Viruses: Structure, Replication, and Host Interactions

Viruses: General Properties

Introduction to Viruses

Viruses are infectious intracellular particles capable of infecting all types of living organisms. Unlike bacteria, fungi, and eukaryotic parasites, viruses lack their own cellular machinery for DNA replication, transcription, translation, and metabolism. Instead, they rely on host cells to reproduce and propagate.

• Obligate intracellular parasites: Viruses require host cells to replicate.

• Genome types: Viral genomes can be DNA or RNA, single-stranded or double-stranded, linear or circular.

• Capsid: Protein shell that encloses the viral genome.

• Envelope: Some viruses have a lipid envelope derived from the host cell membrane.

Viral Replication and Host Interaction

Steps in Viral Replication

Viral replication depends on host cell machinery and typically involves several key steps:

1. Attachment: Virus binds to specific receptors on the host cell surface.

2. Entry: Virus or its genome enters the host cell (via endocytosis or membrane fusion).

3. Disassembly: Viral capsid is removed, releasing the genome.

4. Replication: Viral genome is replicated using host or viral enzymes.

5. Protein synthesis: Host cell machinery translates viral mRNA into proteins.

6. Assembly: New viral particles are assembled from synthesized components.

7. Release: New virions exit the host cell (by lysis or budding).

Viral Genomes

• DNA viruses: Genome is DNA; examples include herpesviruses, adenoviruses, papillomaviruses.

• RNA viruses: Genome is RNA; examples include coronaviruses, influenza viruses, HIV.

• Genome size: Viruses have between ~2,000 and several thousand genes.

Classification of Viruses

Based on Genome Type

• Single-stranded DNA viruses (ssDNA)

• Double-stranded DNA viruses (dsDNA)

• Single-stranded RNA viruses (ssRNA)

• Double-stranded RNA viruses (dsRNA)

Classes of Single-stranded RNA Viruses

• Class I (+) sense RNA: Viral RNA serves as mRNA and is directly translated by host ribosomes (e.g., coronaviruses).

• Class II (-) sense RNA: Viral RNA is a template for mRNA synthesis; host cell must make a complementary copy (e.g., influenza).

• Class III (Retroviruses): Viral RNA is reverse transcribed into DNA by reverse transcriptase (e.g., HIV).

Structure of Viruses

Capsid and Envelope

• Capsid: Composed of protein subunits (capsomeres); protects the viral genome.

• Envelope: Lipid bilayer derived from host cell membrane; contains viral glycoproteins for host cell recognition.

Viral Shapes

• Icosahedral: 20 faces of equilateral triangles (e.g., adenovirus).

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

• Complex: Bacteriophages with head and tail structures.

Bacteriophages

Definition and Structure

Bacteriophages are viruses that infect bacteria. They are among the most abundant life forms and have complex structures, often with a head (capsid) and tail fibers for attachment.

• Head: Contains viral DNA.

• Tail: Injects DNA into the host bacterium.

Phage Replication Cycles

• Lytic cycle: Phage replicates rapidly, lyses the host cell, and releases new virions.

• Lysogenic cycle: Phage DNA integrates into the host genome (prophage), replicates with the host, and can later enter the lytic cycle.

Host Defenses Against Viruses

Restriction Enzymes

Bacteria produce restriction enzymes that cut foreign DNA, such as viral genomes, to protect themselves from infection.

CRISPR-Cas System

The CRISPR-Cas system is an adaptive immune mechanism in bacteria and archaea, providing resistance against viral infections by recognizing and cutting viral DNA.

• CRISPR: Clustered regularly interspaced short palindromic repeats; stores viral DNA sequences as 'spacers'.

• Cas proteins: Enzymes that cut DNA at specific sequences.

Steps in CRISPR Defense

1. Integration: Viral DNA is integrated into the CRISPR locus as a spacer.

2. Transcription: CRISPR locus is transcribed into RNA, which guides Cas proteins.

3. Interference: Cas proteins use guide RNA to recognize and cut matching viral DNA during subsequent infections.

Viral Entry and Replication Mechanisms

Non-Enveloped Viruses

• Entry by endocytosis: Host cell engulfs virus into an internal vesicle (e.g., poliovirus, adenovirus).

• Genome release: Virus releases genome into host cytoplasm after vesicle breakdown.

Enveloped Viruses

• Entry by membrane fusion: Viral envelope fuses with host cell membrane, releasing genome (e.g., HIV, influenza).

• Fusion with endosomal membrane: Virus enters via endocytosis, then fuses with endosomal membrane to release genome.

HIV (Human Immunodeficiency Virus)

Entry and Replication

• GP120 glycoprotein: Binds to CD4 receptor on host immune cells (T cells, macrophages).

• Fusion: Viral envelope fuses with host cell membrane, allowing entry.

• Reverse transcription: Viral RNA is reverse transcribed into DNA, which integrates into host genome.

Replication of Genome

• Viral RNA → DNA → mRNA → proteins

• Provirus: Integrated viral DNA that can remain dormant before replication.

Summary Table: Virus Types and Properties

Virus Type	Genome	Envelope	Replication Strategy	Examples
DNA Virus	dsDNA or ssDNA	May have envelope	Uses host DNA polymerase	Herpesvirus, Adenovirus
RNA Virus (+ sense)	ssRNA (+)	May have envelope	Genome acts as mRNA	Coronavirus, Poliovirus
RNA Virus (- sense)	ssRNA (-)	May have envelope	Genome is template for mRNA	Influenza virus
Retrovirus	ssRNA	Envelope present	Reverse transcription to DNA	HIV
Bacteriophage	dsDNA	No envelope	Lytic or lysogenic cycle	T4 phage, Lambda phage

Key Terms and Definitions

• Capsid: Protein shell enclosing the viral genome.

• Envelope: Lipid membrane surrounding some viruses.

• Prophage: Phage DNA integrated into bacterial genome.

• Reverse transcriptase: Enzyme that synthesizes DNA from RNA template (in retroviruses).

• CRISPR: Bacterial defense system storing viral DNA sequences.

• Virion: Complete, infectious viral particle.

Formulas and Equations

• Viral Replication (Retrovirus):

$\text{Viral RNA} \xrightarrow{\text{reverse transcriptase}} \text{DNA} \xrightarrow{\text{integration}} \text{host genome} \xrightarrow{\text{transcription}} \text{mRNA} \xrightarrow{\text{translation}} \text{viral proteins}$

• CRISPR Spacer Integration:

$\text{Foreign DNA} \xrightarrow{\text{Cas protein}} \text{CRISPR locus (spacer)}$

• General Virus Replication:

$\text{Attachment} \rightarrow \text{Entry} \rightarrow \text{Disassembly} \rightarrow \text{Replication} \rightarrow \text{Protein synthesis} \rightarrow \text{Assembly} \rightarrow \text{Release}$

Additional info:

• Some details inferred from standard biology curriculum, such as the steps of viral replication and CRISPR mechanism.

• Examples and definitions expanded for clarity and completeness.