lesson 3

viral genetics

viruses

• NOT living organisms
• NOT cells
• NO nucleus, organelles, cytoplasm
• replicate ONLY inside living hosts cells
  • are complex nucleoprotein particles
  • are obligate intracellular parasites
• a quality that living matter has (autonomous replication) - which viruses do not have
• utilize host machinery to make components for production of viral particles
• "bad news" - nucleic acids (brain of virus)

viral genome

RNA OR DNA

never both

more on viruses

• require getting in living cells to be able to replicate
• can be in plants, animals, bacteria (bacteriophages)
• have greatest genetic diversity in nature
• genome modification processes -> lead to inc. genome variability

genome modification processes -> lead to inc. genome variability

(what processes are responsible for genome variability)

• mutation
• recombination
• reassortment

natural selection act on the continuously changing genomes due to these 3, and = diversity + evol

some changes can be lethal -> not passed/die off

some changes provide better fit / survival -> fixed in genome

viral infection

• errors in copying nucleic acid -> mutations
• some lethal, some good

non lethal mutations

• eventually eliminated
• OR
• fixed in genome - remain

whether a particular NONLETHAL mutation survives in the genotype, depends on whether the resulting change in the gene product is disadvantageous, neutral, or affords the mutant virus some selective advantage

mutant

genetically changed from wild type

wild type

original strain of a virus from which mutants are selected and to which mutants are compared

original version of a gene

variants could differ by

a single or multiple mutations

mutations (3 types)

• spontaneous
• induced (mutagens, carcinogens, etc.)
• engineered

spontaneous mutations

• due to mistake in normal replication of viral nucleic acid
• accumulate in viral genomes + introduce variations in phenotypes subjected to selection during evol of virus
• DNA spontaneous mutation rate
  • 10^-8 to 10^-11
  • LOW
• RNA spontaneous mutation rate
  • 10^-3 to 10^-4
  • much more common, mutate more
  • due to lack of proofreading activity in RNA replication enzymes
  • ex: flu is RNA, new strains every year
  • majority pathogenic viruses are RNA bc variability/aggressiveness

induced mutations

• occur when wild type viruses are treated w/ mutagen/carcinogen
  1. chemical mutation
     • point mutation - single nucleotide altered
     • gross chromosomal mutations
       • change in #/structure chromosomes (not in viruses)
  2. physical mutagens
     • ionizing: X and gamma rays
     • nonionizing: UV rays

basic unit DNA: nucleotide

nucleotide

• phosphate
• pentose sugar
• nitrogenous base (ATCG)

point mutation

revert to wild type w/ certain frequency

base pair change - change by 1 base in nucleotide

• transitions - purine -> purine or pyrimidine -> pyrimidine
• transversions - pur-> pyr or pyr -> pur

frameshift changes - generate nonfunctional product

• insertion/deletion or 1/2 bases
• cause shift -> codons all change (dont have same 3 bases in each as before)

consequences of base pair changes

• silent - no change in amino acid coding for (doesnt affect outcome)
• missense - change one aa for another
• nonsense- codon termination (UGA, UAA, UAG = stop codon). Transcription of gene stops. Serious mutaion

engineered mutations

molec technique to induce nearly any mutation into viruses

• = expected changes
• know mutations want to produce
• steps before PCR was invented (review it)

types of mutations according to their phenotype

genotype is NOT phenotype

1. null
2. temperature sensitive mutants (TS)
3. cold sensitive mutations
4. plague morphology mutations
5. host range mutation
6. genetic recombination between viruses

phenotype

Phenotype is the observable expression of this genotype – a person's presentation

genotype - DNA sequence

null phenotypic mutation

• mutation completely inactivates the function of a gene
• any type of nucleic acid change can yield a null phenotype (ex: frameshift, point mutation, etc.)
• does not need to be due to large deletion
• null mutant is important to determine if gene is essential for a process

temperature sensitive mutant

phenotypic mutation

• conditional-lethal phenotype
• usually due to missense mutation -> create gene that results in protein product unable to maintain functional configuration at nonpermissive (high) temp
• leaky - retain some functional activity at the nonpermissive temperature
• useful in temperature shift experiments

cold sensitive mutations

phenotypic mutation

• conditionally-lethal at low (nonpermissive) temp
• grow as well as wild type at high (permissive) temp

many times used as attenuation mutations for vaccines (cannot function/grow at low temps)

plague morphology mutations

phenotypic mutation

• altered morphology
  • large plaques release virus from host cell more rapidly than wild type
  • provide useful markers - mutants can illustrate processes like membrane fusion
• center of plaque - original bacteria that died
• large plaque - virus mutation killed everything rapidly
• can use as way to assess number of viruses

chat gpt:

In virology, the term "plaque" typically refers to a clear zone or localized area of cell death on a monolayer of host cells in a culture dish. This occurs when a virus infects and kills the host cells. Plaque assays are commonly used to estimate the concentration of infectious virus particles in a sample.

When we talk about mutations in the virus genome influencing plaque morphology, we mean that changes in the genetic material of the virus can lead to observable differences in the appearance of these clear zones

host range mutations

phenotypic mutation

• conditionally lethal - selected in a number of viruses - can grow in human but not in certain animals, etc.
• can kill in humans that infect us, but not other things

genetic recombination btw viruses

when 2 diff viruses simultaneously infect same cell and exchange pieces of DNA/RNA btw them

• occurs when there is exchange btw new nucleic acid molecules = new nucleic acid molecule