Comprehensive Study Guide: Viruses, Prions, Digestive and Respiratory System Infections

Chapter 6 – Viruses and Prions

Nature of Viruses

• Viruses as Non-Living Entities: Viruses are not considered living organisms because they lack cellular structure, cannot carry out metabolism independently, and require a host cell for replication.

• Key Features:

  • No cellular machinery (e.g., ribosomes, mitochondria)

  • Obligate intracellular parasites

  • Do not grow or respond to stimuli outside a host

Capsids

• Definition: A capsid is the protein shell that encases the viral genome.

• Composition: Made of protein subunits called capsomeres.

• Function: Protects viral genetic material and aids in attachment to host cells.

• Structural Variation:

  • Helical: Rod-shaped, e.g., Tobacco mosaic virus

  • Icosahedral: Spherical, e.g., Adenovirus

  • Complex: Irregular shapes, e.g., Bacteriophage

Viral Envelopes

• Definition: A lipid membrane derived from the host cell, surrounding some viruses.

• Advantages: Helps evade host immune response, facilitates entry into host cells.

• Disadvantages: More sensitive to environmental conditions (e.g., drying, detergents) than naked viruses.

• Naked Viruses: Lack an envelope; more resistant to harsh conditions.

Viral Genome Structures

• Types:

  • DNA or RNA

  • Single-stranded (ss) or double-stranded (ds)

  • Linear or circular

• Examples:

  • dsDNA: Herpes simplex virus

  • ssDNA: Parvovirus

  • dsRNA: Rotavirus

  • ssRNA (+): Poliovirus

  • ssRNA (–): Influenza virus

Antigenic Shift and Drift

• Antigenic Drift: Minor changes in viral antigens due to point mutations; leads to seasonal epidemics (e.g., influenza).

• Antigenic Shift: Major changes due to reassortment of genome segments; can cause pandemics.

• Significance: Both processes hinder long-term immunity and complicate vaccine development.

Tropism and Host Range

• Tropism: Specificity of a virus for a particular host tissue or cell type.

• Host Range: The spectrum of hosts a virus can infect (narrow or broad).

Lytic vs. Lysogenic Replication Pathways (Bacteriophages)

• Lytic Pathway:

  • Virus injects DNA, replicates, assembles, and lyses host cell to release progeny.

• Lysogenic Pathway:

  • Viral DNA integrates into host genome (prophage), replicates with host, can later enter lytic cycle.

• Comparison: Lytic leads to cell death; lysogenic allows viral persistence.

Major Steps of Viral Infection

1. Attachment

2. Penetration

3. Uncoating

4. Replication

5. Assembly

6. Release

Types of Viral Infections

• Acute: Rapid onset, short duration (e.g., influenza).

• Chronic Persistent: Continuous viral production (e.g., hepatitis B).

• Latent Persistent: Virus remains dormant, can reactivate (e.g., herpesviruses).

Viruses and Cancer

• Some viruses (oncogenic viruses) can induce cancer by integrating into host DNA and disrupting cell cycle regulation (e.g., HPV and cervical cancer).

Detection of Viral Proteins and Genetic Material

• Protein Detection: ELISA, Western blot

• Genetic Material Detection: PCR, RT-PCR, hybridization assays

Growth and Measurement of Viruses

• Grown in cell cultures, embryonated eggs, or live animals.

• Measured by plaque assays, TCID50, or hemagglutination assays.

Antiviral Drugs – Mechanisms of Action

• Inhibit viral entry, uncoating, nucleic acid synthesis, assembly, or release.

• Examples: Reverse transcriptase inhibitors, protease inhibitors, neuraminidase inhibitors.

Prions

• Definition: Infectious proteins lacking nucleic acids.

• Diseases:

  • Creutzfeldt-Jakob disease

  • Kuru

  • Bovine spongiform encephalopathy (mad cow disease)

Chapter 19 – Digestive System Infections

GI Tract Features Limiting Infection

• Acidic pH of stomach

• Mucus lining

• Peristalsis

• Normal microbiota competition

Digestive System Microbiome

• Composed of diverse bacteria, archaea, viruses, and fungi.

• Functions: Digestion, vitamin synthesis, immune modulation, pathogen resistance.

Key Terms in Digestive Infections

• Diarrhea: Frequent, watery stools.

• Gastritis: Inflammation of the stomach lining.

• Enteritis: Inflammation of the small intestine.

• Gastroenteritis: Inflammation of stomach and intestines.

• Dysentery: Diarrhea with blood and mucus.

• Dehydration: Excessive loss of body water.

• Hypovolemic Shock: Life-threatening low blood volume due to fluid loss.

Identification of Causative Agents

• Stool cultures, antigen detection, PCR, microscopy for parasites.

Major Digestive System Diseases

Disease	Causative Agent(s)	Symptoms	Transmission	Pathogenesis & Virulence	Treatment/Prevention	Epidemiology	Outcomes
Mumps	Mumps virus (Paramyxovirus)	Parotitis, fever	Respiratory droplets	Infects salivary glands	MMR vaccine	Rare in vaccinated populations	Orchitis, meningitis
Rotavirus	Rotavirus	Severe diarrhea in children	Fecal-oral	Damages intestinal villi	Oral vaccine, rehydration	Global, high child mortality	Dehydration
Norovirus	Norovirus	Acute gastroenteritis	Fecal-oral, contaminated food/water	Low infectious dose	Supportive care	Outbreaks in closed settings	Self-limited
Hepatitis viruses	HAV, HBV, HCV, etc.	Jaundice, fatigue	Varies (fecal-oral, blood)	Liver inflammation	Vaccines (A, B), antivirals (B, C)	Worldwide	Cirrhosis, cancer
Dental Caries	Streptococcus mutans	Tooth decay	Normal flora, diet	Acid production	Oral hygiene	Common	Tooth loss
Periodontal Disease	Mixed bacteria	Gum inflammation	Poor hygiene	Biofilm formation	Dental care	Common	Tooth loss
Stomach ulcer	Helicobacter pylori	Abdominal pain	Oral-oral, fecal-oral	Urease, mucosal damage	Antibiotics, PPIs	Global	Bleeding, cancer

Additional info: For other diseases (e.g., Campylobacteriosis, Shigellosis, EHEC, Salmonellosis, Cholera, C. diff, Giardiasis, Amebiasis, Cryptosporidiosis, Pinworms, Hookworms, Acariasis, Trichinellosis, Schistosomiasis), follow the same structure as above for study purposes.

Foodborne Infection vs. Food Poisoning

• Foodborne Infection: Caused by ingestion of pathogens that colonize the GI tract (e.g., Salmonella).

• Food Poisoning: Caused by ingestion of preformed toxins (e.g., Staphylococcus aureus enterotoxin).

Chapter 16 – Respiratory System Infections

Respiratory System as a Portal of Entry

• Large surface area, constant exposure to air, and moist environment make it the most common entry point for microbes.

• Inhalation of droplets, aerosols, and dust particles facilitates transmission.

Key Terms in Respiratory Infections

• Cilia: Hair-like structures that move mucus and trapped particles out of the respiratory tract.

• Sinusitis: Inflammation of the sinuses.

• Mucociliary Escalator: Mechanism that clears mucus and debris from the respiratory tract.

• Pharyngitis: Inflammation of the pharynx (sore throat).

• Epiglottitis: Inflammation of the epiglottis; can obstruct airway.

• Tracheitis: Inflammation of the trachea.

• Bronchitis: Inflammation of the bronchi.

• Croup: Viral infection causing swelling of the larynx and trachea in children.

• Stridor: High-pitched breathing sound due to airway obstruction.

• Pneumonia: Infection of the lungs.

• Dyspnea: Difficulty breathing.

Respiratory Tract Microbiome

• Upper tract contains diverse bacteria (e.g., Streptococcus, Neisseria).

• Helps prevent colonization by pathogens.

Serovars and the Common Cold

• Serovars: Distinct variations within a species of bacteria or viruses.

• Numerous serovars of rhinoviruses make it difficult to develop a universal cure for the common cold.

Major Respiratory Diseases

Disease	Causative Agent(s)	Symptoms	Transmission	Pathogenesis & Virulence	Treatment/Prevention	Epidemiology	Outcomes
RSV	Respiratory syncytial virus	Bronchiolitis, pneumonia in infants	Respiratory droplets	Syncytia formation	Supportive care	Seasonal outbreaks	Severe in infants
Adenovirus	Adenovirus	Pharyngitis, conjunctivitis	Respiratory droplets, fecal-oral	Stable in environment	Supportive care	Year-round	Self-limited
Covid-19	SARS-CoV-2	Fever, cough, dyspnea	Respiratory droplets, aerosols	ACE2 receptor binding	Vaccines, antivirals	Pandemic	ARDS, death
Otitis media	Streptococcus pneumoniae, others	Ear pain, fever	Respiratory tract	Eustachian tube blockage	Antibiotics	Children	Hearing loss
Pertussis	Bordetella pertussis	Whooping cough	Respiratory droplets	Pertussis toxin	DTaP vaccine	Children	Pneumonia
Tuberculosis	Mycobacterium tuberculosis	Chronic cough, weight loss	Aerosols	Intracellular survival	Antibiotics (long-term)	Global	Latent/reactivation

Additional info: For other diseases (e.g., Blastomycosis, Coccidiomycosis, Typical/Atypical Pneumonia, Legionnaire’s Disease, Q fever, Mucormycosis, Histoplasmosis, Aspergillosis, Pneumocystis pneumonia), follow the same structure as above for study purposes.

SARS-CoV-2 Pathophysiology

• Virus binds to ACE2 receptors in respiratory tract, enters cells, triggers immune response, can cause cytokine storm and ARDS (acute respiratory distress syndrome).

Group A Streptococcus Diseases

• Streptococcus pyogenes causes pharyngitis, scarlet fever, rheumatic fever, and necrotizing fasciitis.

Corynebacterium diphtheriae Disease

• Causes diphtheria: sore throat, pseudomembrane formation, potential airway obstruction.

Clinical Presentations of Pneumonia

• Typical Pneumonia: Rapid onset, productive cough, lobar consolidation (e.g., Streptococcus pneumoniae).

• Atypical Pneumonia: Gradual onset, dry cough, diffuse infiltrates (e.g., Mycoplasma pneumoniae).