Viruses, Viroids, and Prions

Chapter 13: Viruses, Viroids, and Prions

Definition of Virus: Derived from Latin meaning 'poison'.
Historical Context: In 1935, Wendell Stanley isolated the tobacco mosaic virus, marking a significant milestone. The invention of the electron microscope around the same period allowed for visualization of viruses.

Obligatory intracellular parasites:
- Must have living host cells to multiply.
Composition:
- Contain either DNA or RNA.
- Lack ribosomes.
- Do not have an ATP-generating mechanism.
- Surrounded by a protein coat that encases the nucleic acid.
Envelopes:
- Some viruses are encapsulated by an envelope.
- Some have spikes protruding from their surface.
- Host range defined by specific receptor sites and cellular factors on host cells.
Attachment Mechanism:
- For infectivity, the virus's outer surface interacts chemically with receptor sites on host cell surfaces.
- Composed of two complementary components held together by weak bonds.
- Attachment and receptor sites vary by virus type.
- Bacteriophages: Attach to cell walls or fimbriae/flagella of host bacteria.
- Animal Viruses: Attach to receptor sites on plasma membranes of host cells.

Virion: A complete, fully developed infectious viral particle composed of nucleic acid and a protein coat.
Structural Components:
- Nucleic acid can be single-stranded or double-stranded (DNA or RNA).
- Capsid: The protein coat.
- Capsomeres: Protein subunits forming the capsid.
- Envelope: A combination of lipids, proteins, and carbohydrates.
- Spikes: carbohydrate-protein complexes projecting from the envelope that help with host attachment.
- Total amounts of nucleic acid vary from a few thousand up to 250,000 nucleotides.

Types of Capsids:
- Helical: Rigid or flexible rods (e.g., Rabies, Ebola viruses).
- Polyhedral: Regular structures (icosahedrons) like adenovirus and poliovirus.
- Enveloped Viruses: Include Herpes and Influenza viruses.
- Complex Viruses: Bacteriophage, poxviruses.

A healthy human can harbor up to 10 permanent infectious viruses.
Human Virome: The viral portion of the human microbiome, including persistent and latent viruses.
Retrovirus Impact: Genetic material integrated into human chromosomes constitutes about 8% of the human genome. Predominantly, the virome consists of bacteriophages.
Bacteriophage Roles:
- Influence human health and disease by regulating bacterial populations;
- Bacteriophages exist in high numbers within mucosal barriers (mouth, intestines).

“Kill the Winner”: Bacteriophages target dominant bacterial species, thereby preventing pathogenic colonizers.
“Kill the Competition”: Bacteriophages help maintain bacterial diversity within microbiomes by killing competing bacterial strains.

Family Names: End with -viridae.
Genus Names: End with -virus.
Viral Species: Groups of viruses sharing the same genetic information and ecological niche (e.g., Herpesviridae: Herpesvirus).
Examples:
- Herpesviridae -> Herpesvirus -> Human herpesvirus (HHV-1, HHV-2, HHV-3).
- Retroviridae -> Lentivirus -> Human immunodeficiency virus (HIV-1, HIV-2).

Bacteriophage Cultivation:
- Plaques formed on lawns of bacteria by bacteriophage.
- Typically cultured in living animals, embryonated eggs, or cell cultures.
Cell Cultures:
- Normal cells (primary): Often die out after few generations.
- Diploid cell lines: Maintain for about 100 generations.
- Continuous cell lines: Transformed cancerous cells that can replicate indefinitely.

Cytopathic Effects: Changes observed in host cells post-infection.
Serological Tests: Detect antibodies against viruses in a patient or utilize antibodies for identification.
Nucleic Acids: Use of techniques such as PCR (Polymerase Chain Reaction) and RFLPs (Restriction Fragment Length Polymorphisms).
Cytopathic Effects Characteristics:
- Halt macromolecular synthesis in the host cell.
- Induces lysosomal enzymes release.
- Formation of multinucleated giant cells (syncytia).
- Host cell transformations that may lead to cancer.

Lytic Cycle:
1. Attachment: Phage attaches to host cell via tail fibers.
2. Penetration: Lysozyme opens cell wall; phage injects DNA.
3. Biosynthesis: Host's cellular machinery produces phage DNA and proteins.
4. Maturation: Assembly of new phage particles.
5. Release: Host cell lyses and releases new virions.

Phage DNA integration into bacterial chromosome, forming a prophage.
The integrated DNA can be replicated and passed on during numerous bacterial divisions before entering the lytic cycle.

Oncogenic Virus: Viruses that can induce tumors in animals, accounting for approximately 10% of cancers.
Key Characteristics of Transformed Cells:
- Increased growth beyond normal limits.
- Loss of contact inhibition, meaning they continue to divide despite contact with other cells.
- Presence of tumor-specific transplant antigens or T antigens.
Oncogenic DNA Viruses Include:
- Herpesviridae (Epstein-Barr virus associated with lymphomas).
- Papovaviridae (HPV linked to cervical cancer).
- Hepadnaviridae (HBV associated with liver cancer).

Latent Viral Infections: Typically asymptomatic for years and can reactivate (e.g., Cold sores, Shingles).
Persistent Viral Infections: Virions build up slowly over time leading to chronic diseases (e.g., HIV/AIDS).

Prions: Infectious protein particles that cause spongiform encephalopathies leading to brain degeneration (e.g., Mad Cow Disease).
Viroids: Small, infectious, circular RNA molecules that impact plants.
Virusoids: Infectious RNA enclosed in a protein coat, distinct from typical virions.

Transmission: Primarily through wounds or insects since their cell wall is impenetrable.
Classification of some significant plant viruses and their transmission methods noted.

Detailed taxonomy including disease associations, structure, and images of various viruses grouped by DNA and RNA types along with key examples.

These notes encompass a wealth of information about viruses, including their structure, function, replication cycles, impact on human health, and distinctions from other infectious agents such as viroids and prions.