Viruses

Viruses

General Characteristics

• Viruses are not considered living organisms because they cannot reproduce on their own without a host.

• Basic structure:

  • Protein capsule or capsid.

  • Nucleic acid (DNA or RNA, but not both).

Nucleic Acid Types

• Can be circular (resembling bacteria) or linear (resembling eukaryotes).

• Can be single or double stranded.

• RNA viruses may be segmented.

Classification

• Based on the type of genetic material:

  • DNA viruses.

  • RNA viruses.

  • Retroviruses: Contain RNA and use enzymes to reverse transcribe RNA into DNA, which then integrates into the host's genetic material.

Viral Structure

• Capsid: Protein sheet around the nucleic acid core.

• Enzymes: Some viruses store specialized enzymes within their nucleic acid. Example: reverse transcriptase.

• Envelopes: Many animal viruses have envelopes derived from the host cell's membrane, with viral proteins embedded.

Viral Shapes

• Helical: Protein capsid with genetic material inside. Example: Tobacco mosaic virus.

• Isohedral: Protein capsid with genetic material inside. Example: Adenovirus.

• Bacteriophages: Viruses that infect bacteria; protein structure with genetic material.

• Animal Viruses: Example: Influenza (flu virus) with a protein coat (capsid), genetic material (RNA), and an envelope derived from the host.

Viral Infection

• Obligate intracellular parasites: Found in every kind of organism.

• Host range: Viruses are specific and have a limited host range.

• Tissue tropism: Inside a host, viruses may only infect certain types of tissue. Example: Influenza infects respiratory cells.

Viral Replication

• Viral genome: Tricks the host cell into making viral parts.

• Cell damage: The host cell is often damaged during the infection.

• Location: Viruses can only reproduce inside cells; outside, they are inert.

• Mechanism: Viruses hijack the cell's transcription and translation machinery to make proteins.

  • Transcription: Occurs inside the nucleus.

  • Translation: Occurs in the cytoplasm.

• Mature viruses: Assemble and are released when the cell bursts, infecting other healthy cells.

Viral Morphology

• Basic shapes: Helical and isohedral.

• Naked viruses: Lack an envelope. Example: Poliovirus.

• Complex viruses: Example: Bacteriophages.

• Enveloped viruses: Example: Flu.

• Virion: A virus particle outside the host.

Size Comparison

• Viruses are very small compared to eukaryotic cells and bacteria.

• Examples:

  • Poliovirus

  • Herpes simplex virus

  • Rabies

  • HIV

  • Influenza

  • Adenovirus

  • West Nile

Viral Genomes

• Vary in the type of nucleic acid (DNA or RNA) and the number of strands.

• RNA Viruses:

  • Most are single stranded.

  • Examples: Influenza, measles, common cold.

  • Replicate inside the cell's cytoplasm.

  • High mutation rate: Makes it difficult for the immune system to target and create universal vaccines.

• Retroviruses:

  • Single stranded RNA genome is reverse transcribed into double stranded DNA.

  • Enzyme: Reverse transcriptase copies viral RNA into DNA.

  • Example: HIV (human immunodeficiency virus).

• DNA Viruses:

  • Most are double stranded.

  • Replicated in the nucleus of eukaryotic host cells.

  • Examples: Smallpox, herpes virus.

Viral Diseases

• Examples:

  • Chickenpox

  • Hepatitis B

  • Herpes

  • Mono (kissing disease)

  • HPV (can lead to cervical cancer)

  • HIV (can lead to AIDS)

  • Zika virus

  • Guava virus

Classification Methods

• Taxonomy.

• Types of diseases they cause.

• Type of host they infect.

• Genome expression (RNA viruses, DNA viruses, etc.).

Limitations of Classification

• Not all viruses cause diseases.

• Some viruses cause different diseases under different conditions.

• Common cold: Can be caused by several viruses or bacteria.

• Host infection: Some viruses infect different types of organisms, such as influenza (avian flu, swine flu).

Genome Expression

• Baltimore classification: Sorts viruses based on the relationship between genome structure and expression.

Bacteriophages

• Infect only bacteria.

• Phage: Short for bacteriophage.

• Studied phages: Those that infect $E. coli$.

Reproductive Cycles

• Lytic Cycle:

  1. Attachment: Bacteriophage targets the outside of the bacteria cell.

  2. Injection: Viral genome injected into the bacteria cell.

  3. Synthesis: Host starts making viral parts.

  4. Assembly: Viral parts come together to form mature viruses.

  5. Release: Mature virus particles are released through an enzyme that causes the cell to lyse (burst open).

• Lysogenic Cycle:

  1. Attachment: Bacteriophage attaches to the outside of the bacteria cell.

  2. Injection: Viral genome injected into the bacteria cell.

  3. Integration: Virus integrates itself into the bacterial chromosome.

  4. Replication: Every time the bacteria cell divides, it also copies the virus genome.

  5. Trigger: Cell stress (environmental, chemical) can cause the viral genetic material to excise and begin synthesis.

  6. Synthesis: All bacteria cells with viral genetic material start synthesizing viral parts.

  7. Assembly: Viral parts are assembled.

  8. Release: Mature viruses are released.

Lytic vs. Lysogenic

• Lytic: Immediate viral production.

• Lysogenic: Delay (weeks, months, years) with a latent (dormant) phase. The virus does not immediately kill the infected cell but integrates its nucleic acid into the host cell's genome. Integrated genome is called a prophage.

Prophage

• Integrated viral genome in the lysogenic cycle that replicates with the host cell's DNA.

Phage Conversion

• During integration in the lysogenic cycle, some viral genes may be expressed.

• Phenotype or characteristics of the lysogenic bacterium can be altered.

• Example: Vibrio cholerae.

  • Lysogenic phase introduces a gene that codes for a cholera toxin.

  • Harmless bacteria converted into a disease causing form.

  • Causes intestinal epithelial cells to fill with toxin, resulting in diarrhea and dehydration.

  • Benefit for bacteria: Helps it spread more easily from person to person.

  • Common in third world countries due to lack of running water.

Viral Infections: Persistent vs. Acute

• Categorized based on how rapidly and frequently viruses are produced and the appearance of associated symptoms.

• Persistent Infections: Latent or chronic; individuals have it for life.

• Acute Infections: Rapid replication of the virus leads to sudden symptom onset.

Types of Infections

• Acute: Quick infection, symptoms, and recovery (e.g., flu).

• Chronic: Flare ups over many years (e.g., HIV, hepatitis).

• Latent: Virus remains dormant and reappears due to environmental conditions or stress (e.g., herpes virus).

Influenza

• Lethal virus in human history.

• Pandemic of 1918-1919 (Spanish flu): Infected one third of the world's population.

Characteristics

• Enveloped viruses.

• Three basic types (A, B, C) based on capsid proteins.

• Type A: Most serious, causes epidemics in humans and other animals.

• Types B and C: Mild human infections.

• Subtypes differ in their protein spikes (H and N).

  • H: Allows the virus to enter the host cell.

  • N: Allows it to exit.

Antigenic Drift

• H and N molecules accumulate random mutations.

• Small changes in the H and N proteins such that previous vaccine induced immunity is no longer protective.

• Reason for yearly flu shots.

Genetic Recombination

• Occurs when two strains infect the same cell.

• Multiple hosts: Birds, pigs, humans.

• Virus genomes can be reassorted during infection.

• Antigenic shift: Produces strains of the virus with novel combinations.

Flu Virus Mutations

• Quick change artist: Constantly mutating.

• Frequent changes make it hard for bodies to recognize and fend off the virus.

• Need for a new flu vaccine every year.

Hemagglutinin (H) and Neuraminidase (N)

• Found on the outside of influenza A viruses.

• Combinations of H and N give the flu its name (e.g., $H3N2$, $H1N1$).

• Hemagglutinin: Helps the virus attach to cells.

• Immune system: Recognizes hemagglutinin and produces antibodies.

Antigenic Drift and Shift

• Antigenic Drift: Gradual, subtle genetic mutations.

• Antigenic Shift: Sudden, major genetic change, resulting in a novel virus.

• Pandemics: Can occur if a virus carried by a bird or pig mixes with a human strain.

• Universal Vaccine: Scientists are working to create a universal vaccine.

Flu Pandemics

• Spanish Flu (1918): $H1N1$, killed 50-100 million people worldwide.

• Asian Flu (1957): Killed over 100,000 Americans.

• Hong Kong Flu (1968): Affected 50 million in the US, killed 70,000.

Spanish Flu Details

• Second deadliest plague in history.

• Limited knowledge of viruses at the time.

• No vaccine, antiviral drugs, or antibiotics for secondary infections.

• Prevention efforts: Quarantine and personal hygiene.

Origin of New Flu Strains

• Often originate in the Far East.

• Virus hosts: Ducks, chickens, and pigs.

• Simultaneous infection with different strains favors genetic recombination.

• Viral reassortment of avian, human, and swine viruses.

• $H1N1$ Pandemic of 2009: Viral reassortment of avian, human, and swine viruses affected more younger people.

Coronavirus

• Enveloped virus with a plus single stranded RNA genome.

Diseases Caused

• Many different types.

• SARS CoV-2 (COVID-19).

• Four others cause mild cold like symptoms.

• SARS COVID: Severe acute respiratory syndrome.

COVID-19

• Spread globally from China in January 2020.

• Infected 58 million people and caused 1.4 million deaths by November 2020.

• Vaccines: 70-95% protection.

• Infects the respiratory epithelium by binding of spike proteins to the ACE2 protein on the cell surface.

Symptoms

• Asymptomatic.

• Respiratory tract symptoms.

• Neurological symptoms.

• Acute respiratory distress.

• Pneumonia.

• Kidney failure.

• Death.

• Long term complications.