Chapter 19: Viruses – Structure, Function, and Genomes

Chapter 19: Viruses

Introduction to Virology

Virology is the scientific study of viruses, which are unique infectious agents that differ fundamentally from cellular life forms. Understanding viruses is essential for grasping their impact on health, disease, and biological systems.

• Virology: The study of viruses, their structure, function, and role in disease.

• Virus: An acellular, obligate intracellular pathogen that requires a host cell to reproduce.

• Virion: The complete, infectious form of a virus outside a host cell.

• Epidemiology: The study of how diseases affect whole communities, including patterns of outbreaks, pandemics, and endemics.

Example: Recent viral epidemics include SARS-CoV-2 (COVID-19), Zika virus, and Ebola virus.

Characteristics of Viruses

Viruses possess distinct features that set them apart from other microorganisms and living cells.

• Size: Viruses are smaller than bacteria and are submicroscopic.

• Acellular: Viruses lack cellular structure and do not carry out metabolic processes independently.

• Obligate Intracellular Pathogens: Viruses must infect host cells to reproduce, hijacking cellular machinery for replication.

Example: Viruses "trick" host cells into using their own structures to replicate viral genomes and produce new virions.

What is a Virion?

A virion is the complete, infectious particle of a virus, capable of infecting host cells.

• Single infectious virus particle

• Contains genetic material (DNA or RNA) surrounded by a protein coat (capsid)

• Genome codes for new virions

Example: HIV virion infecting a human T cell.

Visualizing Viruses

Viruses are visualized using advanced microscopy techniques due to their small size.

• Transmission Electron Microscope (TEM): Invented in 1931, TEM allows scientists to observe viruses at high magnification.

Example: Images of Ebola virus and other virions are obtained using TEM.

Viral Structures

Basic Components of Viruses

Viruses are composed of several key structural elements that determine their infectivity and classification.

• Genome: The genetic material, either DNA or RNA, single- or double-stranded.

• Capsid: Protein shell that encases the viral genome.

• Capsomeres: Subunits that make up the capsid.

• Envelope: Some viruses possess a lipid membrane derived from the host cell, surrounding the capsid.

• Spike Proteins: Glycoproteins embedded in the envelope, crucial for host cell attachment and entry.

Shapes of Naked Viruses

Naked viruses lack an envelope and exhibit distinct geometric shapes.

• Icosahedral: 20-sided structure formed by capsomeres (e.g., adenovirus).

• Helical: Rod-shaped structure with capsomeres arranged in a spiral (e.g., tobacco mosaic virus).

Shapes of Enveloped Viruses

Enveloped viruses possess a lipid membrane and can have varied shapes.

• Spherical Envelope: The envelope forms a roughly spherical shape around the capsid.

• Helical Envelope: The envelope surrounds a helical capsid, giving a flexible, elongated appearance.

Spike Proteins

Spike proteins are glycoproteins that protrude from the surface of enveloped viruses, playing a key role in host cell recognition and entry.

• Function: Mediate attachment to host cell receptors, facilitating viral entry.

• Example: SARS-CoV-2 spike protein binds to ACE2 receptor on human cells.

Complex Viral Structures

Some viruses, such as bacteriophages and poxviruses, exhibit complex structures beyond simple capsid and envelope arrangements.

• Bacteriophage: Viruses that infect bacteria, often with a complex capsid structure including a tail and baseplate for injecting genetic material.

• Poxvirus: Large, complex viruses with multiple membranes and a lateral body.

Viral Genomes

Types of Viral Genomes

Viruses display remarkable diversity in their genetic material, which can be classified by type and structure.

• Double-stranded DNA (dsDNA)

• Single-stranded DNA (ssDNA)

• Double-stranded RNA (dsRNA)

• Single-stranded RNA (ssRNA)

• Retroviruses: ssRNA viruses that use reverse transcriptase to synthesize DNA from RNA

Example: Most viruses have fewer than 300 genes; their genomes encode capsid proteins, enzymes for replication, and structural factors.

Baltimore Classification of Viruses

The Baltimore classification system groups viruses based on their genome type and replication strategy.

Group	Genome Type	Replication Strategy	Example
I	dsDNA	Transcription of DNA to mRNA	Herpesvirus
II	ssDNA	Conversion to dsDNA, then transcription	Parvovirus
III	dsRNA	Transcription of RNA to mRNA	Reovirus
IV	+ssRNA	Directly serves as mRNA	Poliovirus
V	-ssRNA	Transcription to +ssRNA (mRNA)	Influenza virus
VI	ssRNA-RT (retrovirus)	Reverse transcription to DNA, then transcription	HIV
VII	dsDNA-RT	Reverse transcription during replication	Hepatitis B virus

Additional info: The Baltimore system helps predict how a virus will express its genes and replicate within a host cell.

Protein Synthesis / Gene Expression of Viral Genomes

Viral genomes direct the synthesis of viral proteins using host cell machinery. The number of steps required for protein synthesis depends on the genome type.

• dsDNA viruses follow similar steps as cellular DNA

• ssRNA viruses may require additional steps, such as conversion to mRNA

• Retroviruses use reverse transcriptase to convert RNA to DNA before transcription

Example: Cellular DNA: DNA → mRNA → protein; Retrovirus: RNA → DNA → mRNA → protein

Summary Table: Key Viral Structures and Functions

Structure	Description	Function	Example
Capsid	Protein shell	Protects genome, aids in delivery	Adenovirus
Envelope	Lipid membrane	Helps evade immune system, entry into host	Influenza virus
Spike Proteins	Glycoproteins on envelope	Attachment to host cell	SARS-CoV-2
Capsomere	Capsid subunit	Structural integrity	Poliovirus

Key Terms and Definitions

• Virology: Study of viruses

• Virus: Acellular infectious agent

• Virion: Complete virus particle

• Epidemiology: Study of disease patterns

• Capsid: Protein shell of virus

• Capsomere: Subunit of capsid

• Envelope: Lipid membrane surrounding some viruses

• Spike Protein: Glycoprotein for host cell attachment

• Genome: Genetic material of virus

Equations and Formulas

• Central Dogma (cellular): $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

• Retrovirus gene expression: