Characterizing and Classifying Viruses, Viroids, and Prions

General Characteristics of Viruses

Alive? The Nature of Viruses

Viruses are unique biological entities that blur the line between living and non-living. They are obligate intracellular parasites, meaning they require a host cell to reproduce and cannot carry out metabolic processes independently.

• Genetic Material: Viruses contain either DNA or RNA, but never both.

• Protein Coat: Their genetic material is surrounded by a capsid (protein coat).

• Replication: Viruses hijack the host cell's machinery to multiply, as they lack their own enzymes for metabolism.

• Transfer Structures: They synthesize structures to transfer their nucleic acid to other cells.

Why can’t an antiviral drug inhibit viral multiplication? Most antiviral drugs target viral enzymes or processes, but viruses rely almost entirely on host cell machinery, making selective inhibition difficult.

Characteristics of Viruses

Extracellular and Intracellular States

Viruses exist in two distinct states:

• Extracellular (Virion): The virus is outside a host cell, with a capsid surrounding its nucleic acid. Some have a phospholipid envelope.

• Intracellular: The capsid is removed, and the virus exists as naked nucleic acid within the host cell.

Structure of Viral Genomes

Nucleic Acid Types

Viral genomes are highly variable:

• Can be DNA or RNA (never both).

• May be single-stranded or double-stranded.

• Can be linear or circular.

Structure: Capsid and Envelope

Capsid and Envelope Components

• Capsid: Protein coat composed of subunits called capsomeres, protecting viral nucleic acid.

• Envelope: Some viruses acquire a phospholipid envelope from the host cell during replication or release, often with glycoprotein spikes.

• Mutability: Envelope proteins are highly mutable, affecting antibody and vaccine effectiveness.

Viral Morphology

Shapes and Structures

Viruses display diverse morphologies:

• Helical: Cylindrical capsid with nucleic acid inside.

• Polyhedral: Many-sided, often icosahedral (20 faces).

• Enveloped: Spherical, with helical or polyhedral capsid inside.

• Complex: Capsids with additional structures, such as tail fibers.

Host Range and Specificity

Host Range

Viruses can infect all forms of life, but many are specific to certain cell types or species. This specificity is determined by:

• Attachment Capabilities: Ability to bind to host cell receptors.

• Machinery Compatibility: Host cell must support viral replication.

Bacteriophages (phages) infect bacteria and are used in research and therapeutic applications.

Size Comparison of Virions

Relative Sizes

Viruses are much smaller than cells and organelles.

• Red blood cell: 10,000 nm

• E. coli: 1,000 x 3,000 nm

• Bacterial ribosome: 25 nm

• Poliovirus: 30 nm

• Bacteriophage MS2: 24 nm

• Bacteriophage T4: 50 x 225 nm

• Smallpox virus: 200 x 300 nm

• Tobacco mosaic virus: 15 x 300 nm

Novel Properties of Viruses

Comparison to Cells

Viruses differ fundamentally from cells in several ways:

Viruses	Cells
Inert outside host cell	Metabolize independently
Do not divide or grow	Divide and grow
Obligate intracellular parasites	Cellular
Contain either DNA or RNA	Contain both DNA and RNA
Highly diverse in size (10–500 nm)	200 nm to 12 cm
Protein coat (capsid)	Surrounded by plasma membrane
Replicate using host enzymes	Self-replicating by mitosis/meiosis

Classification of Viruses

Criteria for Classification

Virus classification is based on:

• Type of nucleic acid (DNA or RNA)

• Presence of an envelope

• Shape

• Size

Viral genera are organized into families; relationships among viruses are not fully understood.

Viral Replication in Bacteria

Lytic and Lysogenic Cycles

Viral replication in bacteria occurs via two main cycles:

• Lytic Cycle: Results in host cell lysis and death.

• Lysogenic Cycle: Viral DNA integrates into host genome and remains latent.

Five stages of lytic cycle: Attachment, Entry, Synthesis, Assembly, Release.

Lysogenic Cycle

• Phage DNA integrates into host DNA (prophage).

• Host cell divides, passing prophage to daughter cells.

• Prophage may excise and enter lytic cycle.

Consequences of Lysogeny

• Lysogenic cells are immune to infection by same phage type.

• Phage conversion: Host cell acquires new properties (e.g., toxin production).

• Specialized transduction: Both phage and host DNA are transferred to new host.

Multiplication of Animal Viruses

Attachment and Entry

• Attachment: Chemical attraction between viral proteins and cell receptors.

• Entry: Three mechanisms—direct penetration, receptor-mediated endocytosis, fusion (for enveloped viruses).

• Uncoating: Capsid is removed, releasing viral genome.

Eclipse period: Virus is disassembled and not detectable.

Synthesis, Maturation, and Release

• DNA Viruses: DNA replicated in nucleus; proteins synthesized in cytoplasm.

• RNA Viruses: RNA replicated in cytoplasm; positive-sense RNA acts as mRNA, negative-sense RNA must be transcribed.

• Release: Enveloped viruses bud from cell; non-enveloped viruses cause cell rupture.

Retroviruses

• Contain reverse transcriptase enzyme.

• Copy viral RNA to produce double-stranded DNA, which integrates into host genome as a provirus.

• Provirus is permanent and cannot be excised.

Latent vs Persistent Viral Infections

Types of Infection

• Latent Infection: Virus remains dormant in host cell for long periods without causing symptoms.

• Persistent Infection: Disease develops gradually and is often fatal.

The Role of Viruses in Cancer

Oncogenes and Tumor Formation

• Protooncogenes: Promote cell growth and division.

• Uncontrolled activation leads to cancer.

• Some viruses carry oncogenes or activate host oncogenes.

• Viruses cause 20–25% of human cancers (e.g., Burkitt's lymphoma, Hodgkin's disease, Kaposi's sarcoma, cervical cancer).

Culturing Viruses in the Laboratory

Methods of Culturing

• Viruses require host cells for growth.

• Three types of media: mature organisms, embryonated eggs, cell cultures.

• Bacteriophages: Plaque method used to detect and count viruses (measured in plaque-forming units, PFU).

Culturing Animal Viruses

• Living animals, embryonated eggs, and cell cultures are used.

• Cell lines: primary, diploid, continuous (immortal).

• Cytopathic effect (CPE) is measured to assess viral growth.

Identification of Viruses

Methods

• Electron microscopy for visualization.

• Serological methods (antibody detection).

• Cytopathic effects.

• RFLP and PCR for DNA amplification.

Plant Viruses and Viroids

Plant Virus Effects

• Cause color change, deformed growth, wilting, stunted growth.

• Infection often requires cell wall damage (parasites, wounds, insect feeding).

• Some plant viruses multiply within insects and spread via pollen.

Viroids

• Extremely small, circular pieces of single-stranded RNA.

• Infectious and pathogenic in plants.

• Lack capsid; do not code for proteins.

• Viroid RNA adheres to complementary plant RNA, leading to degradation and disease.

Other Parasitic Particles: Prions

Characteristics of Prions

• Proteinaceous infectious agents.

• Can be destroyed by proteases or incineration.

• Alter normal proteins into infectious forms.

• Cause neurological diseases (spongiform encephalopathies): Mad Cow disease, Creutzfeldt-Jakob, scrapie, kuru.

• Transmitted by ingestion, transplantation, contact with infected tissues, or genetically.

• No standard treatment for prion diseases.

Comparison of Viruses, Viroids, Prions, and Bacterial Cells

Key Differences

Entity	Genetic Material	Structure	Replication	Pathogenicity
Virus	DNA or RNA	Capsid, sometimes envelope	Host cell machinery	Animals, plants, bacteria
Viroid	ssRNA	No capsid	Host cell enzymes	Plants
Prion	None	Protein only	Induces misfolding	Animals (neurological)
Bacterial Cell	DNA	Cell wall, membrane	Binary fission	Animals, plants