Viruses: Structure, Replication, and Acellular Infectious Agents – Study Notes (Microbiology Chapter 13)

Viruses: Structure and Host Range

What Defines a Virus

Viruses are unique infectious agents that differ fundamentally from cellular life forms. They are acellular, lack independent metabolism, and require living host cells for replication.

• Acellular Organization: Viruses are not cells; they lack ribosomes, cytoplasm, and energy-producing systems.

• Obligate Intracellular Parasites: Viruses must infect living cells to reproduce; they do not divide by binary fission but assemble new particles from components.

• Virion: The complete, infectious virus particle outside a host cell.

• Capsid: Protein shell made of capsomeres, protecting the viral genome and often aiding in attachment.

• Nucleocapsid: The viral genome plus its capsid.

• Envelope: An optional lipid membrane derived from the host, containing viral proteins (often glycoprotein spikes).

• Shapes: Helical, polyhedral/icosahedral, and complex (e.g., tailed bacteriophages).

Feature	Viruses	Cellular Organisms
Organization	Acellular particles	Cells with membranes, cytoplasm, ribosomes
Genome	DNA or RNA; single- or double-stranded; may be segmented	DNA genome; RNA for gene expression
Replication	Host-dependent synthesis and assembly	Cell growth and division
Metabolism	No independent ATP production or protein synthesis	Own metabolic machinery

• Why Not Living? Viruses cannot independently metabolize, maintain homeostasis, or reproduce. However, they possess genomes and can evolve.

Host Range and Tissue Tropism

The host range of a virus is determined by the compatibility between viral attachment proteins and host cell receptors, as well as internal cellular factors.

• Host Range: The spectrum of species or cell types a virus can infect.

• Tropism: Preference for specific tissues or cell types within a host.

• Attachment: Viral proteins must match host receptors (e.g., HIV binds CD4 and a coreceptor).

• Example: Bacteriophages infect bacteria; tail fibers recognize specific bacterial molecules.

Discovery and Structure of Viruses

The Tobacco Mosaic Filtration Experiment

Early experiments established viruses as filterable infectious agents distinct from bacteria.

• Ivanovsky (1892): Filtered sap from diseased tobacco leaves through bacteria-retaining porcelain; filtrate remained infectious.

• Beijerinck (1898): Concluded a distinct, filterable agent multiplied in plants—later identified as tobacco mosaic virus.

• Key Point: Filtration showed the agent was smaller than bacteria but did not directly prove acellularity.

Naked Versus Enveloped Virions

Viruses can be classified based on the presence or absence of an envelope, which affects their stability and transmission.

Feature	Naked/Nonenveloped	Enveloped
Outer Surface	Protein capsid	Lipid envelope with viral proteins
Acquisition	No envelope acquired	Budding through host membranes
Environmental Survival	More resistant to drying, detergents, acid	More vulnerable to drying, heat, solvents
Release	Often cell lysis	Often budding or secretion
Examples	Adenovirus, poliovirus, norovirus	Influenza virus, HIV, herpesviruses

• Envelope Origin: Derived from host membrane, but with inserted viral proteins.

• Clinical Note: Enveloped viruses are generally more sensitive to detergents due to their lipid layer.

Bacteriophage Replication

Lytic Versus Lysogenic Cycles

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

Feature	Lytic	Lysogenic
Immediate Outcome	New virions produced	Phage genome maintained
Host Survival	Typically lyses at release	Host survives and reproduces
Key Term	Virulent phage	Temperate phage
Genome State	Active for virion production	Prophage, often integrated
Transition	Ends with release	Induction can initiate lytic cycle

• Lytic Cycle Steps: Attachment → Penetration → Synthesis → Assembly → Release (cell lysis).

• Lysogenic Cycle: Phage genome integrates as a prophage; host cell divides, passing on the prophage.

• Induction: Stress (e.g., UV light) can trigger prophage to enter the lytic cycle.

• Lysogenic Conversion: Prophage genes can alter bacterial traits (e.g., toxin production).

• Terminology: Prophage (bacterial context); provirus (integrated animal-virus DNA).

Animal Virus Entry and Replication

The Animal Virus Replication Sequence

Animal viruses follow a general sequence for replication, with variations in entry and genome replication mechanisms.

• Stages: Attachment → Entry → Uncoating → Biosynthesis → Assembly → Release

• Entry Mechanisms:

  • Direct Penetration: Genome enters cell; capsid remains outside.

  • Membrane Fusion: Enveloped virus fuses with host membrane, delivering nucleocapsid.

  • Receptor-Mediated Endocytosis: Virion is taken into a vesicle, then escapes into cytoplasm.

• Biosynthesis: Viral genome directs synthesis of proteins and genome copies using host (and sometimes viral) enzymes.

• DNA Viruses: Usually replicate in the nucleus.

• RNA Viruses: Usually replicate in the cytoplasm (exceptions: influenza, poxviruses).

Retroviral Replication

Retroviruses, such as HIV, use reverse transcription to integrate their genome into the host DNA.

1. Attachment and entry into the host cell.

2. Reverse transcriptase synthesizes DNA from the RNA genome.

3. Viral integrase inserts the DNA into the host chromosome (provirus).

4. Host transcription produces viral RNA and proteins.

5. Assembly, budding, and maturation yield new virions.

• Reverse Transcriptase: RNA-dependent DNA polymerase packaged in the virion.

• Note: Not all RNA viruses use reverse transcription (e.g., hepatitis B uses a related mechanism).

Virus Release and Infection Patterns

• Release Mechanisms: Lysis (cell destruction), budding (enveloped viruses), exocytosis.

• Latency: Genome persists with little or no infectious particle production between reactivations (e.g., herpesviruses).

• Chronic Productive Infection: Continuous or fluctuating viral production over time.

• Persistent Infection: Encompasses both latency and chronic productive infection.

• Integration: Latency does not always require integration; herpesviruses often persist as episomes.

Viruses and Cancer

How Infection Can Promote Tumors

Some viruses can contribute to cancer development by altering host cell growth controls.

• Proto-oncogenes: Normal genes regulating cell growth; can become oncogenes if mutated or overactive.

• Tumor-Suppressor Genes: Inhibit cell division; loss or inactivation can promote cancer.

• Viral Mechanisms:

  • Insertion near growth-control genes

  • Expression of proteins disrupting cell-cycle regulation

  • Chronic inflammation and immune suppression

  • Some retroviruses carry oncogenes

• Examples:

  • High-risk HPV: Cervical and other cancers (interferes with tumor suppressors)

  • Hepatitis B/C: Liver cancer (chronic inflammation)

  • Epstein-Barr virus: Lymphomas, nasopharyngeal cancer

  • HTLV-1: Adult T-cell leukemia/lymphoma

  • HHV-8/KSHV: Kaposi sarcoma

  • HIV: Indirectly increases cancer risk via immune suppression

• Prevention: Vaccines (HPV, hepatitis B), screening, and treatment of chronic infections.

• Estimate: About 15% of human cancers are associated with viral infections (introductory estimate; check your course edition for specifics).

Cultivating and Counting Viruses

Why Living Cells Are Required

Viruses require living, susceptible, and permissive cells for replication; they cannot multiply on nutrient agar alone.

Method	Description	Strengths and Limitations
Living Animals	Inoculate susceptible animals; observe infection/immune response	Whole-organism study; costly, ethical concerns, species differences
Embryonated Eggs	Inoculate membranes/cavities in live eggs	Supports selected viruses, vaccine production; not universal
Cell Culture	Grow susceptible cells in nutrient medium, then inoculate virus	Controlled, useful for isolation; host choice and contamination matter

• HeLa Cells: Continuous human cell line from Henrietta Lacks; divides indefinitely in culture.

• Primary Culture: Freshly derived from tissue; limited lifespan.

Plaque Assay for Measuring Infectious Virus

Plaque assays estimate the number of infectious virus particles (plaque-forming units, PFU) in a sample.

• Serially dilute virus, apply to susceptible cell monolayer or bacterial lawn under an overlay.

• Each plaque represents local cell destruction from infection.

• PFU/mL Calculation:

$\text{PFU/mL} = \frac{\text{Number of plaques}}{\text{Dilution} \times \text{Volume plated (mL)}}$

• Example: 50 plaques from 0.1 mL of a 10-6 dilution: $50 \div (10^{-6} \times 0.1) = 5 \times 10^8$ PFU/mL.

• Note: PFU is an operational measure; not every virion forms a plaque.

Egg-Based Vaccines and Egg Allergies

• Some vaccines (e.g., influenza) are produced in embryonated eggs; residual egg proteins may be present.

• Current U.S. guidance: Egg allergy does not preclude receiving egg-based influenza vaccines; only severe reactions to previous vaccines require special consideration.

• Other vaccines (e.g., yellow fever) may have different recommendations.

Viruses, Viroids, and Prions

Comparison of Acellular Infectious Agents

Feature	Virus	Viroid	Prion
Structure	Genome inside capsid; some have envelope	Small, circular, single-stranded RNA; no capsid	Infectious misfolded protein
Genetic Material	DNA or RNA	RNA	None
Protein Coding	Encodes viral proteins	Does not encode proteins	No nucleic-acid genome
Multiplication	Genome-directed synthesis and assembly in host cells	Host enzymes copy RNA (rolling-circle)	Abnormal protein templates misfolding of normal host protein
Hosts	Bacteria, archaea, animals, plants	Mainly plants	Humans and other animals
Examples	Influenza, HIV, bacteriophages	Potato spindle tuber viroid	BSE, vCJD, scrapie

• Viroids: Small, circular RNA molecules; infect plants; lack capsid and protein-coding genes.

• Prions: Infectious proteins; no nucleic acid; cause transmissible spongiform encephalopathies (TSEs).

Prion Protein Misfolding

Prion diseases result from the accumulation of misfolded prion proteins, which induce further misfolding in normal host proteins.

• Normal Prion Protein (PrPC): Can be converted to the disease-associated form (PrPSc).

• Propagation: Misfolded PrPSc templates conversion of PrPC without genome replication.

• Pathology: Accumulation causes neuronal loss, gliosis, and spongiform changes in the brain.

• Diseases: BSE (mad cow disease) in cattle; vCJD in humans (linked to BSE exposure); classic CJD (sporadic, inherited, or acquired).

• Transmission: Not all prion diseases are acquired; some arise sporadically or via inherited mutations.

• Disinfection: Prions resist routine sterilization; require specialized protocols.

Practice Questions and Key Concepts

• Viruses are acellular, lack independent metabolism, and require host cells for replication.

• Virion = complete particle; capsid = protein coat; envelope = host-derived lipid membrane with viral proteins.

• Attachment depends on specific host receptors; replication requires compatible internal factors.

• Tobacco mosaic filtration showed a filterable agent, not direct proof of acellularity.

• Enveloped viruses are more sensitive to detergents due to their lipid envelope.

• Lytic cycle: attachment, penetration, biosynthesis, assembly, release.

• Prophage: phage genome maintained in bacteria; induction triggers lytic cycle.

• Animal virus entry: membrane fusion, endocytosis, or direct penetration.

• Retroviral replication: attachment/entry → reverse transcription → integration → RNA/protein production → assembly/release.

• Latent infection: little/no virus production between reactivations; chronic productive: continuous production.

• Proto-oncogene: normal growth; oncogene: excessive growth. Viruses promote cancer by gene insertion, protein expression, inflammation, or immune suppression.

• About 15% of human cancers are virus-associated (introductory estimate).

• Virus cultivation: living animals, embryonated eggs, or cell cultures.

• Plaque assay: $\text{PFU/mL} = \frac{\text{Plaques}}{\text{Dilution} \times \text{Volume (mL)}}$

• Egg allergy does not automatically preclude egg-based influenza vaccines under current U.S. guidance.

• Viroid: circular RNA without capsid; prion: infectious protein, no nucleic acid.

• Prions propagate by templating misfolding, not by genome replication.

• BSE (cattle) and vCJD (humans) are linked prion diseases.

Summary Table: Key Differences Among Viruses, Viroids, and Prions

Agent	Genome	Capsid	Envelope	Replication	Hosts
Virus	DNA or RNA	Yes	Sometimes	Genome-directed in host cell	Bacteria, plants, animals
Viroid	RNA (circular, small)	No	No	Host enzymes copy RNA	Plants
Prion	None	No	No	Protein misfolding templating	Animals, humans

Additional info: These notes are aligned with Pearson Microbiology learning goals for Chapter 13 and include expanded academic context for clarity and exam preparation.