Viral Genetics and Phage Biology Quiz

Virology Overview

• Virology is the study of viruses
• Viruses are not cells; they are nucleic acid molecules that invade cells and replicate within them.
• Viruses have no metabolic processes of their own.
• Viruses are classified as functionally active or inactive, rather than alive or dead.
• Outside a host cell, a virus particle is called a virion and is metabolically inert.
• Viruses lack the majority of enzymes for metabolism (lacking CHON synthesis and ATP generation)

Nature of Viruses

• Viruses are a heterogeneous class of agents varying in size, morphology, complexity, and host range.
• Viruses have a genome (either RNA or DNA, not both) surrounded by a protective protein shell.
• Viruses multiply only in living cells and are dependent on the host's energy-yielding and CHON-synthesizing apparatus.
• Viruses are obligate intracellular parasites.
• Viral genome separation from their protective shell is an initial step of the multiplication cycle.
• A single virus particle can replicate to produce hundreds of progeny viruses while a one cell division creates only two daughter cells.

Viruses vs. Bacteria

Viruses vs. Cells

Host Range of Viruses

• Viruses have a spectrum of host cells they can infect (e.g., invertebrates, vertebrates, plants, protists, fungi, bacteria)
• Most viruses infect specific cell types of a single host species.
• Host range is determined by the virus's requirements for specific attachment sites on the host cell (e.g., receptors).
• Examples determining host range are seen in bacteria (cell wall, fimbriae, flagella) and animals (plasma membrane).

Viral Size

• Viruses range in size from 20 to 1000 nm in length.
• Electron microscopy is used to determine viral size.

Viral Structure Components

• Viral nucleic acids (DNA or RNA)
• Viral proteins (capsid)
• Viral capsid
• Viral envelope

Viral Nucleic Acids

• Viruses can have either DNA or RNA, but not both.
• Viral genomes can be single-stranded (ss) or double-stranded (ds)
• Almost all viruses have a single copy of their genome (haploid) except retroviruses (diploid/dimer)
• Viral genomes can be linear, circular, or segmented (only for RNA)
• Viral genomes vary in size from a few thousand to 250,000 nucleotides.
• Viral genomes encode enzymes and structural proteins.

Viral Classification by Nucleic Acid Type

• DNA viruses: characterized as "HAPPY"
• RNA viruses:
  • Positive (+) stranded RNA
  • Negative (-) stranded RNA
  • Double-stranded RNA
  • Retroviruses

Viral Classification by RNA Viruses mRNA Synthesis Strategy

• Positive (+) stranded RNA: uses their RNA genome directly as mRNA, which is translated in host ribosomes to proteins
• Negative (-) stranded RNA: must first be transcribed into positive stranded RNA by an enzyme in their capsid (RNA-dependent RNA polymerase) to begin translation.
• Double-stranded RNA: carry their own RNA polymerase
• Retroviruses: have negative-polarity single-stranded RNA genomes, but are transcribed into dsDNA by reverse transcriptase enzyme, which is carried by the virus.

Viral Capsid/Envelope

• The capsid protects the virus’s nucleic acid.
• Capsid is made of protein subunits called capsomeres.
• Nucleocapsid is a structure referring to the nucleic acid and capsid.
• Some viruses have an envelope (a lipid bilayer) that surrounds the capsid.
• Envelope spikes/glycoproteins are crucial for attachment to host cells.
• Naked/non-enveloped viruses lack an envelope and are only surrounded by a capsid.

Capsid Morphology

• Enveloped helical
• Naked icosahedral/naked polyhedral
• Enveloped icosahedral/enveloped polyhedral
• Complex viruses

Helical Viruses

• Resemble long rods (rigid or flexible).
• Viral NA is in a hollow cylindrical capsid with a helical structure.
• Most helical viruses have envelopes.

Icosahedral/Polyhedral Viruses

• Common shape for many animal, plant, and bacterial viruses.
• Capsid is an icosahedron with 20 triangular faces and 12 corners.
• Capsomers form equilateral triangles.
• Some may have an envelope.

Complex Viruses

• Have complicated structures, often including bacterial viruses (bacteriophages).
• Often have a polyhedral head and a helical tail sheath.
• Examples include bacteriophages and poxviruses

Viral Proteins

• Capsid proteins protect viral genome/mediate attachment of virus to host cell receptors. Species and organ specificity are determined here.
• Outer viral proteins stimulate Ab production by the host and activate cytotoxic T-cells.
• Internal viral proteins may be structural or enzymes (RNA polymerase, DNA polymerase etc).
• Some viruses produce proteins that act as superantigens
  • Human cells do not have these enzymes in their core mechanisms, so the virus often has to provide them itself inside a capsid

Atypical Virus-Like Agents

• Defective viruses
• Pseudovirions
• Viroids
• Prions
  • Misfolded prion proteins can induce other proteins to misfold into prion form

Viral Replication/Multiplication

• For a virus to replicate, it has to invade a host cell and take over its metabolic machinery.
• Bacteriophages have two main replication cycles: lytic and lysogenic.
• Animal viruses also undergo replication steps, varying from host species and virus to virus, but they always require host cells to replicate

Lytic Cycle

• Attachment (adsorption): virus attaches to host cell
• Penetration: virus injects its DNA, often through a phage lysozyme
• Biosynthesis: viral genes are expressed
• Maturation (assembly): viral pieces are assembled into complete virions
• Release (lysis): host cell is broken open, releasing viral progeny

Lysogenic Cycle

• Phage DNA integrates into the host cell's DNA (now called a prophage).
• Host cell replicates normally, with the prophage DNA replicated as well, with no virus replication in this phase/cycle.
• The prophage can excise from the host's DNA, initiating the lytic cycle under certain conditions.

Replication of Animal Viruses

• Attachment
• Entry (often by endocytosis or fusion with the host cell membrane)
• Uncoating (releasing viral nucleic acid from the capsid)
• Biosynthesis (protein and nucleic acid synthesis)
• Maturation (assembly)
• Release (often by budding or lysis)

Viral Pathogenesis

• Viral infection can lead to several outcomes, such as:
  • Viremia (virus in the blood)
  • Over (infection is halted-immune responses)
  • Tissue damage
  • Latent viral infections (with periods of the virus being inactive and reactivation occurring)
  • Autoimmune pathogenesis (immune reaction against the body's own tissues due to viral infection) - Example: measles causing encephalitis
  • Oncogenic viruses that promote uncontrolled cell growth (e.g., Papillomavirus and others)

Host Defenses

• Nonspecific (innate) defenses:
  • Interferons
  • Natural killer (NK) cells
  • Phagocytosis (macrophages, etc.)
  • a-defensins, CXR4
  • APOBEC3G
  • Fever
  • Mucociliary clearance
• Specific (adaptive) defenses:
  • Active immunity
  • Passive immunity
  • Herd immunity

Antiviral Agents

• Drugs targeting the viral replication cycle
• Examples like Ganciclovir, Efavirenz, etc.

Specimen Selection and Collection

• Specimen collection depends on the virus and disease
• Collection is ideally done early in viral infection when viral titer is highest (typically first 4 days)
• Samples should be collected, ideally, at the infected site directly. An exception is certain viral infections of the CNS. In such cases, stool or throat samples are preferred for culture over CSF.
• Samples should be stored using viral transport media.

Laboratory Diagnosis

• Methods for detecting, culturing, and identifying viruses Include:
  • Cytological or histological examination
  • Electron microscopy
  • Virus isolation in cell or tissue culture (SVCE)
  • Direct antigen/gene detection (DFA, ELISA, PCR)
  • Serological detection of viral antibodies

Viral Vaccines

• Active immunity can be elicited through vaccines containing a live, attenuated (weakened) virus, inactivated (killed) virus, or purified viral proteins.
• Examples include vaccines for measles, mumps, rubella (MMR), polio (live and inactivated), Hepatitis A, B, varicella, influenza, rabies.
• Passive immunity is provided by preformed antibodies from immune globulins (either human or animal origin).
• Passive-active immunity combines passive (immediate) and active (sustained long term protection) approaches.
• Rabies and Hepatitis B are examples of viruses using this two pronged approach.