Viral Structure and Multiplication Lecture Notes

The Position of Viruses in the Biological Spectrum and Discovery

• Viruses demonstrate an incredible range of infection, targeting every known type of cell: bacteria, algae, fungi, protozoa, plants, and animals.

• Environmental prevalence is massive; seawater can contain as many as $10 \, \text{million}$ viruses per milliliter.

• For a significant period, the etiology of viral infections remained a mystery.

• Louis Pasteur hypothesized that rabies was the result of a "living thing" smaller than bacteria.

• Pasteur is credited with proposing the term "virus," which is Latin for "poison."

• Significant discovery milestones include:

  • Ivanovski and Beijerinck: Demonstrated that tobacco disease was caused by a virus.

  • Loeffler and Frosch: Identified the first animal virus, responsible for foot-and-mouth disease in cattle.

• The concept of the "filterable virus" emerged when researchers found that fluids from host organisms remained infectious even after passing through porcelain filters designed to trap bacteria. This proved that infectious agents could be smaller than bacteria.

The Nature of Viruses: The Vital Debate

• The biological status of viruses is a subject of ongoing debate:

  • Argument for Non-living: Because viruses cannot multiply independently of a host cell, they are often viewed as infectious molecules.

  • Argument for Living: Although they lack typical cellular life processes, they can direct those processes within a host, suggesting they are more than inert molecules.

• A more accurate description for viruses is "active" or "inactive," rather than "alive" or "dead."

Evolutionary Role and Biological Significance

• Viruses play a critical role in evolution by infecting cells and influencing their genetic makeup.

• They have shaped the evolution of tissues, bacteria, plants, and animals.

• Human Genome Composition: Approximately $8\%$ of the human genome consists of sequences derived from viruses.

• Bacterial DNA Composition: Between $10\%$ and $20\%$ of bacterial DNA contains viral sequences.

• Obligate Intracellular Parasites: Viruses cannot multiply unless they invade a specific host cell and hijack its genetic and metabolic machinery to produce and release new virions.

General Properties of Viruses

• Viruses are obligate intracellular parasites affecting all forms of life.

• Abundance: There are an estimated $10^{31}$ virus particles on Earth, which is roughly $10$ times the number of bacteria and archaea combined.

• Size: Viruses are ultramicroscopic, ranging in diameter from $20 \, \text{nm}$ up to $1,000 \, \text{nm}$.

• Structure:

  • They are not cells; their structure is compact and economical.

  • They do not independently fulfill the characteristics of life.

  • Basic composition: A protein shell (capsid) surrounding a nucleic acid core.

• Genetics and Metabolism:

  • Nucleic acid is either DNA or RNA, but never both.

  • Viruses lack enzymes for most metabolic processes and lack the machinery for protein synthesis.

  • Molecules on the viral surface provide high specificity for attachment to host cells.

Viral Classification and Taxonomy

• Historical classification was based on host types and the diseases caused.

• Modern systems emphasize:

  • Hosts and disease pathology.

  • Structure and chemical composition.

  • Genetic similarities.

• The International Committee on the Taxonomy of Viruses currently recognizes $8$ orders and $38$ families, with another $84$ families yet to be assigned an order.

Size Range and Relative Scale

• Viruses are the smallest infectious agents:

  • Smallest: Parvoviruses ($20 \, \text{nm}$ in diameter).

  • Largest: Herpes simplex virus (approx. $150 \, \text{nm}$ in length).

  • Cylindrical Viruses: Can reach lengths of $800 \, \text{nm}$ but are only $15 \, \text{nm}$ in diameter, making them difficult to see without an electron microscope.

• Comparative sizes:

  • Yeast Cell: $7 \, \mu \text{m}$.

  • E. coli: $2 \, \mu \text{m}$ long.

  • Streptococcus: $1 \, \mu \text{m}$.

  • Pandoravirus: $1 \, \mu \text{m}$.

  • HIV: $110 \, \text{nm}$.

  • Influenza virus: $100 \, \text{nm}$.

  • Poliovirus: $30 \, \text{nm}$.

  • Hemoglobin molecule: $15 \, \text{nm}$.

Viral Components and Architecture

• Viruses lack protein-synthesizing machinery and bear no resemblance to cells.

• Their structure consists of regular, repeating subunits, often giving them a crystalline appearance.

• Essential parts for invasion and control:

  • External coating (Capsid).

  • Core containing DNA or RNA.

  • Occasionally one or two enzymes.

• Definitions:

  • Capsid: The protein shell surrounding the nucleic acid.

  • Nucleocapsid: The combined unit of the capsid and nucleic acid.

  • Naked Virus: Consists only of a nucleocapsid.

  • Envelope: An external covering (usually host cell membrane) found on some viruses.

  • Spikes: Proteins that project from the envelope or nucleocapsid to allow docking with host cells.

  • Virion: A fully formed, infectious viral particle.

Capsid Structures

• Capsomeres: Identical protein subunits that spontaneously self-assemble into the capsid.

• Helical Capsids: Rod-shaped capsomeres bond to form hollow discs (like a bracelet), which link to form a continuous helix.

  • Naked Helical: Rigid and tightly wound (e.g., Tobacco Mosaic Virus).

  • Enveloped Helical: More flexible.

• Icosahedral Capsids: A 3D, 20-sided figure with 12 corners.

  • Variation: Poliovirus has $32$ capsomeres; Adenovirus has $252$ capsomeres.

  • Examples: Adenovirus (naked), Hepatitis B and Herpes Simplex (enveloped).

• Complex Capsids: Found only in bacteriophages (e.g., T4 bacteriophage). These have multiple protein types, are asymmetrical, and are never enveloped.

Nucleic Acids: The Genetic Core

• Genome: The sum total of genetic information.

• Gene count is small: Hepatitis B has $4$ genes; some Herpesviruses have hundreds.

• DNA Types: Single-stranded (ss) or double-stranded (ds); can be linear or circular.

• RNA Types: Usually single-stranded, but can be double-stranded (dsRNA).

  • Positive-sense RNA: Ready for immediate translation.

  • Negative-sense RNA: Must be converted before translation.

  • Segmented RNA: Genes are on separate pieces of RNA.

  • Retroviruses: Carry enzymes to create DNA from RNA.

• Examples:

  • Variola virus (Smallpox): dsDNA.

  • Parvovirus: ssDNA.

  • Influenza: ss(-)RNA.

  • Rotavirus: dsRNA.

  • HIV: ssRNA + reverse transcriptase.

Additional Viral Substances

• Enzymes for specific operations:

  • Polymerases: Synthesize DNA and RNA.

  • Replicases: Copy RNA.

  • Reverse transcriptase: Synthesizes DNA from RNA (found in retroviruses).

• Borrowed materials:

  • Arenaviruses pack host ribosomes.

  • Retroviruses borrow host tRNA.

The Multiplication Cycle of Animal Viruses

• General Phases:

  1. Adsorption: Virus attaches to host via specific receptors (Host range defines which cells can be infected).

  2. Penetration: Entry into the cell via endocytosis (whole virus engulfed) or direct fusion (envelope merges with membrane).

  3. Uncoating: Release of nucleic acid from the capsid.

  4. Synthesis: Replication and protein production. (DNA viruses usually replicate in the nucleus; RNA viruses in the cytoplasm).

  5. Assembly: Putting together the virus parts.

  6. Release: Budding (enveloped) or lysis (naked).

• Replication times vary: Poliovirus ($8 \, \text{hours}$) vs. Herpesvirus ($36 \, \text{hours}$).

• Release yield examples: Poxvirus ($3,000\text{--}4,000$ virions); Poliovirus ($100,000$ virions).

Viral Genetic Alterations: Influenza

• Mutation and Genetic Reassortment: Segmented viruses can exchange genome segments if two different viruses infect the same cell.

• Antigenic Shift: Major genetic change enabling a strain to jump hosts (e.g., bird to human) or combine segments, potentially causing pandemics.

• Antigenic Drift: Minor mutations in the HA (hemagglutinin) gene that change the shape of antigens, allowing the virus to evade existing antibodies.

Damage to the Host Cell

• Cytopathic Effects (CPEs): Virus-induced damage altering microscopic appearance.

  • Gross changes in size/shape.

  • Inclusion Bodies: Compacted masses of viruses or damaged organelles.

  • Syncytia: Fusion of multiple host cells into large multi-nucleated giant cells.

• Persistent Infections: Cell harbors the virus without immediate lysis.

  • Provirus: Viral DNA incorporated into host DNA.

  • Chronic Latent State: Periodic activation (e.g., Herpes simplex, Herpes zoster).

Viruses and Cancer

• Transformation: The effect of oncogenic (cancer-causing) viruses.

• Roughly $13\%$ of cancers are viral-induced.

• Oncoviruses (e.g., Papillomavirus, Hepatitis B) can carry genes that cause cancer or produce proteins that disrupt growth regulation.

• Transformed cells exhibit increased growth rates, chromosomal changes, and indefinite division capacity.

Bacteriophages: Viruses of Bacteria

• Most contain double-stranded DNA.

• T-Even Bacteriophage Structure: Icosahedral capsid, central tube, sheath, collar, base plate, tail pins, and fibers.

• Lytic Cycle: Adsorption, penetration, duplication of components, assembly, maturation, and lysis for release.

• Lysogenic State (Lysogeny): The host chromosome carries bacteriophage DNA (prophage). The viral DNA is copied during normal cell division.

• Induction: Activation of a prophage to enter the lytic cycle.

• Lysogenic Conversion: Bacteria acquire new traits (like toxins) from the temperate phage (e.g., Diphtheria, Cholera, and Botulinum toxins).

Techniques for Cultivating and Identifying Viruses

• Principal purposes: Isolation/Identification, Vaccine preparation, and Basic research.

• In Vivo Methods:

  • Live animal inoculation (mice, rats, hamsters, etc.).

  • Bird embryos (chicken, duck, turkey eggs) provide a sterile, self-supporting environment.

• In Vitro Methods:

  • Cell/Tissue culture: Cells grown in sterile chambers form a monolayer.

  • Detection of growth: Observation of CPEs or plaques (clear patches in the cell sheet where cells were destroyed).

Coronaviruses and SARS-CoV-2

• Coronaviruses are a large family of ss(+)RNA viruses with club-like projections.

• Reservoirs often include bats; examples include SARS (2002), MERS (2012), and SARS-CoV-2 (2019).

• SARS-CoV-2 Mechanics:

  • Spike (S) protein attaches to the ACE2 receptor on airway cells.

  • Activation of the S protein requires proteolytic cleavage by TMPRSS2.

  • Entry can occur via endocytosis or membrane fusion.

  • Lifecycle involves replication-transcriptase complexes and assembly in the ERGIC (ER-Golgi intermediate compartment).

Other Noncellular Infectious Agents

• Prions: Composed entirely of protein (no nucleic acid). They cause neurodegenerative diseases like Creutzfeldt-Jakob disease, Bovine Spongiform Encephalopathy ("mad cow disease"), and Shy-Drager syndrome.

• Satellite Viruses: Depend on other viruses for replication (e.g., Adeno-associated virus; Delta agent which requires Hepatitis B).

• Viroids: Small ($1/10$ size of a virus), naked RNA strands that parasitize plants (e.g., tomatoes, potatoes).