Chapter 6-Introduction to Viruses, Viroids, and Prions: Structure, Properties, and Classification

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Introduction to Viruses, Viroids, and Prions

Historical Perspective and Discovery of Viruses

The study of viruses began in the late 19th century, with key discoveries that shaped the field of virology. Viruses are unique infectious agents, distinct from cellular life forms.

Louis Pasteur postulated that rabies was caused by an agent smaller than bacteria (1884).
Dmitri Ivanovski introduced the term virus (Latin for "poison").
Ivanovski and Beijerinck demonstrated that tobacco mosaic disease was caused by a virus (1890s).
By the 1950s, virology had become a multifaceted scientific discipline.

Viruses in the Biological Spectrum

Viruses occupy a unique position in the biological world, being the most abundant microbes on Earth and influencing the evolution of all domains of life.

There is no universal agreement on the origin of viruses.
Viruses are considered the most abundant microbes on Earth.
They have played a role in the evolution of Bacteria, Archaea, and Eukarya.
Viruses are obligate intracellular parasites, meaning they require a host cell to replicate.

Properties and Structure of Viruses

General Properties of Viruses

Viruses are noncellular entities with distinct structural and chemical characteristics.

Obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals.
Ultramicroscopic size, typically ranging from 20 nm up to 450 nm in diameter.
Noncellular nature; their structure is compact and economical.
Cannot independently fulfill the characteristics of life.
Inactive macromolecules outside the host cell; active only inside host cells.
Basic structure consists of a protein shell (capsid) surrounding a nucleic acid core.
Nucleic acid is either DNA or RNA, never both.
Nucleic acid can be double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA.
Surface molecules impart high specificity for attachment to host cells.
Multiply by taking control of host cell's genetic material and regulating synthesis and assembly of new viruses.
Lack enzymes for most metabolic processes and machinery for synthesizing proteins.

Viral Size

Viruses are among the smallest infectious agents, requiring electron microscopy for visualization.

Most viruses are less than 0.2 μm in diameter.
The largest viruses, such as Megaviruses and Pandaviruses, can reach 500–1,000 nm, making them 20 times larger than average viruses.

Viral Structure

Viruses are structurally simple, containing only the components necessary for host cell invasion and control.

Viruses bear no resemblance to cells and lack protein-synthesizing machinery.
Components of a virus particle:
- Covering: Capsid (protein coat), Envelope (not present in all viruses)
- Central core: Nucleic acid molecule(s) (DNA or RNA), Matrix proteins, Enzymes (not present in all viruses)

Capsids and Envelopes

The capsid is a protein shell that protects the viral nucleic acid. Some viruses also possess an envelope derived from the host cell membrane.

Capsid together with nucleic acid is called the nucleocapsid.
Viruses lacking an envelope are termed naked viruses.
Capsids are made of identical protein subunits called capsomers.
Two main structural types of capsids:
- Helical: Continuous helix of capsomers forming a cylindrical nucleocapsid.
- Icosahedral: Three-dimensional, symmetrical polygon with 20 sides and 12 corners.
Enveloped viruses acquire their envelope when leaving the host cell; envelope proteins called spikes are essential for attachment to host cells.

Functions of Capsid/Envelope

Protects nucleic acid when the virus is outside the host cell.
Assists in binding to cell surfaces and penetration of viral DNA or RNA into host cells.

Complex Viruses

Some viruses have atypical structures, such as bacteriophages with polyhedral heads and helical tails, or poxviruses with multilayered coverings.

Types of Viral Morphology

Viruses are classified based on their morphology:

Nonenveloped (Naked) Viruses: Helical or icosahedral capsid.
Enveloped Viruses: Helical or icosahedral nucleocapsid surrounded by an envelope.
Complex Viruses: Examples include poxvirus and flexible-tailed bacteriophage.

Viral Genome and Classification

Nucleic Acids

The viral genome consists of either DNA or RNA, encoding genes necessary for host invasion and viral replication.

Number of genes varies from a few to hundreds.
DNA viruses: Usually double-stranded, may be single-stranded, circular or linear.
RNA viruses: Usually single-stranded, may be double-stranded, can be segmented.
Positive-sense RNA: Ready for immediate translation.
Negative-sense RNA: Must be converted to positive-sense before translation.

Other Viral Components

Pre-formed enzymes required for replication:
- Polymerases: Synthesize DNA or RNA.
- Replicases: Copy RNA.
- Reverse transcriptase: Synthesizes DNA from RNA (e.g., HIV).

Classification and Naming of Viruses

Viruses are classified based on structure, chemical composition, and genetic makeup.

The International Committee on the Taxonomy of Viruses recognizes 7 orders, 104 families, and 505 genera.
Families are italicized and end with -viridae; genera end with -virus.
Species are defined by host range, pathogenicity, and genetic makeup.
Placement in families considers capsid type, nucleic acid, envelope presence, size, and site of multiplication.

Important Human Virus Families

Viruses are grouped into families based on their nucleic acid type and other properties.

Family	Genus	Common Name	Disease
Herpesviridae	Herpesvirus	Herpes simplex virus	Herpes, cold sores
Hepadnaviridae	Hepadnavirus	Hepatitis B virus	Serum hepatitis
Papillomaviridae	Papillomavirus	Human papillomavirus	Cervical cancer, warts
Picornaviridae	Enterovirus	Poliovirus	Poliomyelitis
Retroviridae	Lentivirus	HIV	AIDS
Orthomyxoviridae	Influenzavirus	Influenza virus	Flu
Rhabdoviridae	Lyssavirus	Rabies virus	Rabies
Filoviridae	Ebolavirus	Ebola virus	Hemorrhagic fever
Additional info:	Table entries inferred from common human virus families.

Viral Multiplication and Host Interaction

General Phases in Animal Virus Multiplication

Animal viruses follow a specific cycle to infect and replicate within host cells.

Adsorption: Virus binds to specific molecules on the host cell.
Penetration: Genome enters the host cell.
Uncoating: Viral nucleic acid is released from the capsid.
Synthesis: Viral components are produced.
Assembly: New viral particles are constructed.
Release: Viruses are released by budding (exocytosis) or cell lysis.

Adsorption and Host Range

Viruses adsorb specifically to receptor sites on host cell membranes.
Host range: Spectrum of cells a virus can infect (e.g., Hepatitis B infects human liver cells, Poliovirus infects primate intestinal and nerve cells, Rabies infects various mammalian cells).

Penetration and Uncoating

Enveloped viruses enter by fusion with the host membrane.
Enveloped or naked viruses can enter by endocytosis, followed by uncoating.

Synthesis and Assembly

DNA viruses are generally replicated and assembled in the nucleus.
RNA viruses are generally replicated and assembled in the cytoplasm.
Positive-sense RNA is directly translated; negative-sense RNA must be converted first.
Capsid is assembled as an empty shell, then filled with nucleic acid.

Release of Viruses

Budding (exocytosis): Enveloped viruses are released gradually; cell is not immediately destroyed.
Cell lysis: Nonenveloped and complex viruses are released when the cell dies and ruptures.

Cytopathic Effects and Persistent Infections

Viruses can cause visible changes in host cells, known as cytopathic effects (CPE).

Cell damage may include rounding, fusion (syncytia), inclusion bodies, and cell lysis.
Persistent infections occur when the cell harbors the virus without immediate lysis; can last weeks or a lifetime.
Examples: Measles virus (latent in brain cells), Herpes simplex virus (cold sores, genital herpes), Herpes zoster virus (chickenpox, shingles).

Oncogenic Viruses and Transformation

Some animal viruses can permanently alter host genetic material, leading to cancer (oncogenesis).

Transformed cells show increased growth, chromosomal alterations, and indefinite division (tumors).
Oncoviruses: Viruses capable of initiating tumors (e.g., Papillomavirus—cervical cancer, Epstein-Barr virus—Burkitt's lymphoma).

Bacteriophages and Their Replication

Bacteriophage Multiplication Cycle

Bacteriophages are viruses that infect bacteria, following a cycle similar to animal viruses but with key differences.

Adsorption: Binding to specific molecules on the bacterial cell.
Penetration: Genome enters the host cell; only nucleic acid enters, no uncoating required.
Replication: Viral components are produced.
Assembly: Viral components are assembled.
Maturation: Completion of viral formation.
Lysis and Release: Cell lysis releases new phages (lytic cycle).

Lysogeny: The Silent Virus Infection

Some DNA phages enter a reversible state called lysogeny, where the viral genome integrates into the host genome as a prophage.

Prophage is retained and copied during cell division, spreading the virus without killing the host.
Lysogenic conversion can result in production of toxins or enzymes (e.g., Corynebacterium diphtheriae, Vibrio cholerae, Clostridium botulinum).

Comparison of Bacteriophage and Animal Virus Multiplication

Step	Bacteriophage	Animal Virus
Adsorption	Yes	Yes
Penetration	Yes (only nucleic acid)	Yes (entire virus)
Uncoating	No	Yes
Assembly	Yes	Yes
Release	Lysis	Budding or lysis

Cultivation and Identification of Viruses

Methods of Viral Cultivation

Cell (tissue) cultures: Cultured cells support viral replication and allow observation of cytopathic effects.
Bird embryos: Provide a sterile environment and nourishment for viral multiplication.
Live animal inoculation: Animals are injected with viral preparations for study.

Clinical Importance of Viruses

Viruses are the most common cause of acute infections worldwide.
Some viruses have high mortality rates and may be linked to chronic diseases of unknown cause.
Viruses play a major role in Earth's ecosystems.

Detection and Treatment of Viral Infections

Diagnosis is more difficult than for other agents; requires clinical assessment and laboratory tests.
Methods include cell culture, detection of viral components, and immune response (antibodies).
Antiviral drugs can have serious side effects.

Other Nonviral Infectious Particles

Prions

Prions are infectious proteins that lack nucleic acid and cause fatal neurodegenerative diseases.

Extremely resistant to sterilization.
Cause transmissible spongiform encephalopathies (TSEs).
Examples: Scrapie (sheep/goats), Bovine spongiform encephalopathy (mad cow disease), Chronic wasting disease (elk), Creutzfeldt-Jakob Syndrome (humans).

Satellite Viruses and Viroids

Satellite viruses: Require co-infection with another virus for replication (e.g., Adeno-associated virus, Delta agent with hepatitis B).
Viroids: Short pieces of RNA without a protein coat; known to infect plants.

Summary Table: Noncellular Infectious Agents

Agent	Genetic Material	Protein Coat	Host
Virus	DNA or RNA	Yes	Animals, plants, bacteria
Bacteriophage	DNA or RNA	Yes	Bacteria
Prion	None	No	Animals, humans
Satellite Virus	RNA	Yes	Animals (with helper virus)
Viroid	RNA	No	Plants

Key Equations and Concepts

Viral replication rate: Additional info: This equation models the rate of viral infection as proportional to the concentrations of virus and host cells.

Conclusion

Viruses, viroids, and prions represent unique classes of infectious agents with distinct structures, replication strategies, and impacts on health and ecosystems. Understanding their properties and life cycles is essential for microbiology students and for the development of diagnostic and therapeutic approaches.