Microbiology Study Notes: Viral Structure, Replication, and Classification

Prokaryotic Viruses (Bacteriophages)

Introduction to Bacteriophages

Bacteriophages are viruses that infect bacteria. They play a crucial role in microbial ecology and genetics, and are important tools in molecular biology.

• T4 phage: Infects Escherichia coli (E. coli). It is a virulent phage, meaning it undergoes only the lytic cycle.

• Lambda (λ) phage: Also infects E. coli. It is a temperate phage, capable of both lytic and lysogenic cycles.

Lytic Cycle

The lytic cycle is a viral replication process resulting in the destruction of the host cell.

• Attachment: Phage recognizes and binds to specific receptors on the bacterial surface.

• Genome Injection: The phage injects its genetic material into the host cell.

• Synthesis: Early genes encode proteins for phage genome replication; middle and late genes encode structural proteins (capsid, tail fibers).

• Assembly: New phage particles are assembled inside the host.

• Release: Host cell is lysed, releasing new virions.

Lysogenic Cycle

Temperate phages, such as Lambda, can integrate their genome into the host's DNA, becoming a prophage.

• Integration: Phage DNA integrates into the bacterial genome.

• Prophage State: Phage genes are repressed; the host cell survives and replicates with the prophage DNA.

• Induction: Under stress, the prophage may exit the genome and enter the lytic cycle.

Bacterial Defenses Against Phages

• Loss of phage receptors on the cell surface.

• Production of restriction enzymes to degrade foreign DNA.

• CRISPR-Cas system: Provides adaptive immunity against future phage infections.

Eukaryotic Viruses

Introduction to Eukaryotic Viruses

Eukaryotic viruses infect animal, plant, and fungal cells. Their lifecycles are more complex due to cellular compartmentalization.

• Ebola virus: Causes hemorrhagic fever in humans.

• COVID virus (SARS-CoV-2): Causes COVID-19.

• Monkeypox virus: Causes monkeypox disease.

General Lifecycle of Eukaryotic Viruses

• Recognition and Attachment: Virus binds to specific receptors on host cells, determining host and tissue tropism.

• Entry: Viruses enter cells via endocytosis, membrane fusion, or direct penetration.

• Uncoating: Viral capsid is disassembled, releasing the genome.

• Synthesis: Viral genome is replicated and viral proteins are produced.

• Assembly: New virions are assembled.

• Release: Virions exit the cell by lysis or budding.

Viral Entry Mechanisms

• Envelope Fusion: Viral envelope fuses with the host membrane (e.g., influenza, HIV).

• Endocytosis: Virus is engulfed by the cell and released from endosomes (e.g., Dengue, Herpes).

• Direct Injection: Some viruses inject their genome directly into the cytoplasm.

Plant Viruses

Plant viruses typically enter cells through mechanical damage or via vectors (insects, nematodes, fungi).

• Do not bind to specific receptors; have a broad host range.

• Generally lack an envelope and do not lyse plant cells.

• Move cell-to-cell via plasmodesmata and can spread systemically through the vascular system.

Effects of Viruses on Host Cells

• Bacterial viruses: Cause cell lysis or remain dormant as prophages.

• Plant viruses: Cause stunted growth and discoloration.

• Animal viruses: Can cause acute, persistent, latent, or transforming infections.

Types of Animal Virus Infections

• Acute infection: Rapid onset, short duration (e.g., influenza).

• Persistent infection: Long-term, may last years (e.g., hepatitis B).

• Latent infection: Delay between infection and symptoms (e.g., herpes simplex).

• Transformation: Virus induces host cell transformation (e.g., HPV causing cancer).

Subviral Agents

Viroids

Viroids are small, circular single-stranded RNAs that infect plants. They lack a capsid and do not encode proteins.

• Replicated by host RNA polymerase.

• Cause plant diseases by interfering with gene expression.

Prions

Prions are infectious proteins that lack nucleic acids. They cause neurodegenerative diseases in animals and humans.

• Convert normal proteins into abnormal, disease-causing forms.

• Accumulate in neural tissue as amyloid aggregates.

• Diseases include: Scrapie (sheep/goats), Mad cow disease (BSE), Chronic wasting disease (deer/elk), Creutzfeldt-Jakob disease (humans).

Classification of Viruses

Challenges in Virus Classification

Viruses cannot be classified using universal phylogenetic trees because they lack ribosomes and do not share conserved genetic markers with cellular life.

Criteria for Classification

• Genome composition: DNA or RNA, single-stranded (ss) or double-stranded (ds), sense (+) or antisense (-).

• Genome structure: Linear, circular, segmented.

• Virion structure: Capsid symmetry (icosahedral, helical, complex), presence or absence of envelope, particle size.

• Host range: Type of host infected (bacteria, plants, animals, invertebrates).

Summary Table: Comparison of Virus Types

Virus Type	Host	Genome	Envelope	Replication Cycle
Bacteriophage (T4)	Bacteria (E. coli)	dsDNA	No	Lytic only
Bacteriophage (Lambda)	Bacteria (E. coli)	dsDNA	No	Lytic & Lysogenic
Ebola virus	Humans	ssRNA (-)	Yes	Lytic
COVID virus (SARS-CoV-2)	Humans	ssRNA (+)	Yes	Lytic
Monkeypox virus	Humans	dsDNA	Yes	Lytic
Viroid	Plants	ssRNA (circular)	No	Replicates via host enzymes
Prion	Animals	None (protein only)	No	Converts host proteins

Key Equations

• Burst size: Number of virions released per infected cell.

• Latent period: Time between infection and release of new virions.

$\text{Burst size} = \frac{\text{Total number of released virions}}{\text{Number of infected cells}}$

$\text{Latent period} = \text{Time from infection to first release of virions}$

Additional info: Some details about viral entry mechanisms, host defenses, and effects on host cells were expanded for clarity and completeness.