Characterizing and Classifying Viruses, Virions, and Prions

Characterizing and Classifying Viruses, Virions, and Prions

Acellular Infectious Agents

Viruses, viroids, and prions are acellular (noncellular) entities that lack cell membranes and are capable of causing disease in various organisms.

• Viruses: Infectious agents responsible for diseases such as the common cold, influenza, herpes, and AIDS.

• Viroids: Infectious RNA molecules, primarily affecting plants (not detailed in these notes).

• Prions: Infectious proteins that cause neurodegenerative diseases in animals and humans.

Virion refers to a virus particle outside of a host cell. It consists of:

• Capsid: Protein coat that surrounds the nucleic acid core.

• Nucleic Acid Core: Contains the viral genome (DNA or RNA).

• Nucleocapsid: The combination of the nucleic acid core and the capsid.

• Envelope (in some viruses): A lipid membrane derived from the host cell, surrounding the capsid.

• Matrix Proteins: Located between the capsid and envelope, these proteins play roles in viral assembly and structure.

Viral Taxonomy and Nomenclature

Viral genera are organized into families based on special characteristics or the name of an important family member. Unlike the Linnaean system for living organisms, viral family names are usually written in italics and in English.

• Example: Herpesviridae is the family name for herpes viruses.

Bacteriophage Replication: The Lytic Cycle (T4 Phage Example)

The T4 bacteriophage is a double-stranded DNA (dsDNA) virus that infects Escherichia coli (E. coli). The lytic cycle consists of several steps:

1. Attachment: Virions are nonmotile; they encounter host cells by random collision. Tail fibers attach to specific proteins on the E. coli surface.

2. Entry: The phage releases lysozyme to weaken the bacterial cell wall. The tail sheath contracts, injecting the viral genome into the bacterium. Viral enzymes degrade the bacterial DNA.

3. Synthesis: The host cell machinery synthesizes only viral components (genome and proteins).

4. Assembly: Viral components spontaneously assemble into new virions. The exact mechanism is not fully understood.

5. Release: Lysozyme completes degradation of the cell wall, and new virions are released, lysing the bacterium. On agar plates, this results in clear areas called plaques.

• Burst time: The time from attachment to release of new virions.

• Burst size: The number of new virions released from each lysed bacterium.

Bacteriophage Replication: The Lysogenic Cycle (Lambda Phage Example)

The lambda phage is a dsDNA virus that can undergo lysogeny, a process where the viral genome integrates into the host chromosome and remains dormant as a prophage.

1. Attachment: The phage attaches to the host cell via its tail.

2. Entry: Viral DNA enters the host, but the bacterial genome is not destroyed. The virus remains inactive as a prophage, coding for proteins that suppress its own genes.

3. Integration: The prophage DNA fuses with the bacterial chromosome.

4. Replication: The prophage is replicated along with the host chromosome during cell division.

5. Induction: The prophage may be excised from the host chromosome, re-entering the lytic cycle.

6. Synthesis, Assembly, Release: These steps mirror the lytic cycle.

• Lysogenic conversion: The presence of a prophage can convert a harmless bacterium into a pathogen by introducing new genes.

Viral Entry into Animal Cells

Animal viruses can enter host cells by several mechanisms:

• Direct Penetration: Used by naked viruses. The capsid attaches and sinks into the membrane, creating a pore for the genome to enter. The empty capsid remains outside. Example: Poliovirus.

• Membrane Fusion: The viral envelope fuses with the host cell membrane, releasing the capsid into the cytoplasm. The envelope becomes part of the cell membrane. Example: Measles virus.

• Endocytosis: Most enveloped viruses and some naked viruses trigger endocytosis upon attachment, allowing the entire virion to enter the cell. Examples: Adenovirus (naked), Herpesvirus (enveloped).

Viral Genome Replication Strategies

Viruses have diverse genome types and replication strategies:

• Hepatitis B Virus: The genome is transcribed into RNA, which serves as a template for reverse transcriptase to synthesize multiple copies of the viral DNA genome.

• ssDNA Viruses: Host RNA polymerase synthesizes mRNA complementary to the viral single-stranded DNA.

• +ssRNA Viruses: The genome acts directly as mRNA. Example: Poliovirus.

• Retroviruses: Use reverse transcriptase to synthesize DNA from RNA, then mRNA from DNA. Example: HIV.

• -ssRNA Viruses: The genome is complementary to mRNA and must be transcribed before translation. Examples: Rabies, Influenza.

• dsRNA Viruses: Contain double-stranded RNA genomes. Example: Rotavirus.

Viral Release and Persistent Infections

• Budding: Enveloped animal viruses are released from the host cell by budding, acquiring their envelope from the host membrane.

• Persistent Infections: Host cells shed viruses slowly and steadily, often without immediate cell death.

Prions

PrP is a cytoplasmic membrane protein found in mammalian brain cells. Prions are infectious forms of PrP that can induce abnormal folding in normal PrP proteins, leading to neurodegenerative diseases.

• Example: Creutzfeldt-Jakob disease in humans, mad cow disease in cattle.

Summary Table: Viral Genome Types and Replication Strategies

Genome Type	Replication Strategy	Example Virus
dsDNA	Transcription to mRNA by host or viral polymerase	T4 phage, Lambda phage
ssDNA	Host RNA polymerase synthesizes mRNA from complementary DNA	Parvovirus
+ssRNA	Genome acts as mRNA	Poliovirus
-ssRNA	Transcribed to mRNA by viral RNA-dependent RNA polymerase	Rabies, Influenza
dsRNA	Each strand serves as template for mRNA synthesis	Rotavirus
Retrovirus (+ssRNA)	Reverse transcription to DNA, then transcription to mRNA	HIV