Microbiology - Viruses
Viruses: Microbiology - Week 5 Study Notes
Introduction to Viruses
Basic Nature: Viruses are acellular entities, meaning they are not cells and lack cytoplasm. They consist of a nucleic acid core surrounded by a protein coat.
Obligate Intracellular Parasites: This is a defining characteristic of viruses, meaning:
They absolutely require a host cell for their survival and replication.
Their entire life cycle necessitates residing inside a living cell for a period.
Are They Alive?: This is a complex question often debated in biology:
Arguments for not being alive: They are metabolically inert outside of a host cell, lacking their own ribosomes and enzymes for protein and nucleic acid synthesis.
Arguments for being alive: They possess genetic material, can evolve, and reproduce (albeit by hijacking host machinery).
Outside cells, they exist as metabolically inert virions.
Evolutionary Placement: The origin and evolutionary placement of viruses are widely discussed in the scientific community.
Viral Structure
Basic Components:
Nucleic Acid Core: Contains the viral genome, which can be DNA or RNA, circular or linear, and single-stranded (SS) or double-stranded (DS).
Capsid: A protein sheath that surrounds the nucleic acid core.
It is composed of repeating subunits of one to a few proteins.
Nearly all viruses form a capsid.
Specialized Enzymes: Some viruses store specialized enzymes along with their nucleic acid core.
Reverse Transcriptase: An enzyme used by retroviruses to copy viral RNA into DNA.
Envelope: Many animal viruses possess an outer envelope.
This envelope is derived from the host cell membrane during budding.
It contains viral proteins embedded within it.
Main Viral Shapes/Types:
Helical: Rod-like or thread-like shape.
Example: Tobacco Mosaic Virus (TMV) (a plant virus), Influenza (an animal virus with a helical capsid within an envelope).
Icosahedral: Almost spherical shape, a $20$-sided polyhedron.
Example: Adenovirus (an animal virus), Poliovirus (a naked virus).
Complex/Binal: A combination of shapes.
Example: T-even bacteriophages, which have an icosahedral head and a helical tail.
Naked Viruses: Viruses that lack an outer envelope (e.g., poliovirus).
Enveloped Viruses: Viruses that possess an outer envelope (e.g., influenza).
Viral Hosts and Specificity
Ubiquitous Nature: Viruses are found in every kind of organism, from bacteria to plants and animals.
Host Range: Each type of virus has a limited host range, infecting only specific types of organisms.
Tissue Tropism: Within a single host organism, a virus may only infect certain tissues or cell types.
Example: Rhabdovirus (the causative agent of rabies) specifically infects neurons.
Viral Genomes
Nucleic Acid Type:
Viruses can utilize either DNA or RNA as their genetic material.
The genome can be double-stranded (DS) or single-stranded (SS).
The genome can be circular or linear.
DNA Viruses
Characteristics:
Most DNA viruses are double-stranded.
They typically replicate in the nucleus of the eukaryotic host cell.
Examples: Smallpox, herpes simplex virus.
RNA Viruses
Characteristics:
Most RNA viruses are single-stranded.
They typically replicate in the cytoplasm of the host cell.
High Mutation Rates: Replication of RNA genomes is error-prone, leading to high rates of mutation.
This makes them difficult targets for the host immune system, and for the development of vaccines and antiviral drugs.
Examples: Influenza, measles, common cold.
Retroviruses
Unique Replication Cycle:
Retroviruses possess a single-stranded RNA genome.
They employ the enzyme reverse transcriptase to copy their viral RNA into double-stranded DNA.
This newly synthesized viral DNA then becomes integrated and permanently stored within the host cell's DNA.
Genetic Information Transfer: The direction of genetic information flow in a retrovirus is RNA o DNA o mRNA o ext{protein}.
Example: Human Immunodeficiency Virus (HIV).
Viral Replication and Life Cycles
Host Cell Dependence: Viruses lack their own ribosomes and enzymes necessary for protein synthesis and nucleic acid replication. They must hijack the host cell's machinery.
Replication Process: The viral genome essentially tricks the host cell into manufacturing new viral components.
Early genes: Expressed early in the infection cycle.
Intermediate genes: Expressed mid-cycle.
Late genes: Expressed later, often for structural proteins.
Consequences for Host: Cells infected with viruses are often damaged, leading to disease symptoms.
Bacteriophages
Definition: Viruses that specifically infect bacteria, often simply called phage.
Diversity: Highly diverse group, united by their bacterial hosts.
Well-Studied: E. coli-infecting viruses (e.g., the "T" series: T1, T2, etc.) are among the best-studied.
Two Main Reproductive Cycles:
Lytic Cycle
Lysogenic Cycle
Lytic Cycle (also called the Reproductive Cycle of a Bacteriophage)
Outcome: Leads to the rapid replication of the virus and the eventual lysis (bursting) and death of the host cell.
Steps:
Attachment (Adsorption): The phage attaches to specific receptors on the bacterial outer surface.
Penetration (Injection): The phage (e.g., T4) injects its viral genome into the host cell.
Synthesis: The phage takes over the host cell's replication and protein synthesis machinery to synthesize viral components (nucleic acids and proteins).
Assembly: Newly synthesized viral components spontaneously assemble into mature virus particles.
Release: New mature virus particles are released from the host cell, typically by the action of an enzyme that lyses the host cell wall, or through budding.
Lytic phages are also referred to as virulent phages.
Lysogenic Cycle (Latent Phase)
Outcome: The viral DNA integrates into the host genome and is replicated along with it, without immediately killing the cell. The virus enters a latent state.
Steps:
Attachment and Penetration: Similar to the lytic cycle, the phage attaches and injects its DNA.
Integration: The viral nucleic acid (phage DNA) integrates into the host cell's genome, forming a prophage.
Propagation: The host bacterium continues to reproduce normally, copying the prophage along with its own DNA and transmitting it to daughter cells through many cell divisions.
Induction: Under certain conditions (e.g., cell stress), the prophage can exit the bacterial chromosome, initiating gene expression and entering the lytic cycle.
Lysogenic phages are also referred to as temperate phages.
Key Differences from Lytic Cycle:
The lysogenic cycle does not immediately kill the bacteria.
It creates many copies of the viral DNA within a bacterial population without actively producing new phage particles until induction occurs.
Phage Conversion
Mechanism: During the integrated portion of the lysogenic cycle, some viral genes from the prophage may be expressed.
Effect: This can alter the phenotype or characteristics of the lysogenic bacterium.
Example: Vibrio cholerae phage conversion.
A lysogenic phage introduced a gene coding for the cholera toxin into Vibrio cholerae.
This gene became incorporated into the host bacterium's genome.
This process converts a harmless bacterium into a disease-causing, toxigenic form, capable of causing cholera.
Viral Infection Patterns
Viral infections are categorized based on the rapidity and frequency of virus production and the appearance of associated symptoms.
Acute Infections:
Characterized by rapid replication of the virus and sudden onset of symptoms.
Can lead to localized outbreaks, wider epidemics, and global pandemics.
Persistent Infections:
Infections where the virus remains in the host for extended periods.
Can be latent (virus present but not actively replicating or causing symptoms, like the lysogenic cycle) or chronic (virus continually present and replicating, potentially causing ongoing symptoms).
Virus Classification
International Committee on Taxonomy of Viruses (ICTV): Utilizes a hierarchical system including order, family, subfamily, and genus.
Other Classification Methods:
By the Disease They Cause: Limited, as some viruses cause different diseases under varying conditions or times, and some diseases (e.g., common cold) can be caused by multiple viruses.
By the Host They Infect: Limited, as some viruses (e.g., influenza) can infect different types of organisms.
By Genome Expression: How the viral genome is expressed (e.g., Baltimore classification, which categorizes viruses based on their mechanism of mRNA synthesis).
Review Points
Foundational concepts of viruses and their distinction from bacterial cells (e.g., acellular, obligate intracellular parasites, lack organelles).
Zoonotic Diseases: Viral diseases transmitted from animals to humans. Examples might include rabies (rhabdovirus), influenza, SARS-CoV-2.
Identification of virus shapes (helical, icosahedral, complex) from diagrams.
Detailed understanding of the lytic and lysogenic cycles of bacteriophages.
Specific details about HIV, including its structure, the role and mechanism of reverse transcriptase, and its RNA genome that integrates into host DNA.
Understanding of SARS-CoV-2 (while not detailed in this transcript, it's a critical modern example of a virus).