Detection of Viruses

Cultivation Methods

• Bacteriophages: Grown on bacterial lawns; plaques indicate lysis.

• Animal Viruses: Grown in tissue culture, live animals, or embryonated eggs (e.g., influenza vaccine production).

• HeLa Cells: Commonly used human cell line for viral culture.

Plaque Assays

• Clear zones (plaques) on bacterial lawns indicate phage activity.

• Plaque-forming units (PFUs) quantify phage concentration.

• Viral titer: Quantity of virus in a sample.

Diagnostic Techniques

• Latex Agglutination: Detects viral antigens or antibodies using latex beads.

• ELISA (Enzyme-Linked Immunosorbent Assay): Detects antigens or antibodies; color change indicates binding.

• PCR (Polymerase Chain Reaction): Detects viral nucleic acids with high sensitivity and specificity.

• Fluorescent Probes and Sequencing: Used for direct detection of viral genomes.

Diagnostic Test Qualities

• Specificity: Detects only the virus of interest (no false positives).

• Sensitivity: Detects low levels of virus (no false negatives).

Antiviral Drugs and Vaccines

Challenges in Antiviral Therapy

• Viruses are obligate intracellular pathogens with few unique targets.

• Antivirals must be selectively toxic to viruses, not host cells.

• Vaccination is crucial for prevention.

Antiviral Drug Targets

• Attachment

• Penetration

• Uncoating

• Replication

• Assembly

• Release

Examples of Antiviral Agents

Drug/Class	Mechanism	Example/Use
Postexposure prophylaxis	Injectable antibodies	Rabies, HIV
Entry inhibitors	Block viral entry	Docosanol (cold sores), Palivizumab (RSV)
Nucleoside analogs	Mimic nucleotides, inhibit replication	Acyclovir (herpes), Ribavirin (RSV, hepatitis C)
NRTIs	Inhibit reverse transcriptase	AZT (HIV)
Antisense antivirals	Bind viral RNA, inhibit translation	Vitravene
Interferons	Induce antiviral state in cells	Hepatitis treatment
Neuraminidase inhibitors	Prevent viral release	Oseltamivir (Tamiflu), Zanamivir (Relenza)

Prions

Characteristics

• Infectious proteins; lack genetic material.

• Do not replicate like viruses or cells.

• Cause transmissible spongiform encephalopathies (TSEs).

Examples of TSEs

• Gerstmann-Sträussler-Scheinker syndrome

• Creutzfeldt-Jakob disease (CJD)

Summary Table: Virus Properties and Replication

Property	Description
Genome Type	ssRNA, dsRNA, ssDNA, dsDNA
Capsid Symmetry	Helical, Icosahedral, Complex
Envelope	Present (enveloped) or absent (naked)
Replication Site	Cytoplasm or nucleus (animal viruses)
Release Mechanism	Budding (enveloped), lysis (naked)
Mutation Rate	High in RNA viruses (no proofreading)

Additional info:

• Viruses are only visible with electron microscopy due to their small size (20-400 nm).

• Host antibodies against influenza target HA and NA spikes.

• HeLa cells are a widely used human cell line for viral research.

• Vaccines often use attenuated (weakened) viral strains to stimulate immunity without causing disease.