Viruses, Viroids, and Prions: Structure, Classification, and Pathogenesis

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Chapter 13: Viruses, Viroids, and Prions

Viral Structure and Components

Viruses are acellular infectious agents composed of genetic material (either DNA or RNA, never both) surrounded by a protein coat. Some possess additional structures that aid in infection and immune evasion.

Capsid (Protein Coat): The protective protein shell that encloses the viral nucleic acid, composed of subunits called capsomeres.
Envelope: A lipid, protein, and carbohydrate covering derived from the host cell membrane, present in some viruses.
Spikes: Carbohydrate-protein complexes projecting from the surface, facilitating attachment to host cells.
Host Range: The spectrum of host cells a virus can infect, determined by specific attachment sites and cellular factors.

Example: Influenza virus uses spikes (hemagglutinin and neuraminidase) to attach to and enter respiratory epithelial cells.

Viral Morphology

Viruses exhibit diverse shapes, classified by their capsid structure:

Helical Viruses: Capsid forms a hollow, helical cylinder (e.g., Ebola virus).
Polyhedral Viruses: Many-sided, most commonly icosahedral (20 faces, 12 corners; e.g., Adenovirus).
Complex Viruses: Possess complicated structures, such as bacteriophages with polyhedral heads and helical tails. Additional features include tail fibers (attachment) and pins (anchoring).

Viral Size

Viruses range from 20 nm to 1000 nm in length.
For comparison, a human red blood cell is about 10,000 nm wide.

Viral Taxonomy and Classification

Viruses are classified based on genetic material, morphology, and host range.

Family Names: End in -viridae (e.g., Herpesviridae).
Genus Names: End in -virus (e.g., Simplexvirus).
Viral Species: Group of viruses sharing genetic information and ecological niche.
Subspecies: Designated by numbers (e.g., HIV-1).

Growth and Cultivation of Viruses

Viruses require living cells for replication.

Bacteriophages: Grown on bacterial lawns; clear zones called plaques indicate lysis.
Animal Viruses: Grown in embryonated eggs or cell cultures (continuous cell lines).

Example: Influenza virus is commonly grown in chicken eggs for vaccine production.

Viral Identification Techniques

Cytopathic Effects (CPE): Visible changes in host cells due to viral infection.
Serological Tests: Detect antibodies or use antibodies to identify viruses (e.g., ELISA).
Nucleic Acid Techniques: PCR and RFLP analysis for viral genome identification.

Viral Replication Cycles

Bacteriophage Lytic Cycle

Attachment: Phage attaches to host cell via tail fibers.
Penetration: Phage injects DNA into host cell.
Biosynthesis: Host machinery synthesizes viral components.
Maturation: Assembly of viral particles.
Release: Host cell lyses, releasing new virions.

Burst Time: Time from attachment to release (~25 min). Burst Size: Number of virions released per cell (~200).

Lysogenic Cycle

Lysogeny: Phage DNA integrates into host genome as a prophage, remaining latent.
Specialized Transduction: Prophage excises, sometimes carrying host DNA to new cells.

Animal Virus Multiplication

Entry: By endocytosis (engulfment) or fusion (envelope merges with cell membrane).
Uncoating: Removal of capsid to release viral genome.
DNA Virus Replication: Early transcription/translation (enzymes), late transcription/translation (capsid proteins, genome replication).
Retrovirus Replication: Reverse transcriptase synthesizes DNA from RNA; DNA integrates as a provirus.

Viral Pathogenesis

Oncogenesis and Cancer

Oncogenes: Genes that can transform normal cells into cancerous cells when activated by viruses, chemicals, or radiation.
Contact Inhibition: Loss of this property leads to uncontrolled cell growth.
Oncogenic Viruses: DNA (e.g., Herpesviridae, Hepadnaviridae) and RNA (e.g., retroviruses) viruses can induce tumors.
TSTA and T Antigens: Tumor markers on transformed cells.
HTLV-1/2: Human retroviruses causing leukemia.

Latent and Persistent Infections

Latent Infection: Virus remains dormant, reactivates later (e.g., herpes simplex, varicella-zoster).
Persistent Infection: Slow, continuous viral production, often fatal (e.g., measles-induced encephalitis).

Prions

Prions: Infectious proteins (no nucleic acid) causing neurodegenerative diseases.
PrPC: Normal cellular prion protein.
PrPSc: Abnormal, infectious form causing protein aggregation (e.g., Creutzfeldt-Jakob disease, Mad Cow disease).
Spongiform Encephalopathies: Brain tissue develops vacuoles, resembling a sponge.

Plant Viruses and Viroids

Plant Viruses: Infect plants, often transmitted by insects (aphids, leafhoppers) or pollen.
Viroids: Infectious, naked RNA molecules causing plant diseases (no protein coat).

Vector	Role in Transmission
Aphids	Transmit viruses by feeding on plant sap
Leafhoppers	Transmit viruses between plants
Pollen	Can carry viruses to new plants

Major DNA and RNA Virus Families

Family	Genome Type	Envelope	Notable Members/Diseases
Parvoviridae	ssDNA	No	Human Parvovirus (Fifth Disease)
Adenoviridae	dsDNA	No	Respiratory infections, conjunctivitis
Papovaviridae	dsDNA	No	Papillomavirus (warts, cervical cancer)
Poxviridae	dsDNA	Yes	Smallpox, cowpox
Herpesviridae	dsDNA	Yes	Herpes simplex, varicella-zoster
Hepadnaviridae	dsDNA (uses RT)	Yes	Hepatitis B
Picornaviridae	ssRNA (+)	No	Polio, rhinovirus (common cold)
Caliciviridae	ssRNA (+)	No	Norovirus (gastroenteritis)
Coronaviridae	ssRNA (+)	Yes	Coronavirus (SARS, COVID-19)
Filoviridae	ssRNA (–)	Yes	Ebola, Marburg
Orthomyxoviridae	ssRNA (–), segmented	Yes	Influenza A, B, C
Retroviridae	ssRNA (+), 2 copies	Yes	HIV, HTLV

Additional info: ss = single-stranded, ds = double-stranded, (+) = positive sense, (–) = negative sense, RT = reverse transcriptase

Coronavirus Structure and Life Cycle (COVID-19 Focus)

Structural Proteins: S (Spike), E (Envelope), M (Membrane), N (Nucleocapsid).
Replication: Uses RNA-dependent RNA polymerase to synthesize a negative-sense template for new genomes.
Exit: Viral proteins are inserted into the ER; virions bud into the ER lumen and are transported via the Golgi to the cell membrane for release.
Incubation Period: 2–14 days for SARS-CoV-2.
R0 (Reproductive Number): Indicates contagiousness:
- R0 < 1: Disease will decline.
- R0 = 1: Disease remains stable.
- R0 > 1: Disease spreads rapidly (epidemic).

Example: COVID-19's R0 was estimated between 2 and 3 in early outbreaks.

Viral Transmission and Epidemiology

Host Tropism: Specificity for certain hosts or tissues (e.g., bird flu vs. human flu).
Zoonotic Diseases: Diseases that originate in animals and infect humans (e.g., SARS, Ebola).

Laboratory Techniques in Virology

Plaque Assay: Quantifies bacteriophage by counting clear zones on bacterial lawns.
Embryonated Eggs: Used for mass production of animal viruses (e.g., influenza vaccine).
Serological and Molecular Tests: ELISA, PCR, and RFLP for virus detection and identification.

Summary Table: Key Differences in Viral Replication

Replication Step	Bacteriophage (Lytic)	Animal Virus
Attachment	Tail fibers to cell wall proteins	Spikes to cell membrane receptors
Penetration	Injection of nucleic acid	Endocytosis or fusion
Uncoating	Not required	Required (capsid removal)
Biosynthesis	Cytoplasm	Cytoplasm (RNA) or nucleus (DNA)
Release	Host cell lysis	Lysis or budding (enveloped viruses)

Key Terms and Definitions

Virion: A complete, fully developed viral particle.
Prophage: Phage DNA integrated into bacterial chromosome (lysogeny).
Provirus: Viral DNA integrated into eukaryotic host genome (retroviruses).
Oncogene: Gene that can cause cancer when activated.
Prion: Infectious protein causing neurodegenerative disease.

Selected Equations

R0 (Basic Reproductive Number):

Viral Burst Size:

Additional info: This guide integrates foundational concepts, taxonomy, replication cycles, and clinical relevance for college-level microbiology students.