5. Viruses: Structure, Life Cycle, and Infection

Viruses and Viral Structure

Definition and Basic Properties

Viruses are unique genetic elements that require a living host cell to multiply. They exist in an extracellular form known as the virion, which facilitates transmission between hosts.

• Virus: A genetic element that can only replicate inside a living cell.

• Virion: The extracellular form of a virus, containing the nucleic acid genome surrounded by a protein coat (capsid), and sometimes additional layers.

• Virions enable transmission from one host cell to another.

• Viruses are obligate intracellular parasites; they cannot replicate outside a host cell.

Example: The influenza virus is transmitted via virions that infect respiratory tract cells.

Viral Genomes

Viral genomes are highly diverse and can be composed of either DNA or RNA, which may be linear or circular. Most viral genomes are significantly smaller than those of cellular organisms.

• Genome types include: dsDNA, ssDNA, dsRNA, ssRNA (+ or - sense), and RNA→DNA (retroviruses).

• Viral genomes encode all information necessary for replication and infection.

Example: SARS-CoV-2 has a single-stranded positive-sense RNA genome.

Structure of the Virion

Size and Shape

Viruses exhibit a wide range of shapes and sizes, but are generally much smaller than prokaryotic cells, typically ranging from 0.02 to 0.3 μm in diameter.

• Common shapes: helical, icosahedral, complex, and enveloped forms.

• Viruses can be visualized using electron microscopy due to their small size.

Example: Bacteriophage T4 is a complex virus that infects Escherichia coli.

Capsid and Capsomeres

The capsid is the protein shell that surrounds the viral genome, composed of repeating protein subunits called capsomeres. The arrangement of capsomeres is highly ordered and repetitive, providing structural stability.

• Capsids protect viral nucleic acids and aid in host cell recognition.

Symmetry in Viral Structure

Nucleocapsids (capsid + nucleic acid) are arranged with specific symmetry:

• Helical symmetry: Rod-shaped viruses (e.g., tobacco mosaic virus).

• Icosahedral symmetry: Spherical viruses (e.g., human papillomavirus).

Additional info: Icosahedral symmetry provides maximal internal volume for genome packaging with minimal protein usage.

Enveloped Viruses

Some viruses possess a lipoprotein envelope derived from the host cell membrane, surrounding the nucleocapsid. Envelope proteins are critical for host cell attachment and entry, especially in animal viruses.

• Enveloped viruses are generally more sensitive to environmental conditions than non-enveloped viruses.

Example: Influenza virus and SARS-CoV-2 are enveloped viruses.

Virion-Associated Enzymes

Certain virions contain enzymes essential for infection:

• Lysozyme-like enzymes: Degrade bacterial cell walls (e.g., bacteriophages).

• Neuraminidases: Cleave glycosidic bonds, facilitating virus release from host cells.

• Nucleic acid polymerases: Required for replication of viral genomes, especially in RNA viruses.

Structure of SARS-CoV-2

SARS-CoV-2 is an enveloped virus with helical symmetry and a positive-sense single-stranded RNA genome. Key structural proteins include:

• Spike (S1 & S2): Mediates attachment to host cell receptors.

• Nucleocapsid (N): Encapsulates the RNA genome.

• Membrane (M) and Envelope (E): Contribute to virion structure and assembly.

Comparison of Viruses and Bacteria

Similarities and Differences

• Both can cause disease and contain genetic material (DNA or RNA).

• Bacteria are living cells; viruses are not considered alive and require a host for replication.

• Bacteria are larger, have cellular structures, and can reproduce independently.

• Viruses are smaller, lack cellular machinery, and are obligate intracellular parasites.

Table: Comparison of Viruses and Bacteria

Feature	Viruses	Bacteria
Cellular Structure	No	Yes
Genome	DNA or RNA	DNA
Replication	Only in host cell	Independent
Size	20–300 nm	~1–5 μm
Living?	No	Yes

Harmful and Beneficial Effects of Viruses

• Harmful: Cause diseases, kill host cells, can lead to disabilities, and affect plants and animals.

• Beneficial: Used in phage therapy, molecular biology research, gene transfer, and as tools in biotechnology.

Culturing, Detecting, and Counting Viruses

Methods of Cultivation

• Viruses replicate only in specific host cells or whole organisms.

• Bacterial viruses (bacteriophages) are easiest to grow and serve as model systems.

• Animal and plant viruses are cultivated in tissue cultures.

Measuring Virus Infectivity

• Titer: Number of infectious units per volume of fluid.

• Plaque assay: Quantifies virus infectivity by counting clear zones (plaques) on a lawn of host cells.

Example: Each plaque on an agar plate corresponds to infection by a single virus particle.

Overview of the Virus Life Cycle

Replication Cycle of a Bacterial Virus

The replication cycle involves several distinct steps:

1. Attachment (adsorption): Virion binds to host cell surface.

2. Penetration: Viral nucleic acid enters the host cell.

3. Synthesis: Host machinery synthesizes viral nucleic acids and proteins.

4. Assembly: New virions are assembled from synthesized components.

5. Release: Mature virions are released, often lysing the host cell.

One-Step Growth Curve

• Latent period: Time between infection and appearance of mature virions (includes eclipse and early maturation phases).

• Burst size: Number of virions released per infected cell.

Attachment and Entry of Bacteriophages

Attachment Specificity

Attachment of a virion to a host cell is highly specific, requiring complementary receptors on the host cell surface. These receptors are often normal cellular proteins or glycoproteins.

• Common receptors: glycoproteins, lipids, flagella, pili, iron transport proteins, LPS (lipopolysaccharide).

Bacteriophage T4

Bacteriophage T4 infects E. coli and utilizes one of the most complex penetration mechanisms, involving tail fibers and lysozyme to breach the bacterial cell wall.

• Lysozyme: Enzyme that degrades peptidoglycan in the bacterial cell wall, facilitating DNA entry.

Phage T4 Infection Time Course

• T4 genome encodes early, middle, and late proteins, each expressed at different stages of infection.

• Early proteins: involved in takeover of host functions.

• Middle proteins: involved in DNA replication.

• Late proteins: involved in assembly and release of new virions.

Packaging of DNA into T4 Phage Head

Viral DNA is packaged into the preformed capsid head using a motor complex and ATP hydrolysis. Scaffold proteins are discarded after assembly.

Temperate Bacteriophages and Lysogeny

Viral Life Cycles

• Virulent mode: Virus lyses host cell after infection (lytic cycle).

• Temperate mode: Virus genome integrates with host genome and replicates without killing the host (lysogenic cycle).

• Lysogeny can result in lysogenic conversion, where the host acquires new properties (e.g., increased virulence).

• Temperate viruses can switch to the lytic pathway under certain conditions.

Overview of Animal Virus Infection

Entry and Replication

• Entire virion enters the animal cell, often by fusion or endocytosis.

• Many animal viruses replicate in the cell nucleus.

• Viral infection is mediated by binding to specific host cell receptors, which vary by tissue and organ.

Release of Animal Viruses

• Enveloped viruses exit host cells by budding (acquiring part of the host membrane) or by cell lysis.

Effects of Virus Infection in Animal Cells

• Transformation: Virus induces tumor formation.

• Lysis: Death of the cell and release of virus.

• Persistent infection: Slow release of virus without cell death.

• Latent infection: Virus remains dormant within the cell, may reactivate later.

Additional info: Some animal viruses can integrate into the host genome, leading to long-term genetic changes.