Virology Lecture Notes Review
Relative sizes of host cell, viruses, and bacteria
- Advenovirus: 225\ \text{nm}
- Bacteriophage T4: 90\ \text{nm}
- Rhinovirus: 30\ \text{nm}
- Bacteriophages f2, MS2: 24\ \text{nm}
- Bacteriophage M13: 800\times 10\ \text{nm}
- Tobacco mosaic virus: size not provided in the list
- Prion: size not provided in the list
- Poliovirus: 200\times 20\ \text{nm}; diameter ~30\ \text{nm} (listed values include both
dimensions and a standalone diameter in the source) - Vaccinia virus: 300\times 200\times 100\ \text{nm}
- E. coli (a bacterium): 3000\times 1000\ \text{nm}
- Human red blood cell: 10{,}000\ \text{nm in diameter}
- Rabies virus: 170\times 70\ \text{nm}
- Chlamydia elementary body: 300\ \text{nm}
- Viroid: 300\times 10\ \text{nm}
- Ebola virus: 970\ \text{nm}
- Plasma membrane of red blood cell: 10\ \text{nm thick}
- Other notables listed: Tobacco mosaic virus, Prion
Discovery of Viruses
- Viruses studied in the late 19th century
- 1886: Mayer demonstrated that tobacco mosaic disease (TMD) was transmissible from a diseased plant to a healthy plant
- 1892: Iwanowski found that the infectious agent could pass through a filter designed to capture bacteria; could infect healthy plants with the filtered fluid
- The agent was filterable and not obviously bacterial at the time
Definition of a Virus (basic criteria)
- Not bacterial or fungal; not a cellular organism
- Small in size (filterable)
- Obligatory intracellular parasites: absolutely require living host cells to multiply
- Contain a single type of nucleic acid, either ext{DNA} or ext{RNA}
- Contain a protein coat (capsid) surrounding the nucleic acid
- Multiply inside living cells by using the host cell's synthesizing machinery
- Cause synthesis of specialized structures that can transfer the viral nucleic acid to other cells
To live or not to live
- Virus is Latin for poison
- Viruses are technically not living organisms
- They are inert outside living host cells
- Do not perform metabolic processes on their own; cannot replicate independently
Viral Structure
- Nucleic acid: can be ext{dsDNA}, ext{ssDNA}, ext{ssRNA}, ext{dsRNA}
- Capsid and optional envelope
- Capsid protects the nucleic acid; capsid is made of capsomeres
- Envelope may surround the capsid (enveloped viruses)
- Spike proteins on envelope or capsid mediate attachment to host cells and can aid in identification
- Non-enveloped virus: nucleic acid inside with a capsid composed of capsomeres; no viral envelope
- Example morphology: polyhedral (icosahedral) form
- TEM size example: ~40\ \text{nm} (as labeled in the figure)
- Enveloped virus: capsid plus envelope with spike proteins; envelope derived from host membranes; generally spherical appearance
- Example: Influenza (enveloped polyhedral);
- Herpes simplex virus is an enveloped virus with a polyhedral capsid
- Spikes on envelope or capsid function in host attachment and are useful for identification
Viral Morphology
- Morphological types (classifications based on capsid structure, mainly via electron microscopy):
- Helical
- Polyhedral (icosahedral)
- Enveloped (can be helical or polyhedral in the capsid overall form)
- Complex (e.g., bacteriophages with tail and tail fibers)
Helical viruses
- Showcapsomere arrangement forming a helical nucleocapsid; nucleic acid coils inside
- Example: Ebola virus
- Typical TEM size around ~100\ \text{nm} (as illustrated in the figure)
Polyhedral viruses
- Capsid with many faces, commonly icosahedral
- 20 triangular faces, 12 corners
Enveloped viruses
- Capsid surrounded by envelope; envelope confers rough spherical appearance
- Example: Influenza virus; some herpesviruses are enveloped and have polyhedral capsids
Complex Viruses
- Often bacteriophages with intricate structures
- Example: T-even bacteriophage
- Head (capsid) ~65\ \text{nm}; tail sheath; baseplate; tail fibers; DNA inside
Viral taxonomy
- Early classification relied on symptoms; not reliable for precise grouping
- High-speed sequencing allows grouping by nucleic acid sequence and structure
- Current grouping: family and genus
- Family name endings: -viridae
- Genus name endings: -virus
- Viral species are subgroups of a genus; immunologically distinct within the genus
- Example: AIDS
- Family: \text{Retroviridae}
- Genus: \text{Lentivirus}
- Species: \text{HIV}
Cultivation of Viruses
- Viruses must be grown in living cells
- Bacteriophages are the easiest to grow
- Host range and tissue tropism are important concepts to consider before growth
Host range
- Host range describes which organisms a virus can infect
- Typically narrow in number; mediated by attachment proteins on the virus and receptors on the host cell
- Example: Smallpox infects only humans
- Rabies can infect many warm-blooded animals (broader host range)
Tropism
- Even within a susceptible host, not all cells are infected
- Tissue or cell-type specificity (cell/tissue tropism) determines which cells are susceptible
Growing Bacteriophages in the Laboratory
- Bacteriophages infect bacteria; they lyse bacterial cells and are easy to grow
- Plaque method: mix phages with host bacteria on nutrient agar
- After cycles of multiplication, the area around the original virus clears; this is a plaque
- Each plaque originates from a single virus particle
- Phage concentration is expressed as plaque-forming units (PFU)
Viral Plaques
- Plaques visually represent successful infection and lysis on a bacterial lawn
Multiplication of Bacteriophages
- Two main life cycles:
- Lytic cycle: phage replicates, lyses the host cell, releases new virions
- Lysogenic cycle: phage DNA integrates into the host genome as a prophage; host cell remains alive and replicates normally with prophage
The Lytic Cycle (T-even phage example)
- Stages: Attachment/absorption -> Penetration -> Biosynthesis -> Maturation/assembly -> Release
- Result: host cell death and release of progeny virions
The lysogenic cycle
- Lysogenic infection: phage DNA integrates into bacterial chromosome as prophage
- Lysogenic bacterium reproduces normally, passing prophage to progeny
- Prophage may excise and enter the lytic cycle under certain conditions -> phage DNA circularizes and may begin lytic cycle
Bacteriophage therapy
- Phages offer a potential approach to treat bacterial infections due to their host-range specificity
- Drawbacks: phages are foreign to the host and can be cleared by the immune system within ~7–10 days
- Similar issues with oncolytic (tumor-targeting) viruses: immune clearance limits efficacy
Animal Viral Multiplication
- Like bacteriophages, animal viruses hijack host cell machinery and lack own energy production or protein-synthesis enzymes
- Multiplication requires entry into a host cell and subversion of host metabolism
Steps to animal virus replication
- 1) Attachment: virion binds to host cell via surface proteins (spikes, tail fibers) to specific receptors
- 2) Penetration: nucleic acid (and sometimes the whole nucleocapsid) enters cytoplasm; nucleic acid is transported to the expression/replication site
- 3) Biosynthesis: viral genome replicated; viral proteins (capsid, spike/tail proteins) synthesized
- 4) Assembly: nucleocapsids formed; if enveloped, envelope may be acquired during budding from a membrane
- 5) Release: new virions released by lysis or budding; enveloped viruses acquire envelope during budding from the membrane
- Latency: some viruses can enter a latent state, delaying replication until later
Replicative infection by DNA-containing enveloped viruses
- A) Following attachment, the host cell membrane may fuse with the viral envelope, allowing nucleocapsid entry
- B) Nucleocapsid uncoats; genome replicated in the nucleus
- C) Viral mRNAs transcribed in the nucleus and translated on cytoplasmic ribosomes
- D) Translation yields capsid and spike proteins
- E) Capsid proteins enter the nucleus to assemble with viral genomes into nucleocapsids
- F) Viruses bud through the nuclear membrane and acquire their final envelope and spikes in a Golgi/secretory pathway before exocytosis
Provirus (retrovirus) infection
- Retroviruses transcribe their RNA into DNA via reverse transcriptase
- The newly synthesized dsDNA is transported to the host nucleus and integrates as a provirus into the host chromosome
- Viral genome remains latent or actively transcribed depending on cellular context
- Diagram flow (simplified): ssRNA viral genome → reverse transcription to dsDNA → integration as provirus → transcription/translation in the host
Growing animal viruses in the laboratory
- Some viruses require whole animals for cultivation
- Animal models: Simian AIDS and feline AIDS models provide insights into human AIDS
- Embryonated eggs can be used for cultivation
- Cell culture (animal cells in culture media) is a common alternative
Viral Identification
- Prompt diagnosis is essential for effective antiviral therapy
- Not all infections require laboratory tests (e.g., chickenpox, common cold, influenza) but many do
- Serological tests: screen patient sera for virus-specific antibodies (antibody detection indicates exposure)
- Molecular methods: Restriction Fragment Length Polymorphism (RFLP) and Polymerase Chain Reaction (PCR)
PCR (polymerase chain reaction)
- A laboratory technique to copy a specific region of nucleic acid many times
- Diagnostic if a region unique to a particular virus is amplified
- Positive amplification indicates presence of target; no amplification indicates absence (negative)
Restriction Fragment Length Polymorphism (RFLP)
- Detects small differences in genome sequence by cutting nucleic acids with restriction enzymes
- Enzymes recognize specific sequences and cut DNA
- Analyzing fragment patterns after digestion allows distinguishing between different viruses
Cytopathic effects (CPE)
- Viruses grown in host cells often cause visible changes in those cells (cytopathic effects)
- CPEs can be diagnostic patterns, identifiable under a microscope
Common viral cytopathic effects
- Examples by virus families include: structural changes in cells, nuclear changes, vacuolization, cell rounding, syncytia (cell fusion), chromosomal breakage, detachment from culture, virion inclusions in nucleus or cytoplasm, and formation of viral factories or Negri bodies in cytoplasm
- Specific patterns are associated with certain viral families (e.g., Herpesviridae, Adenoviridae, Picornaviridae, Rhabdoviridae, Poxviridae, Paramyxoviridae, Coronaviridae, Papovaviridae)
Viruses and cancer
- Some viruses can alter host genetic material and potentially transform normal cells into cancerous cells
- Cancer = unregulated cellular division; Oncogene: gene product involved in transformation or induction of tumors
- Oncogene products often participate in cellular replication; mutations in these genes can drive cancer
- Approximately 10–20% of cancers are virus-associated; more may be virus-related but not yet detected
Oncogenic viruses and mechanism of activation
- Oncogenic viruses may carry oncogenes; these genes may be mutated during infection
- Virus attachment, entry, and genome integration can lead to expression of oncogene products that disrupt normal cell regulation
- Mechanism overview: attach → penetrate → viral DNA/RNA enters nucleus → integration (provirus) or expression of oncogene → altered cellular regulation → cancer
Types of viral infections
- Acute infections
- Latent infections
- Persistent infections
Acute infection
- Virus replicates after entry, causes tissue damage and immune response
- In most cases, immune system clears the virus and the host survives
- In some cases, infections can be fatal
Latent viral infections
- Virus remains in host cell for long periods without active infection
- Classic example: herpes simplex virus (causes cold sores); persists in nerve cells and reactivates under stimuli (fever, sun exposure)
- Most people carry herpes simplex virus; only 10–15% show disease symptoms
Latent infections (Varicella-zoster system)
- Varicella-zoster virus (VZV) may remain latent after chickenpox
- Virus may disseminate, enter nerves, and remain latent; immune changes (e.g., T-cell response) can reactivate
- Reactivation causes shingles, occurring in about 10–20% of people who had chickenpox
Persistent viral infections
- Long-lasting, generally fatal disease processes
- Caused by conventional viruses; viruses accumulate over long periods
- Immune system is thought to gradually fail in clearing the virus
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