Viral Replication - Vocabulary Flashcards

Viral Replication: Key Concepts

  • Based on the transcript by Bo-Young Hong, M.S., Ph.D., covering step-by-step viral replication, replication mechanisms across virus types, mutation consequences, and antigenic drift vs. shift.
  • Learning objectives (paraphrased): describe the replication steps, differentiate replication strategies of different viruses, review mutation impacts, and compare antigenic drift and antigenic shift in epidemics/pandemics.

Invasion, Latency, and Clinical Presentation (Contextual Background)

  • Invasion of epithelial cells by virus at the site of exposure followed by intracellular replication at the primary exposure site.
  • Retrograde movement of virus to host nervous system (examples of ganglia): trigeminal, cervical, lumbosacral.
  • Replication and persistence in a dormant state throughout life (latency).
  • Example clinical note: intraoral presentation of herpetic ulcers in the palate (latency/reactivation of herpesviruses).

Viral Genome Types and Replication Overview

  • Viral genomes and transcription:
    • dsDNA viruses (double-stranded DNA): use DNA transcription machinery.
    • ssDNA viruses: require complementary DNA synthesis for transcription.
    • dsRNA viruses: genome is double-stranded RNA; transcription performed by viral RNA-dependent RNA polymerases.
    • ssRNA viruses: genome is single-stranded RNA; polarity determines replication strategy:
    • ssRNA(+) (plus-sense): infectious RNA, 5′→3′; can serve directly as mRNA for translation.
    • ssRNA(−) (minus-sense): genome is complementary to mRNA, 3′→5′; cannot be translated directly; serves as template to synthesize (+) RNA.
    • Retroviruses: RNA genome acts as mRNA-like and is reverse-transcribed into DNA; the resulting dsDNA integrates into the host genome and is transcribed by host machinery.
  • Key concept: Some viruses code their own polymerases; others rely on host polymerases. Retroviruses use reverse transcription; para-retroviruses use reverse transcription for genome replication as well.
  • Important note: Packaging signals in viral genomes guide genome encapsidation during assembly.

Major and Minor Points in RNA/DNA Replication (Detailed)

  • RNA viruses rely on specialized enzymes to use RNA genomes as templates:
    • RNA→RNA: use RNA-dependent RNA polymerase (RdRP).
    • RNA→DNA→RNA: reverse transcription (RNA-dependent DNA polymerase).
  • DNA viruses may code their own polymerases or use host cellular polymerases.
    • DNA→DNA: use DNA polymerase (DNA-dependent DNA polymerase).
    • DNA→RNA→DNA: para-retroviruses use reverse transcriptase.
  • For ssRNA(+): the genome can function directly as mRNA and be translated by host ribosomes; for ssRNA(−): must be transcribed into a positive-sense RNA first.

Stepwise Viral Life Cycle (7 Stages)

1) Attachment/Adsorption

  • Attachment mechanisms differ for naked (non-enveloped) vs. enveloped viruses.
  • Naked viruses attach via direct capsid contact to receptors.
  • Enveloped viruses attach via viral glycoproteins (spikes) to host receptors and may enter via membrane fusion or endocytosis.
  • Examples and factors mentioned:
    • Spikes mediate attachment for enveloped viruses.
    • For entry barriers, host factors like LY6E, IFITM, CH25H, NCOA7 influence fusion/endosomal processing.
    • Endocytosis can lead to fusion in late endosomes; H+ and endosomal conditions promote fusion.
  • Example (Rhinovirus): attachment via receptor ICAM-1 on nasal epithelial cells.

2) Penetration/Uptake

  • Direct penetration (mainly naked viruses).
  • Fusion at the plasma membrane (enveloped viruses).
  • Fusion within the plasma membrane or endosomal membranes can occur for various viruses depending on entry route and morphology.

3) Uncoating and Eclipse

  • Removal of genome from the capsid occurs:
    • At the cell membrane upon entry.
    • In endocytic vesicles via low pH or virion conformational changes.
    • In the cytosol via cellular enzymes.

4) Transcription

  • Viral genomes must serve as templates to produce new viral genomes and mRNAs.
  • Viruses may use viral enzymes, host enzymes, or both.
  • Viruses often shut down host nucleic acid replication and host protein production to favor virion production.
  • Note: ssRNA(+) can often bypass some transcription steps and proceed toward translation after uncoating.

5) Translation (and Genome Synthesis)

  • Viral mRNAs are translated into viral proteins by host ribosomes.
  • For ssRNA(+) viruses, translation can begin directly from the genome, producing viral proteins needed for replication and assembly.
  • For other genome types, translation requires transcription first to generate mRNAs compatible with translation.

6) Assembly (Nucleocapsid Formation)

  • Nucleocapsid is created; capsid assembles spontaneously around the genome.
  • Packaging signals in the genome guide incorporation into the virion.
  • This step culminates in the mature virion ready for release.

7) Release (Egress)

  • Three primary mechanisms for release:
    • Lysis: occurs for naked and enveloped viruses, often associated with host cell death.
    • Budding: primarily for enveloped viruses; virions acquire a lipid envelope from cellular membranes during egress.
    • Exocytosis: used by some naked and enveloped viruses; involves trafficking through the Golgi/secretory pathway and vesicular transport.
  • Release mechanism can influence virion morphology and host cell fate.

Details of Attachment and Entry Mechanisms

  • Attachment (Naked Virus)
    • Direct capsid-contact with host receptor.
  • Attachment (Enveloped Virus)
    • Viral glycoproteins (spikes) engage host receptors and mediate fusion or endocytosis.
    • Endosomal processing may involve host factors such as LY6E, IFITM, CH25H, NCOA7; fusion occurs in endosomes or at the plasma membrane depending on virus.
  • Specific example: Rhinovirus attaches via ICAM-1 receptor on nasal epithelial cells; docking occurs at a nasal cell docking port.
  • Penetration outcomes:
    • Direct penetration for naked viruses.
    • Fusion at the plasma membrane for enveloped viruses.
    • Fusion inside the plasma membrane for both naked and enveloped viruses under certain conditions.

Antiviral Therapies and Targets (How Therapies Intercept Replication)

  • Antiviral modalities include:
    • Monoclonal antibodies (mAbs): used in HIV, CMV, RSV.
    • Entry inhibitors: block adsorption or fusion (used in HIV, HSV).
    • Uncoating inhibitors: used against influenza A and picornaviruses.
    • Viral DNA polymerase inhibitors: block DNA synthesis.
    • Viral RNA polymerase inhibitors: block RNA synthesis.
    • Reverse transcriptase inhibitors (RT inhibitors): used in HIV and HBV.
    • Protease inhibitors: block viral protein processing.
    • Integrase inhibitors: used in HIV.
    • Neuraminidase inhibitors: used in influenza.
  • Conceptual targets aligned with life cycle stages:
    • Entry (adsorption/fusion)
    • Uncoating
    • Replication
    • Maturation
    • Release
    • Integration (for retroviruses)

Consequences of Mutation and Antigenic Variation

  • Mutations enable:
    • Changes in tissue tropism (e.g., influenza shifts between animal hosts; SARS-CoV-2 from bats to humans).
    • Altered antigenic properties, aiding immune evasion (antibody escape).
    • Drug resistance (e.g., influenza resistance to amantadine; HIV requires combination ART due to resistance).
    • Changes in virulence (e.g., some strains become more deadly when crossing species barriers).

Antigenic Drift vs Antigenic Shift (Epidemics vs Pandemics)

  • Antigenic drift:
    • Minor antigenic changes in Hemagglutinin (H) and Neuraminidase (N) proteins due to random mutations by the viral RNA polymerase.
    • No change in viral subtype.
    • Can lead to epidemics: increased disease incidence in a localized region.
  • Antigenic shift:
    • Major change in antigenicity due to reassortment of viral genome segments; occurs infrequently (approximately every 10–20 years).
    • Results in a new viral subtype with pandemic potential across wide geographic areas.

Reassortment and Coinfection (Genetic Mixing in Viruses)

  • When two viruses co-infect the same cell (coinfection/superinfection), genome segments can reassort.
  • This process can generate novel combinations of genome segments, leading to new viral phenotypes.
  • Conceptual depiction: virus A and virus B co-infecting can produce offspring viruses with mixed segments (illustrated as input A and B producing outputs A, B, or reassorted viruses).

Summary of Release Pathways and Virion Diversity

  • Release mechanisms (Lysis, Budding, Exocytosis) influence virion structure (naked vs enveloped) and host cell fate.
  • Enveloped virions acquire their lipid envelope via budding or exocytosis from host membranes such as plasma membrane, ER, Golgi, or endosomal membranes.
  • Naked virions typically lyse cells or are released by exocytosis without acquiring an envelope.
  • Tegument and envelope proteins (examples: US3, UL34, UL31, gE, gI, gM) participate in assembly and egress in some viruses; these details are illustrated in the exocytic pathway diagram.

Reference Context and Exam Preparation

  • Core sources cited in the transcript include: Essential Microbiology for Dentistry (Chapter 4), Oral Microbiology and Immunology (3rd ed., Chapter 16).
  • The material includes a 40-question assessment format noted at the end of the slide deck.

Key Takeaways for Exam

  • Know the 7 steps of viral replication and what occurs at each step.
  • Be able to distinguish replication strategies of different genome types: dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(−), and retroviruses.
  • Understand how antigenic drift and shift differ in cause and epidemiologic outcome (epidemics vs pandemics).
  • Recognize the impact of mutations on tropism, antigenicity, drug resistance, and virulence.
  • Recall major antiviral targets and the corresponding stages of the viral life cycle that they affect.
  • Appreciate the role of host factors and viral entry mechanisms in shaping infection outcomes.

Notation and Equations Used

  • Positive-sense RNA: ssRNA^{+}, ext{ 5' to 3' infectious RNA, can function as mRNA}
  • Negative-sense RNA: ssRNA^{-}, ext{ 3' to 5', cannot be translated directly; serves as template for }(+)RNA
  • General transcription/translation relationships summarized as:
    • ext{DNA viruses}
      ightarrow ext{RNA transcripts}
      ightarrow ext{proteins}
    • ext{RNA viruses}
      ightarrow ext{RNA synthesis (RdRP)}
      ightarrow ext{proteins}
  • Reassortment conceptually described as coinfection producing mixed genome segments rather than a fixed algebraic equation, but genetically represented by segment exchange between viruses A and B.