🧬 Viruses in the Environment — Comprehensive Notes

1. Viral Basics

What is a Virus?

  • A virus is an obligate intracellular parasite:

    • Can only replicate inside living host cells

  • Size: 20–400 nm → too small for light microscopy

Core Components

All viruses contain:

  • Nucleic acid (DNA or RNA)

  • Capsid (protein coat)

Some viruses also have:

  • Envelope (lipid bilayer derived from host membrane)

2. Viral Classification — Baltimore System

Classifies viruses based on:

  • Genome type (DNA vs RNA)

  • Strand type (ss vs ds)

  • mRNA production strategy

7 Baltimore Classes

Class

Genome Type

Key Feature

I

dsDNA

Uses host machinery

II

ssDNA

Converted to dsDNA

III

dsRNA

Carries RNA polymerase

IV

+ssRNA

Genome = mRNA

V

−ssRNA

Must be transcribed

VI

ssRNA-RT

Reverse transcription

VII

dsDNA-RT

RNA intermediate

3. Viruses in the Environment

Abundance & Distribution

  • ~10³¹ virus particles globally

  • 10× more viruses than microbial cells

  • Found in:

    • Oceans (10⁶–10⁸ viruses/mL)

    • Soil (10⁷–10⁹ viruses/g)

    • Atmosphere & extreme environments

Hosts

  • Infect all domains:

    • Bacteria

    • Archaea

    • Plants

    • Animals

    • Fungi

4. Why Viruses Matter

Biological & Environmental Importance

  • Control microbial populations

  • Drive nutrient cycling

  • Influence evolution (gene transfer)

Human Relevance

  • Cause diseases

  • Affect agriculture & food security

  • Used in:

    • Gene therapy

    • Vaccines

    • Phage therapy

    • Molecular biology tools

🌱 5. Plant Viruses

Key Features

  • Require living plant cells

  • Cannot enter via:

    • Endocytosis

    • Membrane fusion

      (due to rigid cell wall)

Entry Methods

  • Mechanical damage

  • Insect vectors (e.g. aphids)

  • Agricultural practices

Spread

  • Cell-to-cell via plasmodesmata

  • Systemic via vascular tissue

Symptoms

  • Mosaic leaf patterns

  • Leaf curling

  • Stunted growth

⚠ Disease results from metabolic disruption, NOT cell lysis

Genome & Structure

  • Mostly:

    • +ssRNA

    • Non-enveloped

  • Shapes:

    • Rod-shaped

    • Filamentous

    • Some icosahedral

Example: Tobacco mosaic virus (TMV)

Key Features

  • +ssRNA (Baltimore Class IV)

  • Non-enveloped

  • Rod-shaped

  • Extremely stable

Transmission

  • Mechanical contact (tools, handling)

  • No receptor needed

TMV Life Cycle

  1. Entry

    • Through plant wounds → cytoplasm

  2. Uncoating

    • RNA released and binds ribosomes

  3. Early Gene Expression

    • Viral replicase produced

  4. Genome Replication

    • −RNA intermediate → new +RNA

    • Produces subgenomic RNAs

  5. Assembly

    • Coat protein + RNA → virions

  6. Cell-to-cell movement

    • Movement protein modifies plasmodesmata

  7. Systemic Spread

    • Via vascular system → whole plant

🧍 6. Animal Viruses

General Features

  • Infect vertebrates & invertebrates

  • Can be:

    • DNA or RNA

    • Enveloped or non-enveloped

Infection Outcomes

  • Asymptomatic → severe disease

  • Acute or chronic

Viral Pathogenicity

Determined by:

Virus Factors

  • Tissue tropism

  • Replication rate

  • Immune evasion genes

Host Factors

  • Genetics

  • Immune status

  • Age, nutrition, stress

Environmental Factors

  • Dose

  • Transmission route

  • Population density

Common Viral Diseases

Respiratory

  • Influenza

  • SARS-CoV-2

  • RSV

Herpesviruses

  • Herpes simplex virus

  • EBV, CMV

Gastrointestinal

  • Norovirus

  • Rotavirus

Blood-borne

  • HIV

  • HBV, HCV

Example: Herpes simplex virus (HSV-1 & HSV-2)

Key Features

  • dsDNA (Baltimore Class I)

  • Enveloped, icosahedral

  • Causes lifelong infection

Types

  • HSV-1 → oral herpes

  • HSV-2 → genital herpes

HSV Life Cycle

  1. Attachment & Entry

    • Membrane fusion

  2. Transport to Nucleus

    • DNA remains episomal

  3. Gene Expression

    • Immediate-early → regulatory

    • Early → replication

    • Late → structural proteins

  4. Assembly & Release

    • Exocytosis

  5. Latency

    • Dormant in neurons

  6. Reactivation

    • Triggered by stress, UV, illness

🦠 7. Bacteriophage (Phage)

Key Features

  • Infect bacteria

  • Most abundant biological entities on Earth

  • Found everywhere:

    • Soil, oceans, gut

Infection Types

1. Lytic Cycle

  • Replication → host cell lysis → release

2. Lysogenic (Temperate)

  • Viral DNA integrates into host genome

  • Host survives

Ecological Roles

  • Control bacterial populations

  • Drive evolution (horizontal gene transfer)

  • Influence nutrient cycles

Example: CTXφ bacteriophage

Host

  • Vibrio cholerae

Key Concept

  • Bacterium becomes pathogenic only after phage infection

Disease Link: Cholera

  • Caused by toxin encoded by CTXφ genes (ctxA, ctxB)

CTXφ Life Cycle

  1. Attachment

    • Binds toxin-coregulated pilus (TCP)

  2. Entry

    • ssDNA enters cell → converted to dsDNA

  3. Integration

    • Viral DNA inserts into chromosome

  4. Gene Expression

    • Cholera toxin genes expressed

  5. Toxin Production

    • Causes severe diarrhoea

  6. Phage Release

    • Without killing host cell

🧾 8. Summary (Exam Gold)

  • Viruses are ubiquitous and highly abundant

  • Drive:

    • Ecosystem processes

    • Evolution

    • Disease dynamics

Key Comparisons

Feature

Plant Viruses

Animal Viruses

Phage

Entry

Wounds/vectors

Receptors

Receptors

Spread

Cell-to-cell

Systemic

Within bacteria

Cell death

Rare

Common

Often (lytic)

Example

TMV

HSV

CTXφ

🔥 Key Takeaways

  • TMV → simple +ssRNA virus, no cell lysis

  • HSV → latency + reactivation

  • Phage → major ecological regulators

  • CTXφ → converts harmless bacteria into pathogens

If you want next:

  • ultra-condensed 1-page cheat sheet

  • predicted exam questions

  • flashcards (Anki-ready)

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