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

Chapter 6 – Viruses and Prions

Viruses: Living or Non-living?

Viruses are unique infectious agents that challenge the definition of life. They are considered non-living because they lack the cellular machinery necessary for independent metabolism and reproduction.

• Not Living: Viruses cannot carry out metabolic processes or reproduce independently; they require a host cell for replication.

• Obligate Intracellular Parasites: Viruses depend entirely on host cells for energy, enzymes, and biosynthetic machinery.

• No Cellular Structure: Viruses lack organelles, cytoplasm, and a plasma membrane.

Capsids

The capsid is the protein shell that encases the viral genome, providing protection and aiding in host cell attachment.

• Composition: Made of protein subunits called capsomeres.

• Function: Protects viral genetic material and facilitates transfer into 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

Some viruses possess a lipid envelope derived from the host cell membrane.

• Enveloped Viruses: Have a lipid bilayer with embedded proteins.

• Naked Viruses: Lack an envelope; only have a capsid.

• Advantages of Enveloped Viruses: Can evade host immune responses more easily, but are more sensitive to desiccation and disinfectants.

• Advantages of Naked Viruses: More resistant to environmental stresses.

Viral Genome Structures

Viral genomes are highly diverse in structure and composition.

• DNA Viruses: Can be double-stranded (dsDNA, e.g., Herpesvirus) or single-stranded (ssDNA, e.g., Parvovirus).

• RNA Viruses: Can be double-stranded (dsRNA, e.g., Rotavirus) or single-stranded (ssRNA, e.g., Influenza virus).

• Genome Polarity: ssRNA viruses can be positive-sense (e.g., Poliovirus) or negative-sense (e.g., Rabies virus).

Antigenic Shift and Antigenic Drift

These are mechanisms by which viruses, especially influenza, alter their surface proteins to evade immune detection.

• Antigenic Drift: Gradual accumulation of mutations in viral genes encoding surface proteins. Leads to seasonal flu variation.

• Antigenic Shift: Abrupt, major change due to reassortment of genome segments, often resulting in pandemics.

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

Tropism and Host Range

Tropism refers to the specificity of a virus for a particular host tissue, while host range is the spectrum of hosts a virus can infect.

• Determined by: Viral surface proteins and host cell receptors.

• Example: HIV targets CD4+ T cells; Rabies virus infects many mammals.

Lytic vs. Lysogenic Replication Pathways (Bacteriophages)

Bacteriophages can replicate via two main pathways:

• Lytic Pathway:

  1. Attachment

  2. Penetration

  3. Biosynthesis

  4. Maturation

  5. Release (host cell lysis)

• Lysogenic Pathway:

  1. Attachment and Penetration

  2. Integration of phage DNA into host genome (prophage)

  3. Replication with host cell

  4. Induction into lytic cycle under stress

• Comparison: Lytic cycle results in host cell death; lysogenic cycle allows viral genome persistence.

Major Steps of Viral Infection

1. Attachment

2. Penetration

3. Uncoating

4. Biosynthesis

5. Assembly

6. Release

Types of Viral Infections

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

• Chronic Persistent: Continuous viral replication (e.g., Hepatitis B).

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

Viruses and Cancer

Some viruses can induce cancer by integrating into host DNA and disrupting normal cell regulation (oncogenic viruses).

• Examples: Human papillomavirus (HPV), Hepatitis B and C viruses, Epstein-Barr virus.

Detection of Viral Proteins and Genetic Material

• Protein Detection: ELISA, Western blot, immunofluorescence.

• Genetic Material Detection: PCR, RT-PCR, nucleic acid hybridization.

Growth and Measurement of Viruses

• Cell Culture: Viruses are grown in living cells (cell lines, embryonated eggs, or animals).

• Plaque Assay: Quantifies infectious virus particles by counting plaques on a cell monolayer.

Antiviral Drugs: Mechanisms of Action

• Entry Inhibitors: Block viral attachment or fusion.

• Polymerase Inhibitors: Inhibit viral genome replication.

• Protease Inhibitors: Prevent viral protein processing.

• Integrase Inhibitors: Block integration of viral DNA (e.g., HIV drugs).

Prions

Prions are infectious proteins that cause neurodegenerative diseases by inducing abnormal folding of normal proteins.

• Examples of Prion Diseases:

  • Creutzfeldt-Jakob disease (CJD)

  • Bovine spongiform encephalopathy (BSE, "mad cow disease")

  • Kuru

Chapter 19 – Digestive System Infections

GI Tract Features Limiting Infection

• Acidic pH: Stomach acid destroys many pathogens.

• Mucus: Traps microbes and facilitates removal.

• Peristalsis: Moves contents, preventing colonization.

• Normal Microbiota: Compete with pathogens for resources.

Digestive System Microbiome

• Composition: Diverse bacteria, archaea, fungi, and viruses.

• Functions: Aid digestion, synthesize vitamins, modulate immunity, and outcompete pathogens.

Key Terms in Digestive Infections

• Diarrhea: Frequent, watery stools due to increased intestinal motility or secretion.

• Gastritis: Inflammation of the stomach lining.

• Enteritis: Inflammation of the small intestine.

• Gastroenteritis: Inflammation of the stomach and intestines, often causing vomiting and diarrhea.

• Dysentery: Diarrhea with blood and mucus, often due to invasive pathogens.

• Dehydration: Excessive loss of body water, a major risk in diarrheal diseases.

• Hypovolemic Shock: Life-threatening drop in blood volume due to severe fluid loss.

Identification of Causative Agents

• Stool Culture: Isolation and identification of bacteria.

• Antigen Detection: ELISA, rapid tests for specific pathogens.

• Molecular Methods: PCR for pathogen DNA/RNA.

Major Digestive System Diseases and Organisms

Disease/Organism	Causative Agent(s)	Symptoms	Transmission	Pathogenesis & Virulence	Treatment/Prevention	Epidemiology	Outcomes/Complications
Mumps	Mumps virus (Paramyxovirus)	Parotitis, fever, headache	Respiratory droplets	Infects salivary glands	MMR vaccine	Rare in vaccinated populations	Orchitis, meningitis
Rotavirus	Rotavirus (Reovirus)	Severe diarrhea, vomiting	Fecal-oral	Destroys enterocytes	Oral vaccine, rehydration	Common in children	Dehydration
Norovirus	Norovirus (Calicivirus)	Acute gastroenteritis	Fecal-oral, contaminated food/water	Low infectious dose	Supportive care	Outbreaks in closed settings	Dehydration
Hepatitis viruses	HAV, HBV, HCV, HDV, HEV	Jaundice, fatigue, liver dysfunction	Varies (fecal-oral, blood, sexual)	Infect hepatocytes	Vaccines (HAV, HBV), antivirals	Global distribution	Cirrhosis, liver cancer

Additional info: For brevity, only a subset of diseases is shown. Students should refer to class materials for full details on all listed diseases.

Foodborne Infection vs. Food Poisoning

• Foodborne Infection: Illness caused by ingestion of pathogens that grow in the host (e.g., Salmonella).

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

• Comparison: Infections have longer incubation, may involve fever; intoxications have rapid onset, often without fever.

Chapter 16 – Respiratory System Infections

Respiratory System as a Portal of Entry

• Large Surface Area: Exposed to air, facilitating pathogen entry.

• Constant Airflow: Inhalation brings in microbes.

• Thin Epithelial Barriers: Allow easy access to bloodstream.

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 lungs.

• 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, leading to a barking cough.

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

• Pneumonia: Infection of the lung alveoli.

• Dyspnea: Difficulty breathing.

Respiratory Tract Microbiome

• Upper Respiratory Tract: Diverse microbiota, including Streptococcus, Staphylococcus, and Neisseria.

• Lower Respiratory Tract: Generally sterile in healthy individuals.

• Role: Competes with pathogens, modulates immune responses.

Serovars and the Common Cold

• Serovars: Distinct variations within a species of bacteria or viruses, based on antigenic properties.

• Impact: Multiple serovars of cold viruses (e.g., rhinoviruses) make it difficult to develop a universal cure or vaccine.

Major Respiratory Diseases and Organisms

Disease/Organism	Causative Agent(s)	Symptoms	Transmission	Pathogenesis & Virulence	Treatment/Prevention	Epidemiology	Outcomes/Complications
RSV	Respiratory syncytial virus	Bronchiolitis, pneumonia in infants	Respiratory droplets	Syncytia formation in airways	Supportive care	Common in young children	Respiratory failure
Adenovirus	Adenovirus	Pharyngitis, conjunctivitis	Respiratory droplets, fecal-oral	Stable in environment	Supportive care	Outbreaks in close quarters	Pneumonia
Covid-19	SARS-CoV-2	Fever, cough, dyspnea, loss of taste/smell	Respiratory droplets, aerosols	ACE2 receptor binding, cytokine storm	Vaccines, antivirals, supportive care	Pandemic, global	ARDS, long COVID

Additional info: For brevity, only a subset of diseases is shown. Students should refer to class materials for full details on all listed diseases.

SARS-CoV-2 Pathophysiology

• Entry: Binds ACE2 receptors in respiratory tract.

• Immune Response: Can trigger excessive inflammation (cytokine storm).

• Complications: ARDS, multi-organ failure, long-term sequelae.

Group A Streptococcus (Streptococcus pyogenes) Diseases

• Pharyngitis (strep throat): Sore throat, fever.

• Scarlet fever: Rash, strawberry tongue.

• Rheumatic fever: Autoimmune sequelae affecting heart, joints.

• Glomerulonephritis: Kidney inflammation.

Corynebacterium diphtheriae Disease

• Diphtheria: Sore throat, pseudomembrane formation, potential airway obstruction.

• Virulence: Diphtheria toxin inhibits protein synthesis.

• Prevention: DTaP vaccine.

Typical vs. Atypical Pneumonia

• Typical Pneumonia: Caused by Streptococcus pneumoniae; rapid onset, productive cough, lobar consolidation.

• Atypical Pneumonia: Caused by organisms like Mycoplasma pneumoniae; gradual onset, dry cough, diffuse infiltrates.

• Clinical Presentation: Typical pneumonia is more severe and acute; atypical is milder but more prolonged.