Virology Basics, Pathogenesis and Yellow Fever Virus


Virus?

  • Definition: A virus is a non-cellular particle that infects a host cell and directs it to produce progeny particles.

Size and Structure of Viruses

  • Viruses are generally small.

  • Example: Pandoravirus measures approximately 1 mm x 0.5 mm (Philippe et al. Science July 19, 2013)

Genome Sizes of Representative Organisms

  • Phage T7: 40 kb

  • Circovirus: 1.8 kb

  • Phage T4: 170 kb

  • Megavirus: Various sizes

  • DNA Viruses: Generally larger sizes

  • MS2: 3.5 kb

  • Coronaviruses:

    • RNA Viruses can range vastly in size.

Virus Definition II: Mode of Replication

  • Modes of Replication:

    • Replication by Division: The virus replicates by splitting its components.

    • Replication by Assembly: Most viruses replicate by assembling pre-formed components.

Are Viruses Alive?

  • Historically, viruses were defined as nonliving particles.

  • Characteristics:

    • Must enter and infect a host cell to produce progeny virions.

    • Some viruses carry genes for tRNAs and some ribosomal components, yet cannot independently synthesize proteins. However, they rely on the host's cellular machinery to replicate and assemble new virus particles.

General Parts of a Virion

  • Viral Nucleic Acid:

    • Encodes viral proteins, requiring replication through host enzymatic machinery.

    • Can be RNA or DNA (not both).

  • Viral Proteins:

    • Protect the viral genome.

    • Deliver the genome to correct cells.

    • Facilitate the infectious cycle by interacting with cellular components.

    • Provide enzymes essential for viral infection.

    • Help evade the host immune system.

Structure of Virion

  • Outline of virion components:

    • Capsid: Composed of capsomeres, determines the shape and structure.

    • Nucleic acid: Core genetic material.

    • Viral Envelope (when present): Composed of lipids and proteins that assist in cell entry.

The Infectious Cycle

  1. Attachment and Entry:

    • Infection initiation occurs after collisions of virions and susceptible host cells.

    • Binding requires specific interactions with cellular receptors.

    • Failure to bind the correct receptor results in no infection.

  2. Genome Replication, Transcription, and Translation

    • Following entry, the viral genome is replicated.

    • Translation of viral proteins occurs, involving cellular machinery.

  3. Assembly:

    • Viral proteins and genomic components are assembled into progeny particles.

  4. Release:

    • New virions exit the host cell. This may occur via lysis or budding, depending on the virus type.

Metrics of Viral Replication

  • Viral Replication Kinetics:

    • Eclipse Period: Time from infection to the appearance of viral progeny.

    • Rise Period: Time during which virions are released and increase in number in the environment.

    • Burst Size: The number of virions released per infected cell.

Measuring and Counting Viruses

  • Plaque Assays: Method to quantify viral particles based on cytopathic effects in tissue culture.

  • Observed Effects: Describes the cellular changes due to viral infection at different time points (e.g., Poliovirus replication).

Classification of Viruses

  • Classification criteria include:

    • Genetic and physical characteristics

    • Types of infected cells or organisms

    • Presence or absence of an envelope

    • Size of viral particle or genome

    • Type of viral symmetry and genome type

Symmetry of Viruses

  • Types of Symmetry:

    • Helical (Filamentous): Rod-shaped appearance under microscopy.

    • Icosahedral (Spherical): 20 faces made of equilateral triangles, providing structural support.

  • Complex Structure: Includes phages with elements like a tail and tail fibers.

Baltimore Classification of Viruses

  • Categorization based on viral genome and replication strategies:

    • Group I: Double-stranded DNA (dsDNA)

    • Group II: Single-stranded DNA (ssDNA)

    • Group III: Double-stranded RNA (dsRNA)

    • Group IV: Positive-sense single-stranded RNA (+ssRNA)

    • Group V: Negative-sense single-stranded RNA (-ssRNA)

    • Group VI: Retroviruses (RNA reverse-transcribing viruses)

    • Group VII: Pararetroviruses (DNA reverse-transcribing viruses)

YFV Overview

  • Flavivirus Characteristics:

    • Enveloped, + RNA virus, Icosahedral capsid.

  • Yellow Fever Virus (YFV):

    • Historical Perspective: Once endemic to the Southeastern U.S.; introduced via the African Slave Trade.

    • Current Endemics: Latin America, Caribbean, and Sub-Saharan Africa.

    • Transmission Cycles:

    1. Sylvatic Cycle: Involves non-human primates and mosquitoes.

    2. Urban Cycle: Involves humans and mosquitoes.

    3. Intermediate Cycle: Non-human primates, humans, and mosquitoes.

Yellow Fever Virus Genotype and Symptoms

  • YFV has a single serotype with 7 genotypes (5 native to Africa, 2 native to South America).

  • Clinical Symptoms: Ranges from mild (flu-like) to severe (potentially fatal); severe cases involve major organs like the liver, kidneys, and myocardium.

    • Symptoms include jaundice, hepatorenal syndrome, hemorrhage, and shock.

    • Transmission: Primarily transmitted through the bite of infected mosquitoes, particularly Aedes aegypti. It can also occur through contact with the bodily fluids of infected individuals.

YFV Genome Structure and Proteins

  • Structural Proteins:

    • Envelope (E) Protein: Critical for receptor binding and entry.

    • Capsid (C) Protein: Protects the RNA genome.

  • Non-structural Proteins:

    • NS1: Involved in genome replication and immune evasion.

    • NS2A/B: Components of the replicase complex and viral assembly.

    • NS3: Responsible for polyprotein cleavage.

      • Targets: Serine Proteases, nuclear pore, STINGTargets include host serine proteases that facilitate viral replication, components of the nuclear pore that assist in viral entry, and the STING pathway which is crucial for detecting cytosolic DNA and initiating immune responses.

      • Outcome: Decreased immune activation, decreased IFN-y (interferon warns neighbors of invader+ establish+ recruit defending cells), decreased host protein synthesis (important to prod. specialized tools and cell popul. needed to ID +eliminate specific pathogens…..NS3 hinders the adaptive immune systems responses.

    • NS4A/B: Also components of the replicase.

    • NS5: Acts as the RNA-dependent RNA polymerase.

      • Targets: STAT1/STAT2 pathway

      • Outcome: Decreased type 1 interferon signaling—>impairing/suppressing innate immune responses=enhanced viral replication and increased severity of infection.

YFV Replication Cycle

  1. Attachment: E protein binds to a known receptor, triggering endocytosis.

  2. Uncoating: Invoked by changes in environmental pH; allows genome release into cytoplasm.

  3. Translation: Host machinery translates viral proteins, creating replication organelles.

  4. Replication: - RNA produces + RNA that is necessary for progeny formation.

  5. Assembly: Formation of immature virions along the rough endoplasmic reticulum.

  6. Maturation: Viral proteins are modified during transit to the trans-Golgi apparatus.

  7. Release: Mature virions budding from the host cell.

YFV Pathogenesis

  • Infects Kupffer cells in the liver within 24 hours of exposure, leading to systemic infection.

  • Involvement of renal tissues can lead to kidney failure through eosinophilic degeneration.

  • Potential injuries include myocardial fiber injury through apoptosis and cytokine dysregulation affecting TNF-a, INF-b, IL-2, and CTL activity leading to severe disease.
    - TNF-α: Mediates inflammation and regulates immune responses; involved in apoptosis, leading to tissue injury.

    - INF-β: Key in the antiviral response; promotes antiviral gene expression and enhances immune response.

    - IL-2: Crucial for T cell growth and differentiation; supports immune cell activation and tolerance.

    - CTL: Essential for killing infected cells; activation influenced by IL-2 and INF-β, enhancing infection clearance.