Virology Quiz on Polyomaviruses

Viral Structures and Symmetries

• Helical symmetry: Virus particles formed from a single protein subunit arranged in a spiral structure. A 10 nm axial rise indicates the vertical distance the helix moves upward after a full rotation. Three protein subunits are required to make one full turn (μ = 3).
• Tobacco Mosaic Virus (TMV): Axial rise per subunit is typically around 0.14 nm; number of subunits per turn (n) is 16.3.
• Vesicular Stomatitis Virus (VSV): The N protein (nucleoprotein) wraps around the viral RNA, forming a helical structure. The scale bar of 100 Å represents the nucleocapsid diameter.

Enveloped RNA Viruses

• Paramyxoviridae (Measles and Mumps viruses): Nucleocapsid surrounded by a lipid envelope studded with glycoproteins.
• Rhabdoviridae (Rabies virus): Bullet-shaped with a nucleocapsid tightly coiled inside.
• Orthomyxoviridae (Influenza virus): Contain segmented RNA genomes wrapped by nucleoproteins, forming multiple helical nucleocapsids. The genome is surrounded by the viral matrix protein, and the RNA polymerase complex (PB2, PB1, PA) helps initiate transcription.
• Filoviridae (Ebola viruses): Filamentous structure with RNA genome tightly packed into a helical nucleocapsid.

Icosahedral Symmetry

• Watson and Crick: Spherical capsids built with icosahedral symmetry (20 triangular faces, 12 vertices, 30 edges). This minimizes genetic material needed while maximizing stability.
• Icosahedron: A Platonic solid, characterized by 5-fold, 3-fold, and 2-fold symmetry axes.

Viral Capsid Complexity

• Triangulation number (T): Represents the complexity of the capsid's arrangement—how many subunits form one triangular face. T=1 is the simplest, whereas T=3 and higher values indicate more complex structures.
• Quasiequivalence: Subunits in a capsid higher than T=1 occupy similar but not identical positions.
• Adeno-associated virus 2: An example of a T=1 icosahedral structure.

Viral Proteins and Functions

• Nucleocapsid: The core that encapsulates viral RNA, composed of nucleoprotein bound to RNA.
• Lipid envelope: Acquired from host cell membranes during viral replication; embedded with viral glycoproteins for attachment and entry.
• Spike proteins (S): Protrude from the surface; give virus its crown-like appearance. Critical for attachment to host cells.
• Adenovirus structure: Follows T=25 icosahedral symmetry; contains 720 copies of the viral hexon protein (major component of the capsid). Fibers at 12 vertices aid in host cell attachment.
• Herpes Simplex Virus (HSV) capsid: Highly organized structure with multi-viral proteins (VPs) and a specialized portal for DNA/RNA entry/exit.
• Viral proteins (VPs): Varies by specific virus; major structural components for forming capsids and playing roles in genome packaging, assembly and functions.

Genome Packaging

• Viral genomes are highly condensed, often analogous to packing wire into a tennis ball for optimal confinement.
• Some viruses use specialized viral proteins, or cellular proteins like histones, to package the genome.
• Structures of viral genomes: Linear, circular, gapped, segmented, single-stranded (+ or - strand), double-stranded, and ambisense characteristics.

Viral Genomes and Types

• RNA and DNA-based genomes. RNA genomes appeared before DNA in evolution (RNA World), and DNA genomes are generally more complex.
• Baltimore system: Seven types of genomes and descriptions, such as linear, circular, gapped, segmented, single-stranded, double-stranded, and ambisense, based on the relationship to mRNA.
• Viral genome diversity is critical for viral function.

Genome Replication and Viral Protein Synthesis

• Viral genomes code for unique methods such as ribosomal frameshifting, IRES-related translation of nested mRNAs, and polyprotein processing.
• There are many varieties of viral enzymes including polymerase, transcriptases, proteases, helicases, and ligase.
• Viral genomes are structurally diverse to encode, package, transcribe and translate unique proteins for replication and expression.

Other Viral Components

• Viral proteins not directly part of structure, but involved in functions such as:
  • Nucleic acid replication, transcription, and translation
  • Host cell function shutdown
  • Inhibition of innate immunity.
  • Cellular machinery interference
  • Synthetic activities

Viral DNA Genomes

• dsDNA viruses dominate the bacterial virosphere; many DNA viruses emulate the host, based on DNA.
• However, almost all viral DNA genomes are NOT like cell chromosomes, but have evolved unexpected, unique tricks for replication.

ssDNA Genomes

• Circular or linear forms with a single strand.

RNA Genomes

• RNA viruses dominate eukaryotic virosphere (rare in bacteria), have their own RdRp (RNA-dependent RNA polymerase) enzymes.

Other Viral Structures

• Enveloped viral structures, with envelopes formed from host cell membranes, contain viral proteins, glycoproteins, and oligosaccharides.
• Viral membrane interactions using glycoproteins and internal domains.
• Multiple glycoprotein spike structures.

Viral Mutations and Genetic Methods

• Mutations: Changes in nucleic acids and proteins; these changes can alter viral function but have not been altered in the past.
• Genetic methods for virus manipulation: Transfection to introduce specific DNA to cultures or cells. Cloning techniques for manipulating viral DNA sequences.

Large Virus Groups

• Bacteriophage T4: A large virus with multiple structural elements for various functionalities such as head, connector, tail sheath, whiskers, tail fibers, and baseplate.
• Herpesviruses: Large viruses with specific protein subunits to produce a nucleocapsid, tegument envelope, and envelope.
• Poxviruses: Large viruses with dumbbell-shaped cores and specific layering membranes.
• Pithovirus: Large virus observed using electron microscopy.