ch 11

Viral Genomics, Diversity, and Ecology

Genetic Diversity of Viruses

Viruses exhibit remarkable genetic diversity, which influences their replication strategies, host range, and evolutionary potential. This diversity is especially notable when comparing bacteriophages (viruses that infect bacteria) and human viruses.

• Bacteriophages: Often have double-stranded DNA genomes, but can also possess single-stranded DNA or RNA genomes. They display a wide range of genetic arrangements and replication mechanisms.

• Human Viruses: Can have DNA or RNA genomes, which may be single- or double-stranded. Human viruses include retroviruses (e.g., HIV), hepadnaviruses (e.g., Hepatitis B), and others with unique replication strategies.

• Key Point: The diversity in viral genomes leads to differences in replication, mutation rates, and adaptability.

Viral Replication Strategies

Viruses replicate using various mechanisms, depending on their genome type and host cell.

• DNA Viruses: Typically replicate in the host cell nucleus using host enzymes. Example: Herpesviruses.

• RNA Viruses: Usually replicate in the cytoplasm and often encode their own RNA-dependent RNA polymerase. Example: Influenza virus.

• Retroviruses: Use reverse transcriptase to convert their RNA genome into DNA, which integrates into the host genome. Example: HIV.

• Bacteriophages: Can undergo lytic (destroying the host cell) or lysogenic (integrating into the host genome) cycles.

Key Differences: Location of replication, type of genome, use of host vs. viral enzymes, and potential for genome integration.

Positive-Strand vs. Negative-Strand RNA Viruses

Single-stranded RNA viruses are classified based on the polarity of their RNA genome.

• Positive-Strand RNA Virus: Genome can serve directly as mRNA for protein synthesis.

• Negative-Strand RNA Virus: Genome is complementary to mRNA and must be transcribed into a positive strand before translation.

Example: Poliovirus is a positive-strand RNA virus; Influenza virus is a negative-strand RNA virus.

Reverse Transcription and Retroviruses

Retroviruses have a unique genetic information flow, using reverse transcription to convert RNA into DNA.

• Reverse Transcriptase: Enzyme that synthesizes DNA from an RNA template.

• Retrovirus Example: HIV, which causes AIDS.

Equation:

$\text{RNA} \xrightarrow{\text{reverse transcriptase}} \text{DNA}$

Unique Features of Selected Viruses

• Poxviruses: Large, complex DNA viruses that replicate in the cytoplasm. Cause skin lesions (e.g., smallpox).

• Adenoviruses: Infect respiratory tract, gastrointestinal tract, eyes, and urinary tract.

• Herpesviruses: Cause cold sores (Herpes Simplex 1), chickenpox, and shingles (Varicella-Zoster).

• Coronaviruses: Cause respiratory diseases such as the common cold, SARS, MERS, and COVID-19.

• Rabies Virus: Bullet-shaped, RNA virus in the Rhabdoviridae family; causes rabies.

• Reoviruses: Double-stranded RNA viruses with icosahedral symmetry; include rotavirus, a cause of gastroenteritis.

• Hepadnaviruses: Infect liver cells (hepatocytes); example: Hepatitis B virus.

Antigenic Drift and Shift

Influenza viruses undergo genetic changes that help them evade the immune system.

• Antigenic Drift: Gradual accumulation of mutations in viral genes, leading to new strains.

• Antigenic Shift: Abrupt, major change due to reassortment of genetic material between different viral strains, resulting in new subtypes.

Associated Virus: Influenza A virus.

Viral, Viroid, and Prion Diseases

Viruses, viroids, and prions are all infectious agents, but differ fundamentally in structure and the diseases they cause.

Agent	Composition	Diseases	Hosts
Virus	DNA or RNA + protein coat (sometimes lipid envelope)	Colds, influenza, AIDS, etc.	Animals, plants, bacteria, archaea
Viroid	Short, circular single-stranded RNA (no protein coat)	Plant diseases (e.g., potato spindle tuber)	Plants only
Prion	Protein only (no nucleic acid)	Neurodegenerative diseases (e.g., Creutzfeldt-Jakob)	Animals, humans

Viroids

Viroids are the smallest infectious agents, consisting solely of a short, circular RNA molecule. They lack a protein coat and infect only plants, causing diseases that can stunt growth or cause abnormal development.

Prions

Prions are infectious proteins that lack nucleic acids. They cause disease by inducing misfolding of normal host proteins, leading to neurodegenerative disorders.

• Native Form (PrPC): Normal, alpha-helix-rich structure; non-infectious.

• Pathogenic Form (PrPSc): Misfolded, beta-sheet-rich structure; infectious and resistant to degradation.

Key Point: Prions are unique among infectious agents for being composed solely of protein.

Comparison: Prions vs. Viroids vs. Viruses

• Prion vs. Viroid: Prion is protein only; viroid is RNA only.

• Prion vs. Virus: Prion is protein only; virus contains nucleic acid and protein coat.

Examples of Prion Diseases

• Scrapie: Sheep

• Mad Cow Disease (Bovine Spongiform Encephalopathy): Cattle

• Chronic Wasting Disease: Deer and elk

• Creutzfeldt-Jakob Disease: Humans

Key Vocabulary

• Hepadnavirus: Virus with DNA genome replicating via an RNA intermediate.

• Negative Strand: Nucleic acid strand complementary to mRNA.

• Positive Strand: Nucleic acid strand with the same sense as mRNA.

• Prion: Infectious protein lacking nucleic acid.

• Retrovirus: Virus with RNA genome replicated via a DNA intermediate.

• Reverse Transcription: Copying genetic information from RNA into DNA.

• RNA Replicase: Enzyme producing RNA from an RNA template.

• Viroid: Infectious RNA lacking a protein coat.

Summary Table: Types of Viral Replication

Type	Genome	Replication Site	Key Enzymes	Example
DNA Virus	DNA	Nucleus	Host enzymes	Herpesvirus
RNA Virus	RNA	Cytoplasm	RNA-dependent RNA polymerase	Influenza virus
Retrovirus	RNA	Cytoplasm & Nucleus	Reverse transcriptase	HIV
Bacteriophage	DNA or RNA	Bacterial cytoplasm	Phage or host enzymes	Lambda phage

Additional info: This guide expands on the provided study questions with definitions, examples, and summary tables for clarity and exam preparation.