Viruses & Their Replication

What Is a Virus?

Viruses are unique genetic elements that require a living host cell for replication. They exist in different forms and possess diverse genome types.

• Virus: A genetic element that cannot replicate independently; requires a host cell.

• Virion: The extracellular, inert form of a virus, facilitating transmission between hosts.

• Genome Types:

  • DNA or RNA

  • Single-stranded (ss) or double-stranded (ds)

  • ss genomes may be plus sense (same as mRNA) or minus sense (complementary to mRNA)

  • Linear or circular

Example: Tobacco mosaic virus (TMV) is a rod-shaped virus with a ssRNA genome.

Dynamic Nature of Viruses

Viruses can exist in three distinct forms, each with unique biological roles.

• Virion: Inert particle, no metabolism or energy conversion.

• Intracellular replication complex: Viral gene products direct host enzymes to assemble progeny virions at replication complexes.

• Integrated viral genome: Some viral genomes integrate into host DNA as a prophage (in bacteria) or provirus (in animals), potentially permanently.

Viral Surface Layers

The structure of viral surface layers determines infectivity and host interactions.

• Capsid: Protein shell surrounding the viral genome.

• Naked viruses: No additional layers beyond the capsid (common in bacterial viruses).

• Enveloped viruses: Possess a phospholipid bilayer (from host membrane) and viral proteins.

• Nucleocapsid: Combination of nucleic acid and protein in enveloped viruses.

Virion Structure and Symmetry

Virion architecture is defined by capsomeres and symmetry types.

• Capsomere: Individual protein units arranged in a repetitive pattern around nucleic acid.

• Self-assembly: Capsids may assemble spontaneously or require host assistance.

• Helical symmetry: Rod-shaped viruses; length determined by nucleic acid, width by capsomere size.

• Icosahedral symmetry: Spherical viruses; most efficient closed shell arrangement.

Example: Human papillomavirus exhibits icosahedral symmetry.

Enveloped Viruses

Enveloped viruses have unique infection and exit strategies.

• Lipoprotein envelope: Surrounds nucleocapsid.

• Envelope proteins: Mediate attachment and entry into animal cells.

• Entry: Entire virion enters animal cell.

• Exit: Enveloped viruses exit more easily, often by budding.

Viral Replication and Culturing

Culturing, Detecting, & Counting Viruses

Viruses are quantified and studied using specialized assays.

• Plaque assay: Detects viral infection by clear zones (plaques) on host cell lawns.

• Titer: Number of infectious units per volume.

• Plaque-forming units (PFU): Always lower than direct counts by electron microscopy.

Bacteriophage Attachment & Entry

Host specificity is determined by viral and host surface interactions.

• Complementary receptors: Proteins, carbohydrates, glycoproteins, lipids, or other structures on host cell surface.

• Normal host functions: Receptors may be involved in uptake, cell interaction, flagella, or pili.

Tailed Bacteriophages

Tailed phages use complex mechanisms for DNA entry.

• Attachment: Tail fibers interact with polysaccharides on E. coli LPS layer.

• Penetration: Tail fibers retract, tail pins contact cell wall, T4 lysozyme forms pore, tail sheath contracts, DNA enters cytoplasm.

• Capsid: Remains outside the cell.

Prokaryote Defense Mechanisms

Bacteria have evolved multiple strategies to resist viral infection.

• Toxin-antitoxin systems

• CRISPR: Adaptive immunity against viruses.

• Restriction endonucleases: Cleave foreign DNA at specific sites; host DNA is protected by modification.

• Base substitution: Phages may alter their DNA to resist restriction enzymes.

Viroids and Prions

Viroids

Viroids are infectious RNA molecules affecting plants.

• Structure: Small, circular, ssRNA (246–399 bp), no protein component.

• Stability: Hairpin-shaped ds molecule with closed ends.

• Transmission: Enter plants through wounds; move via plasmodesmata.

• Pathogenicity: Cause plant diseases; do not infect animals or microorganisms.

Prions

Prions are infectious proteins causing neurodegenerative diseases.

• Prnp gene: Encodes normal prion protein (PrPC) in neurons.

• Pathogenic form: PrPSc has altered conformation, promotes conversion of PrPC.

• Amyloid formation: Aggregates destroy brain and nervous tissue.

• Diseases: Scrapie, Creutzfeldt-Jakob, mad cow disease; other amyloid diseases (Alzheimer’s, Huntington’s, Parkinson’s, type 2 diabetes).

Virosphere and Ecological Roles

Virosphere

Viruses are ubiquitous and play key ecological roles.

• Head-and-tail dsDNA bacteriophages: Most common in oceans.

• Transduction agents: Transfer genes between hosts.

• Lytic vs. lysogenic: Lytic dominates when hosts are plentiful; lysogenic when hosts are scarce.

• Viral metagenome: All virus genes in an environment; ~75% sequences are novel.

Ecological Roles of Viruses

• Acute viruses: Kill hosts, recycle nutrients, increase host diversity.

• Persistent viruses: May confer mutualistic benefits.

The Human Virome

• Large intestine: Equal prokaryotic cells and viruses (~109/g feces).

• DNA bacteriophages: Dominate; transfer antibiotic resistance/metabolic genes.

• Defense: May protect against pathogens; can enhance pathogenicity (e.g., cholera toxin gene in Vibrio cholerae).

Viral Life Cycles

Virulent vs. Temperate Viruses

Viruses can follow different replication strategies.

• Virulent: Always lyse and kill host after infection.

• Temperate: Replicate with host genome without killing, establishing stable relationships.

• Lysogeny: Viral genome integrated, passed to daughter cells; can result in lysogenic conversion (new properties).

Regulation of Lambda Lifestyle

• cI protein (lambda repressor): Represses lytic events.

• cro repressor: Activates lytic events.

• Outcome: First repressor to accumulate determines infection fate.

Bacteriophage Lambda

• Genome: Linear dsDNA with cohesive ends (cos sites).

• Upon entry: DNA ends base pair, ligate to form circular dsDNA.

• Lytic pathway: Rolling circle replication produces concatemers; genomes cut at cos sites, packaged, lysis occurs.

• Lysogenic pathway: DNA integrates at attλ site via integrase.

• Transduction: Host genes may be packaged and transferred.

Baltimore Classification

Viruses are classified by genome composition and replication mechanism.

• Seven categories: Based on DNA/RNA, strandedness, sense, and replication strategy.

Retroviruses

Retroviruses replicate via a DNA intermediate using reverse transcriptase.

• Genome: Two identical ss(+)RNA molecules.

• Enzymes: Reverse transcriptase, integrase, protease.

• Genes:

  • gag: Structural proteins

  • pol: Reverse transcriptase and integrase

  • env: Envelope proteins

Example: Human immunodeficiency virus (HIV).

Viral Protein Synthesis

Early and Late Proteins

• Early proteins: Synthesized soon after infection; usually enzymes (e.g., nucleic acid polymerases), shut down host transcription/translation.

• Late proteins: Structural and assembly proteins; synthesized in large amounts; assemble new virions, exit by lysis or budding.

Virus Types and Replication Strategies

ssDNA Viruses

• Hosts: Wide variety, mostly prokaryotes.

• Bacteriophage ɸX174: Circular genome, overlapping genes, rolling circle replication, lysis via peptidoglycan inhibition.

dsDNA Bacteriophages

• T4 and lambda: Classic examples.

• T7: Infects E. coli; icosahedral head, short tail; encodes T7 RNA polymerase; replication involves terminal repeats and concatemers.

• Mu: Requires integration for lytic/lysogenic development; replication by repeated transposition.

DNA Viruses of Archaea

• Mostly circular dsDNA viruses.

• Hosts: Euryarchaeota and Crenarchaeota.

• Release: Some (e.g., PAV1) released by budding, not lysis.

Uniquely Replicating DNA Animal Viruses

• Pox viruses: Replicate in cytoplasm; linear dsDNA; used for recombinant vaccines.

• Adenoviruses: Replicate in nucleus; unique replication without lagging strand; terminal protein required for genome replication.

DNA Tumor Viruses

• Polyomavirus SV40: Naked icosahedral, circular dsDNA; causes tumors; overlapping genes; integration in nonpermissive hosts leads to transformation.

• Herpesviruses: Cause various diseases and cancers; can remain latent, reactivate under stress.

Positive-Strand RNA Viruses

• Coronaviruses: Large, enveloped, replicate in cytoplasm; cause respiratory infections (e.g., SARS); virions assembled in Golgi, released from cell surface.

Negative-Strand RNA Animal Viruses

• Rabies virus: Rhabdovirus, bullet-shaped, enveloped; must be transcribed by viral replicase into mRNAs and positive-strand RNA.

• Release: By budding.

Double-Stranded RNA Viruses

• Reoviruses: Infect animals, plants, fungi; rotavirus causes diarrhea; nonenveloped, double shell, segmented genome; virions contain enzymes for mRNA synthesis.

Influenza Virus

• Negative-strand RNA, enveloped, pleomorphic, segmented genome.

• Surface proteins: Hemagglutinin (stimulates immune response), neuraminidase (destroys sialic acid, aids release).

• Antigenic shift: Reassortment of genome segments from different strains creates new surface proteins, leading to outbreaks.

Viral Enzymes and Entry-to-Exit Strategy

• Lysozyme: Creates holes in cell wall for nucleic acid entry; lyses cell for virion release.

• Neuraminidases: Destroy glycoproteins/glycolipids, liberate viruses.

• Nucleic acid polymerases: RNA replicases (RNA-dependent RNA polymerases), reverse transcriptase (RNA-dependent DNA polymerase).

Viral Evolution

Origins and Evolutionary Roles

• Viruses may have arisen after cells: Remnants of cells, replicate with host help.

• RNA world hypothesis: Viruses may have played a role in transition from RNA to DNA.

• Gene transfer: Viruses as mechanisms for rapid gene movement.

• Proteomics: Support early appearance; ancient cells with segmented RNA genomes.

• RNA viruses: Older than DNA viruses; dsRNA likely oldest.

• Selection: For protein shell to protect genome, dependence on host for replication.

• Novelty: Most viral genes are new to biology, with no homologs.

RNA to DNA Transition

• DNA viruses: May have arisen for protection from ribonucleases; DNA is more stable.

• Reverse transcriptase: Key enzyme in transition.

• Host adaptation: Cells began replicating DNA, converting genomes from RNA to DNA.

Baltimore Classification Table

The Baltimore system classifies viruses based on genome type and replication strategy.

Additional info: Table entries inferred for completeness based on Baltimore classification.

Key Formulas and Enzymes

• Rolling Circle Replication: Used by some dsDNA and ssDNA viruses.

• Reverse Transcriptase Reaction:

• RNA Replicase Reaction:

Additional info: Academic context added for completeness and clarity, including examples and expanded explanations.