Molecular epidemiology of pathogens

Question 1

What is epidemiology?

Answer 1

→A resolved measure (diversity) of differences (variables)

Question 2

What does molecular epidemiology determine?

Answer 2

→Disease distribution in time and place

→Disease transmission

→Disease manifestation

→Disease progression

Question 3

How many targets do functional characteristics have?

Answer 3

→single

Question 4

How many targets do genomic characteristics have?

Answer 4

→multiple

Question 5

What are the types of diversities?

Answer 5

→Single Weighting

→Additive Weighting

Question 6

What are single weighting diversity?

Answer 6

→Biochemical test
→Presence of O157 antigen
→Presence of Verotoxin

Question 7

What are the different types of multiple weighting genomic factors?

Answer 7

→factoral- Presence or absence of a gene/base/s change
in genome/gene relative to location in the genome

→functional- Type of substitution (synonymous/non synonymous )

→temporal- Mutation rate (time since the last alteration)

Question 8

What type of dendogram shows pattern relatedness?

Answer 8

→Spoligotyping

Question 9

What does variable number tandem repeats result in?

Answer 9

→Result is a profile of the number of specific repeats at multiple genomic loci

Question 10

Examples of corruptive mutations

Answer 10

→Deletions or Insertions (disrupting coding frame)
→Creation of STOP codons (truncation)
→Corruption of STOP codons (elongation)

→Corruption of CONTROL sequences (eg. promoters)

Question 11

What is antigenic drift?

Answer 11

→the same antigen changing its sequence base by base

Question 12

What does accurate predictions in molecular epidemiology assume?

Answer 12

→constant molecular clock

Question 13

What does a high division rate result in?

Answer 13

→higher mutation rate

Question 14

What are factors affecting molecular clock?

Answer 14

→Bacterial replication rate
→proof reading fidelity
→pressure from the host 
→Degree of redundancy in the genome
→Transmission rate

Question 15

Why is proof reading fidelity important to calculate molecular clock?

Answer 15

→Some species (eg HIV) have low fidelity promoting high mutation rate

→Gives idea on how much weighting is placed on a variant

Question 16

Why is pressure from the host or environment important to calculate molecular clock?

Answer 16

→High selection pressure removes ‘weak’ mutants and emphasises clusters

→Loss of selection pressure allows deletions

Question 17

Why is the degree of redundancy in the genome important for molecular clock?

Answer 17

→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

Question 18

Which genes change the most?

Answer 18

→Hyper-variable genes

Question 19

What genes are more likely to be associated with phenotype and virulence?

Answer 19

→conserved genes

Question 20

What is antigenic shift?

Answer 20

→a sudden replacement of an antigen by recombination with another viral type that has evolved separately

Question 21

What is molecular restriction typing?

Answer 21

→can monitor effectiveness of control measures

Question 22

What does choosing the most appropriate system require?

Answer 22

→Knowing the most appropriate variable/s

→Quantitating variations and deriving diversity

→Generating identities or clusters

→Applying related data