Viruses and Prions: Structure, Classification, and Impact on Human Health

Chapter 07: Viruses and Prions

Section 7.1: Introduction to Viruses

Viruses are extremely abundant and infect all types of cells, including bacteria, algae, fungi, protozoa, plants, and animals. Their unique nature challenges traditional definitions of life.

• Viruses as Biological Entities: It is more accurate to describe viruses as active or inactive rather than alive or dead. Most viruses cannot multiply independently and require a host cell for replication.

• Obligate Intracellular Parasites: Viruses must invade specific host cells and use the cell's genetic and metabolic machinery to produce new viruses.

• Role in Evolution: Viruses have influenced the genetic makeup of their hosts and may account for a significant portion of the human genome (estimated 40–80% as remnants of ancient viral infections).

• Viruses in the Microbiome: Some viruses are part of the normal human microbiome and can shape cellular evolution.

Additional info: Viruses are not considered living organisms because they lack independent metabolic processes and cellular structure.

Section 7.2: The General Structure of Viruses

Viruses are much smaller than most bacteria and have a simple structure designed for infecting host cells.

• Size Range: Viruses range from 20 nm to 1,500 nm. For example, parvoviruses are about 0.02 μm, while pandoraviruses can be as large as some bacteria.

• Basic Structure: All viruses have a core of genetic material (DNA or RNA) surrounded by a protein coat called a capsid. Some viruses also have an outer envelope derived from the host cell membrane.

• Capsid Types:

  • Helical capsid: Rod-shaped capsomeres form a continuous helix around the nucleic acid.

  • Icosahedral capsid: Three-dimensional, 20-sided structure with 12 corners.

  • Complex capsid: Found in bacteriophages; may have multiple proteins and asymmetrical shapes.

• Enveloped vs. Naked Viruses: Enveloped viruses have a lipid membrane with viral proteins (spikes) for host attachment. Naked viruses lack this envelope.

• Viral Genome: Viruses may have double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA, but never both DNA and RNA.

• Surface Proteins (Spikes): Glycoproteins essential for attachment to host cells.

Additional info: Viral genomes are typically much smaller than cellular genomes, encoding only the proteins necessary for replication and infection.

Table: Comparison of Capsid Types

Capsid Type	Structure	Example Virus
Helical	Continuous helix of capsomeres	Tobacco mosaic virus
Icosahedral	20-sided, 12 corners	Adenovirus
Complex	Multiple proteins, asymmetrical	T4 bacteriophage

Table: Viral Genome Types

Genome Type	Example Virus	Disease
dsDNA	Herpes simplex	Herpes
ssDNA	Parvovirus B19	Skin rash
dsRNA	Rotavirus	Gastroenteritis
(+)ssRNA	Poliovirus	Polio
(-)ssRNA	Influenza virus	Influenza
ssRNA-RT	HIV	AIDS
dsDNA-RT	Hepatitis B virus	Hepatitis B

Section 7.3: How Viruses Are Classified and Named

Viruses are classified based on structure, chemical composition, and genetic makeup. The formal system uses orders, families, and genera.

• Order: Suffix -virales

• Family: Suffix -viridae

• Genus: Suffix virus

• Examples:

  • Herpesviridae (family) includes Simplexvirus (genus), which causes herpes.

  • Rhabdoviridae (family) includes Lyssavirus (genus), which causes rabies.

Table: Important Human Virus Families and Diseases

Family	Genus	Example Virus	Disease
Herpesviridae	Simplexvirus	HSV-1, HSV-2	Herpes
Hepadnaviridae	Orthohepadnavirus	Hepatitis B virus	Hepatitis B
Picornaviridae	Enterovirus	Poliovirus	Polio
Coronaviridae	Coronavirus	SARS-CoV-2	COVID-19
Filoviridae	Ebolavirus	Ebola virus	Ebola fever
Retroviridae	Lentivirus	HIV	AIDS

Section 7.4: How Viruses Multiply

Viruses replicate through a series of steps within host cells. The multiplication cycle varies between animal viruses and bacteriophages.

• Six-Step Multiplication Cycle (Animal Viruses):

  1. Adsorption: Virus attaches to host cell receptors.

  2. Penetration: Virus enters the host cell (often by endocytosis).

  3. Uncoating: Viral envelope and capsid are removed, releasing genetic material.

  4. Synthesis: Viral genome directs host machinery to produce viral components.

  5. Assembly: New viral particles are assembled.

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

• Cytopathic Effects (CPEs): Virus-induced damage alters cell appearance, may cause cell death, inclusion bodies, or syncytia (multinucleate cells).

• Persistent and Transforming Infections: Some viruses integrate into host DNA (provirus) or cause cancer (oncogenic viruses).

• Bacteriophage Life Cycles:

  • Lytic cycle: Results in destruction of the bacterial cell.

  • Lysogenic cycle: Phage DNA integrates into host genome (prophage), may later reactivate.

  • Lysogenic conversion: Acquisition of new traits (e.g., toxin production) by bacteria due to prophage genes.

Table: Comparison of Animal Virus and Bacteriophage Replication

Step	Bacteriophage	Animal Virus
Attachment	Tail fibers to cell wall	Capsid to cell surface receptors
Penetration	Injection of nucleic acid	Endocytosis or fusion
Uncoating	Not required	Required
Synthesis	In cytoplasm	In cytoplasm and/or nucleus
Release	Cell lysis	Budding or cell lysis

Section 7.5: Techniques in Cultivating and Identifying Viruses

Viruses are cultivated for research, vaccine production, and clinical identification using several methods.

• Live Animal Inoculation: Viruses are injected into laboratory animals to study infection and disease.

• Bird Embryos: Embryonated eggs provide a sterile, nourishing environment for viral growth.

• Cell (Tissue) Culture: In vitro systems using animal cells in dishes or bottles; allows observation of cytopathic effects and plaque formation.

• Primary vs. Continuous Cell Lines:

  • Primary cell cultures: Derived directly from animal tissue, retain original characteristics.

  • Continuous cell lines: Altered chromosome numbers, rapid growth, can be subcultured indefinitely.

Section 7.6: Viruses and Human Health

Viruses are a major cause of human disease, with some leading to acute infections and others to chronic or fatal outcomes.

• Common Viral Diseases: Colds, chickenpox, influenza, herpes, warts.

• High Mortality Viruses: Rabies, Ebola.

• Long-Term Debility: Polio, neonatal rubella.

• Antiviral Therapies: Difficult to design due to rapid mutation rates; vaccines are the primary preventive measure. Few antiviral drugs are available; antibiotics are ineffective against viruses.

• Interferon (IFN): A human cell product used in some antiviral treatments.

Section 7.7: Prions and Other Noncellular Infectious Agents

Besides viruses, other noncellular agents can cause disease, including prions, satellite viruses, and viroids.

• Prions: Infectious proteins causing spongiform encephalopathies (e.g., Creutzfeldt-Jakob Disease, mad cow disease). Prions lack nucleic acids and replicate by an unknown mechanism.

• Satellite Viruses: Depend on other viruses for replication (e.g., adeno-associated virus).

• Viroids: Infect plants; consist only of naked RNA strands, lack capsids.

Table: Noncellular Infectious Agents

Agent	Composition	Host	Example Disease
Prion	Protein	Animals, humans	Creutzfeldt-Jakob Disease
Satellite virus	DNA or RNA	Animals, plants	Adeno-associated virus
Viroid	RNA	Plants	Potato spindle tuber disease

Key Equations and Concepts

• Viral Replication Rate: $\text{Rate} = k[\text{Virus}][\text{Host Cell}]$

• Genome Types: $\text{Virus Genome} = \text{DNA} \text{ or } \text{RNA}$

Summary Table: Virus Classification Suffixes

Taxonomic Level	Suffix	Example
Order	-virales	Herpesvirales
Family	-viridae	Herpesviridae
Genus	virus	Simplexvirus