L10 - Molecular and Genomic Epidemiology of Infections Flashcards
What is meant by a single weighting test?
to test for the presence or absence of something
What is meant by a additive weighting test?
combination of single tests
What is Spoligotyping?
use of PCR to identify pathogens and strain-dependant polymorphisms in lab specimens
Describe functional diversity in terms of DNA?
phylogenetic progression occurs = single base subsitutions which leads to changes in DNA
What is meant by silent mutations in the genome?
Mutations that are Intragenic (between genes) or Synonymous (not altering coding)
What is meant by Non-synonymous mutations in the genome?
Substitutions causing coding to be altered
What is meant by corruptive mutations in the genome?
Deletions or Insertions (disrupting coding frame)
` Creation of STOP codons (truncation)
Corruption of STOP codons (elongation)
Corruption of CONTROL sequences (eg. promoters)
What is meant by drift?
Gradual alteration in DNA sequence
What is meant by Antigenic drift?
Refers to the same antigen changing its sequence base by base.
This leads to changes in the surface proteins of the virus
What is meant by the Molecular clock?
a measure of evolutionary change over time at the molecular level.
Describe the Bacterial Replication rate as a factor affecting speed of molecular clock?
A high division rate provides a higher mutation rate
Describe the DNApol/RNApol proof-reading fidelity as a factor affecting speed of molecular clock?
Some species (eg HIV) have low fidelity promoting high mutation rate
Describe the selection pressure from the host as a factor affecting speed of molecular clock?
High selection pressure removes ‘weak’ mutants and emphasises clusters
Loss of selection pressure allows deletions
Describe the Degree of redundancy in the genome as a factor affecting speed of molecular clock?
Multiple copies of a single gene in the genome allow for
mutations in one copy without compromising overall functionality
Movement or recombination within genome may not effect phenotype
Describe the Transmission rate as a factor affecting speed of molecular clock?
High transmission rates relative to the mutation rate
results in dissemination and single strain outbreaks
(Flu A = 2-3 bases per year and 1.5 transmissions per infection)
