Viruses: Structure, Replication, and Diversity

Viruses: Structure, Replication, and Diversity

What Is a Virus?

Viruses are genetic elements that can only multiply inside living host cells. They are not considered living organisms and are not included on the tree of life. Viruses are obligate intracellular parasites, relying on their host for energy, metabolic intermediates, and protein synthesis. Each virus contains its own nucleic acid genome, which may be either DNA or RNA.

• Virion: The extracellular form of a virus, existing outside the host and enabling transmission between hosts. Replication occurs only after infection.

• Obligate intracellular parasite: Requires a host cell for replication and metabolic processes.

Viral Components

Viruses are composed of several key structural elements that facilitate infection and replication.

• Capsid: The protein shell surrounding the viral genome, built from repeating protein units called capsomeres.

• Nucleocapsid: The combination of the genome and capsid, which may be enclosed within an envelope.

• Surface Proteins: Mediate host recognition, cell attachment, and sometimes enzymatic functions.

Types of Viruses

Type	Description
Naked virus	Only nucleic acid + capsid
Enveloped virus	Has lipid membrane from host + viral proteins

Viral Life Strategies

Viruses employ different strategies to propagate within their hosts.

• Lytic (Virulent) Infection: Virus replicates, redirects host metabolism, and causes cell lysis, releasing new virions.

• Lysogenic (Temperate) Infection: Viral genome integrates into the host genome as a prophage, remaining dormant until induced to enter the lytic cycle.

Viral Genomes

Viral genomes are highly diverse and can be composed of either DNA or RNA, which may be single- or double-stranded. These genomes are much smaller than those of cellular organisms.

• Hosts: Viruses infect bacteria (bacteriophages), archaea, animals, plants, protozoa, and even other viruses.

Virus Size & Structure

Viruses vary greatly in size and structural complexity.

• Size: Most viruses range from 0.02 to 0.3 μm, with some giant viruses exceeding 1 μm.

• Capsid Assembly: Often self-assemble, though some require host folding proteins.

Virus Symmetry

Viruses exhibit different forms of symmetry, which influence their shape and assembly.

• Helical: Rod-shaped (e.g., Tobacco Mosaic Virus).

• Icosahedral: Spherical with 20 triangular faces (e.g., Human papillomavirus).

• Complex: Head and tail structures (e.g., T4 bacteriophage), or giant viruses (e.g., Mimivirus).

Enveloped Viruses

Some viruses possess a lipid membrane envelope derived from the host cell, which facilitates easier exit (budding) and is common in animal viruses such as Ebola and HIV. Enveloped viruses are rare in bacteria and plants due to the presence of cell walls.

Enzymes in Virions

Certain viruses package enzymes within their virions to facilitate infection and replication, especially when the host cell cannot provide the necessary functions.

Enzyme	Function
Lysozyme	Breaks bacterial cell wall
Neuraminidase	Helps release influenza virus
RNA replicase	RNA → RNA synthesis
Reverse transcriptase	RNA → DNA (retroviruses)

Culturing & Counting Viruses

Viruses are quantified using plaque assays, where clear zones (plaques) indicate areas of cell lysis. Each plaque corresponds to one infectious virus, allowing calculation of the titer (number of infectious virions per volume). Plating efficiency is always less than 100% due to defective virions, and electron microscopy (EM) counts are typically higher than plaque counts.

Viral Replication Cycle

The viral replication cycle consists of five main steps:

1. Attachment (adsorption)

2. Penetration

3. Synthesis

4. Assembly

5. Release

The one-step growth curve includes an eclipse phase (no detectable virions), maturation (assembly), and a latent period (eclipse + maturation). The burst size refers to the number of virions released per infected cell.

Bacteriophage T4 (Model Lytic Virus)

Bacteriophage T4 infects Escherichia coli and serves as a model for lytic viral infection.

• Attachment: Uses LPS receptors on the host cell.

• Penetration: Tail fibers bind, tail sheath contracts, and DNA is injected into the host like a syringe, leaving the capsid outside.

• Host Defenses: CRISPR, restriction enzymes, and toxin-antitoxin systems.

• Virion Production: Early proteins are replication enzymes; late proteins are structural. The genome is pumped into the capsid using ATP, and over 100 virions can be released per cell.

Temperate Phages (Lambda)

Temperate phages, such as lambda, can integrate their DNA into the host genome, becoming a prophage. A repressor protein keeps the virus inactive until induction (triggered by stress, such as DNA damage) causes the virus to enter the lytic cycle.

Viruses of Eukaryotes

Viruses infecting eukaryotes differ from those infecting prokaryotes in several ways:

• The entire virion enters the cell.

• Replication often occurs in the nucleus.

• Viral factories, or viroplasms, are sites of viral replication within the host cell.

Animal Virus Infection

Animal viruses enter host cells via membrane fusion or endocytosis. The outcome of infection can vary, including cell lysis, latency, persistent infection, or transformation (cancer).

Plant Viruses

Plant viruses are mostly RNA viruses and are usually not enveloped. They have a wide host range and typically enter through wounds or are transmitted by vectors such as insects, nematodes, or fungi. Movement proteins facilitate cell-to-cell spread via plasmodesmata.

Retroviruses (HIV)

Retroviruses, such as HIV, have an RNA genome and use reverse transcriptase to convert RNA into DNA, which then integrates into the host genome as a provirus.

Comparison: Virus vs Bacteria Growth

Feature	Virus	Bacteria
Growth curve	One-step	Exponential
Reproduction	Only in host	Independent
Metabolism	None	Full metabolism
Division	Assembly	Binary fission

Possible Results of Viral Infections

Type	Result
Virulent	Cell lysis
Latent	Viral DNA silent
Persistent	Slow release
Transformation	Cancer

Key Review Questions

• How does a virus differ from a cell? Viruses lack metabolism, ribosomes, and cellular structure, and can only replicate inside host cells.

• Why does a virus need a host cell? Viruses rely on the host for energy, enzymes, ribosomes, and metabolic intermediates.

• What is unusual about viral genomes? They can be DNA or RNA, single- or double-stranded, and are much smaller than cellular genomes.

• Capsid vs capsomere & common symmetry: Capsid is the whole protein shell; capsomere is an individual protein unit. Common spherical symmetry is icosahedral.

• Naked vs enveloped virus: Naked viruses have only a capsid; enveloped viruses have a capsid plus a lipid membrane from the host.

• Enzymes in RNA virus virions & why: RNA-dependent RNA polymerases and reverse transcriptase are packaged because host cells cannot make RNA from RNA.

• What is packaged into capsids during maturation? The viral genome (DNA or RNA).

• Explain burst size: The number of virions released from a single infected cell.