Viruses, Replication Cycles & Antiviral Strategies

Central Dogma & Viral Exceptions

• Canonical flow: \text{DNA}\xrightarrow{\text{Transcription}} \text{RNA}\xrightarrow{\text{Translation}} \text{Protein}.

• RNA viruses violate by performing \text{RNA}\to \text{RNA} (enzyme = RNA-dep RNA pol) or \text{RNA}\to \text{DNA} (Reverse Transcriptase).

Antiviral Drugs Targeting Synthesis

1. Nucleoside/Base Analogs (chain terminators)
   • Fake nucleotides lacking 3′-OH block elongation.
   • Examples: Acyclovir (G analog) for HSV; AZT (T analog) for HIV.
   • Chemical similarity illustrated: double-ring purine/pyrimidine mimics.

2. RNA-dep RNA Pol Inhibitors
   • Block active site ⇒ no complementary RNA.
   • Examples: Remdesivir & Molnupiravir (SARS-CoV-2, Ebola).

• No drugs block viral Translation: would harm host ribosomes.

Assembly (Maturation)

• Self-assembly: capsomeres + genome attract electrostatically.

• Enzymes (except lysozyme) packaged inside nucleocapsid.

• Enveloped viruses: peplomers (spike glycoproteins) traffic to host membrane; matrix/tegument proteins line interior.

• Multi-protein precursors require viral Protease to cleave & fold subunits.
  • Protease inhibitors (e.g. Paxlovid, saquinavir) stop assembly; historic game-changer for HIV (Magic Johnson anecdote).

Release Mechanisms

• Bacteriophages & some naked animal viruses: accumulate Lysozyme → digest peptidoglycan/cell membrane → osmotic lysis; virions explosively ejected.

• Alternative for naked viruses lacking cell wall: permeabilize membrane or exocytosis.

• Enveloped viruses: always bud through a membrane containing pre-located peplomers.
  • If budding at cell membrane → simultaneous release.
  • If budding at internal membranes (ER/Golgi/nuclear) → secondary exocytosis required.
  • Drug example: Tamiflu (neuraminidase inhibitor) prevents influenza budding; effective only if taken ≤ 48–72 h after symptom onset.

Lytic vs Lysogenic Life Cycles (Bacteriophage then Animal-Cell Context)

• Five lytic stages: Attachment → Penetration → Synthesis → Assembly → Release ⇨ host death.

• Lysogenic = lytic + detour after Penetration

  1. Incorporation: viral dsDNA integrates into host genome via Integrase.
     • Viral genes in chromosome = Provirus (always dsDNA).
     • RNA or ssDNA viruses must first convert to dsDNA (Reverse Transcriptase or DNA pol) before Integrase acts.

  2. Dormancy until trigger (chemical, physical, hormonal, UV, age, illness, diet arginine > lysine).

  3. Upon induction → resume Synthesis, Assembly, Release as in lytic.

• Enzyme summary per stage
  • Penetration (phage): Lysozyme.
  • Incorporation: Integrase ± Reverse Transcriptase.
  • Synthesis (RNA viruses): RNA-dep RNA pol.
  • Assembly: Protease.

Reactivation Triggers & Epidemiology

• Documented triggers
  • Chemical (acidic juices, alcohol, aluminium can contact).
  • Physical trauma (dentist, wrestling mats, lip injury).
  • Emotional stress (sympathetic hormones).
  • Ageing (> 50 y: shingles risk).
  • Illness (immune diversion).
  • Radiation (especially UV – hence SPF lip balms).
  • Amino-acid ratio: High arginine / low lysine favors outbreaks; opposite ratio suppresses (≈40 % able to control HSV via diet; arginine-rich: nuts, beans, chocolate, coffee, alcohol; lysine-rich: dairy, breads).

• Persistent vs Latent vs Oncogenic outcomes (animal lysogeny)

  1. Latent: provirus silent ⇒ episodic outbreaks (classic HSV-1 cold sore).

  2. Persistent: continuous low-level virion release while cell lives (HIV; ~15 % genital HSV carriers!).

  3. Oncogenic: proviral insertion disrupts tumor-suppressor/onco-genes → uncontrolled mitosis (HPV, EBV, HBV, etc.).

Retrovirus (HIV-1) Complete Animation Highlights

• Structure: Enveloped; nucleocapsid core; glycoproteins gp120/gp41 spikes.

• Host receptor: CD4 + co-receptor CCR5/CXCR4.

• Key steps & enzymes
  • Fusion penetration.
  • Reverse Transcriptase → RNA/DNA hybrid → dsDNA.
  • Integrase docks dsDNA into host chromosome.
  • Transcription of provirus → mRNA → polyproteins.
  • Protease cuts Gag-Pol multiprotein; folded parts self-assemble.
  • Budding from membrane with spikes; maturation completes after protease action.

• Drug targets highlighted: Attachment blockers, RT inhibitors (nucleoside & non-nucleoside), Integrase inhibitors (e.g. Raltegravir), Protease inhibitors (e.g. saquinavir), budding blockers.

Bacteriophage-Specific Quick Sheet

Stage | Key Protein/Enzyme | Drug Target
Attachment | Tail fibers | (bacterial receptor mutation)
Penetration | Lysozyme | n/a
Synthesis | RNA-dep RNA pol (for RNA phage) | base analogs
Assembly | Protease | protease inhibitors
Release | Lysozyme burst | (hypothetical lysozyme blocker)

Group Exercise – Nafamostat & SARS-CoV-2 (class discussion)

• Nafamostat: existing anticoagulant that strongly inhibits spike-mediated membrane fusion via TMPRSS2 protease blockade.
  • Blocks either “Penetration” or “Attachment + Penetration complex” depending on viewpoint.

• Other plausible drug targets drawn from life-cycle diagram

  1. RNA-dep RNA pol inhibition (Remdesivir) ⇒ stop genomic replication.

  2. Protease (Mpro/3CLpro) inhibition ⇒ block polyprotein processing.

  3. Budding/Neuraminidase-like exocytosis interference (not yet observed for SARS-CoV-2).

Numerical & Statistical Nuggets

• 16 activity items reported by one student.

• Attendance: 10/30 present initially (33 %).

• Study ratio 3{:}1 hours outside:inside.

• Dietary control: 40\% of HSV patients outbreak-free via lysine > arginine.

• Persistent HSV-2 shedders: 15\% of carriers.

• Shingles typical age >50\,\text{y}.

• Tamiflu effective window: \le48–72\,\text{h} of symptoms.

Ethical, Practical & Philosophical Points

• Public-health advice: “Know your HIV status” because latency/persistence hide infectious phase.

• Social stigma history: HIV in 1990s; protease inhibitors shifted disease to chronic manageable → financial counseling case.

• Prescription stewardship: Early administration of antivirals (e.g., Tamiflu, Paxlovid) critical for efficacy — misuse may foster resistance.

• Personal responsibility: sharing beverages, engaging in sexual activity without visible lesions still transmits herpes; informed consent.

• Equity: Access to costly multi-drug HIV cocktails, protease/RT/integrase inhibitors — global disparity.

Connections & Reminders for Exam

• Lecture Test 2 covers Topic 3B only: Viruses, Prions, Cancer.

• Review old Test 1 virus questions (indicated in Joint Announcement).

• Fill comparison chart: Virus types vs genome vs required enzymes vs exit strategy.

• Practice drawing all five lytic syntheses and three lysogenic scenarios (dsDNA, ssDNA → dsDNA, Retrovirus).