Viruses: Structure, Classification, and Replication (Microbiology Study Notes)

Viruses as Nonliving Microbes

Definition and General Properties

Viruses are considered nonliving microbes because they cannot carry out metabolic processes or reproduce independently. They require a host cell to replicate and are classified as obligate intracellular parasites.

• Obligate intracellular parasites: Viruses must invade a specific host cell to reproduce.

• Size: Typically range from 20-400 nm; much smaller than bacteria.

• Virology: The study of viruses.

• Bacteriophages: Viruses that infect bacteria.

• Animal viruses: Viruses that infect animals and humans.

Additional info: There are thousands of known viruses, with approximately 220 causing human diseases.

Viral Structure

Overview of Viral Components

Viruses are composed of a nucleic acid core surrounded by a protein coat (capsid), and sometimes an envelope. These structures protect the viral genome and aid in host infection.

• Virion: A complete virus particle capable of infecting a cell.

• Capsid: Protein layer that covers and protects the viral genome.

• Envelope: Lipid membrane covering outside the capsid (present in some viruses).

• Spikes: Glycoproteins on the outside of the capsid/envelope, used for attachment to host cells.

Capsid Structure

The capsid is made of protein subunits called capsomeres and determines the shape of the virus.

• Capsomeres: Subunits that assemble to form the capsid.

• Shapes: Helical (cylindrical), Icosahedral (20-sided polygon), Complex (e.g., bacteriophage with head, tail, sheath).

Envelope Structure

Some viruses possess a lipid-based envelope derived from the host cell membrane during viral budding. Others lack an envelope and are termed naked viruses.

• Enveloped viruses: Acquire envelope by budding off the host cell, incorporating host membrane lipids.

• Naked viruses: Lack an envelope and are released by lysing the host cell.

Spikes

Spikes are glycoproteins that protrude from the capsid or envelope and are essential for host cell recognition and attachment.

• Function: Allow viruses to attach to and infect host cells.

• Examples: Influenza virus spike proteins include Neuraminidase (NA) and Hemagglutinin (HA), which are frequently mutated.

Viral Genome

Genetic Material and Arrangements

Viral genomes are much smaller than those of cellular organisms and can be composed of either DNA or RNA, but never both.

• Genome size: Usually about 300 genes.

• Types: Double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), single-stranded RNA (ssRNA).

• Segmented genomes: Some viruses have genomes split into segments.

Viral Classification

Criteria for Classification

Viruses are classified by the International Committee on Taxonomy of Viruses (ICTV) using several key properties.

• Nucleic acid type: DNA or RNA.

• Capsid symmetry: Helical, icosahedral, or complex.

• Envelope presence: Enveloped or naked.

• Genome architecture: ssDNA, dsDNA, ssRNA, dsRNA, segmented or nonsegmented.

Additional info: Viral nomenclature is typically at the genus and species levels.

Viral Host Range and Tropism

Definitions and Examples

Host range and tropism refer to the specificity of viruses for particular hosts and cell types.

• Host range: The spectrum of species a virus can infect. Some viruses infect only one species (e.g., measles virus infects only humans).

• Tropism: The specificity for certain tissues or cell types within a host, determined by the ability of the virus to attach to host cell receptors.

Bacteriophage Replication

Lytic and Lysogenic Cycles

Bacteriophages (phages) can replicate via two main pathways: lytic and lysogenic.

• Lytic cycle: Results in active virion production and destruction of the host cell.

• Lysogenic cycle: Viral DNA integrates into the host genome as a prophage, replicating with the host cell without killing it immediately.

Lytic Replication Steps

1. Attachment (adsorption): Phage binds to bacterial cell surface.

2. Entry: Phage injects its genetic material into the host.

3. Synthesis: Host machinery is commandeered to produce viral components.

4. Maturation: Viral genomes are packaged into new phage particles.

5. Release: Host cell lyses, releasing new phages.

Lysogenic Replication Steps

1. Integration: Phage genome incorporates into host DNA as a prophage.

2. Replication: Prophage is copied with host genome during cell division.

3. Induction: Under stress, prophage may excise and enter the lytic cycle.

Additional info: Lysogeny can confer new pathogenic properties to bacteria, such as toxin production (e.g., Corynebacterium diphtheriae, Clostridium botulinum).

Animal Virus Replication

Generalized Steps

Animal viruses follow a multi-step replication process within host cells.

1. Attachment: Virus binds to host cell membrane via specific interactions.

2. Entry: Virus enters the cell by fusion or endocytosis.

3. Uncoating: Removal of capsid to release viral genome.

4. Replication: Viral genome is replicated and viral proteins are synthesized.

5. Assembly: New viral particles are assembled.

6. Release: Viruses exit the cell by budding (enveloped viruses) or lysis (naked viruses).

Persistent and Oncogenic Viral Infections

Types of Persistent Infections

Some viruses establish persistent infections, evading immune clearance and remaining in the host for extended periods.

• Chronic infection: Continuous production of virus (e.g., HIV).

• Latent infection: Periods of inactivity and reactivation (e.g., Herpes virus).

Oncogenic Viruses

Oncogenic viruses can induce uncontrolled cell growth, leading to cancer.

• Mechanism: Stimulate cell proliferation and/or inhibit cell death.

• Examples: Human papillomaviruses (HPVs), lymphotropic viruses.

Virus Cultivation Techniques

Bacteriophage vs Animal Virus Cultivation

Viruses require specific host cells for growth, and cultivation techniques differ for bacteriophages and animal viruses.

• Bacteriophages: Grown on bacterial lawns; plaques indicate areas of cell lysis and can be used to quantify phage numbers.

• Animal viruses: Cultivated in cell cultures, embryonated eggs, or live animals.

Viral Classification Table

The following table summarizes key parameters used to classify viruses:

Parameter	Examples	Description
Nucleic Acid Type	DNA, RNA	Genetic material of the virus
Capsid Symmetry	Helical, Icosahedral, Complex	Shape of the protein coat
Envelope Presence	Enveloped, Naked	Lipid membrane surrounding capsid
Genome Architecture	ssDNA, dsDNA, ssRNA, dsRNA	Single or double stranded, segmented or nonsegmented

Key Equations

While viruses do not have metabolic equations, the following formula is used to calculate viral titer from plaque assays:

$\text{Viral Titer} = \frac{\text{Number of Plaques}}{\text{Dilution Factor} \times \text{Volume Plated}}$