Molecular and Genomic Epidemiology of Infections Flashcards
What kind of questions can molecular epidemiolgy answer?
What kind of things do we look for in molecular epidemiology?
What is meant by single weighting vs additive weighting?
Single weighting is the presence or absence of something in a biochemical test.
- powerful but prone to false negatives/positives
Additive weighting is a combination of single tests.
- has quantitation
What kind of weighting is a culture on selective media?
Single weighting - is usually yes or no
What is meant by factoral multiple weighting?
This is when we also use genomic factors:
Presence or absence of a gene/ base/s change in genome/ gene relative to location in the genome
Name an example of when we use factoral system in multiple weighting
- Tuberculosis
- Is hard to culture. We need to understand exactly what strain it is as well as identifying it is Tb - and we can do this by looking for the presence or absence if specific repeats at one locus
- Is this spoligotyping?
What is a spoligotype?
Spacer oligonucleotide typing, or spoligotyping, is a rapid, polymerase chain reaction (PCR)-based method for genotyping strains of the Mycobacterium tuberculosis complex (MTB)
Explain what is meant by VNTR?
variable number tandem repeats = VNTR
- is another factoral multiple copy system (multiple weighting test)
- basically microsatellites?
- tellls us the number of specific repeatds at multiple genomic loci
- by PCR (length of the amplicon on the gel)
- then make a tree
What are the 3 types of multiple weighting?
- Factoral is asking if some gene is there is there or not and maybe how much of it is there.
- Functional is asking what type of substitution.
- Temporal is the mutation rate.
Describe what functional diversity is and how we can use this
- Can use it in functional multiple weighting tests - explains how substitution mutations can lead to many different genotypes/phenotypes
- we can then trace them back and make a tree to see the evolution
Describe the difference between a silent, non-synonmous and corruptive mutation
What is antigenic drift?
Antigenic drift is the same antigen changing its sequence base by base
What is temporal diversity?
If we assume a mutation rate/ mutation rate is constant then we can produce evolutionary trees (dendograms) this way
Name some different factors that affect the speed of the ‘molecular clock’
Molecular clock meaning the mutation rate
What is meant by the degree of redundancy of a genome?
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
Do different genes vary in mutation rate?
Yes
Conserved genes are more likely to be associated with {?} - these genes mutate less rapidly than {?}
Conserved genes are more likely to be associated with phenotype and virulence - these genes mutate less rapidly than hyper-variable genes
What is meant by convergent evolution?
Not all changes are new
Some may revery back to an older profile (convergent evolution)
What is meant by shift as opposed to drift?
This is when there is a large change - drift being slow change by small mutations and shift is a large change
How does antigenic SHIFT occur?
Antigenic shift is a sudden replacement of an antigen by recombination with another viral type that has evolved separately (either in another animal or another human population). New types will not be protected against by previous infection or vaccination - leading to new epidemics.
