Viral Genetics and Genetic Mutations

Study Notes

Viruses exhibit diverse genetic material, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), and RNA with DNA intermediate.
Some DNA viruses have genomes that are partially single-stranded and partially double-stranded (e.g., hepadnaviruses).
RNA viruses can have positive-sense, negative-sense, or ambisense RNA.
Viral genomes can be circular or linear.

Genotypic classification of mutants: Includes point mutations, insertions, deletions, and reassortment.
Phenotypic classification of mutants: This includes plaque mutants, antibody escape mutants, "hot" mutants, attenuated mutants, antigenically drifting mutants, and conditionally lethal mutants.
Additional mutant types: This list also includes host-range mutants and temperature-sensitive mutants/cold-adaptive mutants.

Transition mutations involve the substitution of a purine for another purine (A ↔ G) or a pyrimidine for another pyrimidine (C ↔ T).
Transversion mutations involve the substitution of a purine for a pyrimidine (A ↔ T or G ↔ C) or a pyrimidine for a purine.

Plaque assay is a method used to visualize viral infections on a plated substrate, and observe the number of plaques as an indicator of viral population.

Antibodies can recognize viral epitopes, binding to specific regions of viral proteins.
Antibody binding or unbinding can be represented by the presence or absence of a graphical line connecting an antibody to a viral epitope on a diagram.

Reassortment: Genetic material exchange between different viral strains.
Complementation: Recovering a functional virus from two non-functional viruses.
Multiplicity reactivation: A greater chance of survival for bacteria when infected with multiple viruses that contain defective viruses or mutations.
Defective viruses: Genetically imperfect viruses that cannot replicate themselves.
Defective interfering particles (DI): Viruses that interfere with the replication of normal viral particles by taking over replication processes.
Phenotypic mixing: Formation of progeny that have the capsid proteins from two different viruses, but with the genetic material from only one virus. The type of virus in the progeny is determined by the type of genetic material observed.

Influenza A virus can cross between species (e.g., birds, pigs, and humans).
The constant interchange of viruses between species, including pigs, can result in reassorting viral genomes resulting in a new and dangerous virus, e.g., 2009 H1N1.

Reassortment occurs when different viral strains infect a cell at the same time.
Migratory water birds and poultry (e.g. chickens) often carry viruses and can infect humans. Humans can get infected from other humans.

Wild water birds serve as the reservoir for many influenza A viruses, which can spread to other animal species like pigs, which can act as a "mixing vessel".
Pigs can contract multiple influenza viruses from different sources, including those from birds and humans.
Pigs can genetically recombine these different viral strains and potentially produce new and more dangerous strains.

Cells infected with a virus can become resistant to subsequent infection with a similar virus.
Mechanisms include cytoplasmic accumulation of viral components, blocking nucleic acid injection, or masking cell surface receptors.

Some viruses (e.g., reticuloendotheliosis virus) are embedded within the genome of other viruses (e.g., fowlpox virus).
The presence of embedded viruses can affect the characteristics of the host virus, such as its ability to cause immunosuppression.

Many viruses encode transactivating proteins that can activate the transcription of other viral or cellular genes.
These proteins can interact with different promoters or genes coming from other viruses.
Examples include HIV-1 and cytomegalovirus proteins.