Epidemiology Flashcards
(40 cards)
Why are models used?
- as a representation of a system
- to make predictions and generate new hypotheses
- allows investigation of system properties
What is epidemiological model used for?
To consider the number of infections through time, with infection rate and removal rate
How is R0 calculated?
Rate of new infections/average infection duration
What are the 4 different mutation types?
- Nucleotide only
- Change amino acids
- Insertions and deletions
- Recombination and gene transfer
What is a phylogeny?
A diagram representing ancestral relationships among characters or genetic sequences
Why are phylogenetic trees useful?
- phylogeny is most complete representation of evolutionary relationships
- provides a framework for asking scientific questions
Differences in replication and evolution speeds of RNA viruses, DNA viruses, and bacteria?
RNA viruses = fast but error prone
DNA viruses = slower and more conserved
Bacteria = very slow, but horizontal gene transfer can take place
Differences in genome size and mutation rate of RNA viruses, DNA viruses, and bacteria?
RNA virus = 8-30kb with 10-100 mutations per year
DNA virus = 20-200kb with 1-20 mutations per year
Bacteria = 4Mb with 0-1 mutations per year
What are the main points of rooted trees?
- single node represents earliest point in time
- have directionality as nodes can be ordered in terms of earlier or later
- branch lengths are measured in substitutions per site
- distance between nodes is represented along x-axis only
What are the main points of unrooted trees?
- no directionality, cannot tell if a node is earlier or later in time
- distance along branches directly represents node distance, which is the genetic distance measured in substitutions per site
What are the 3 things needed in order to build a tree?
- sequence data
- model of substitution
- ability to determine branch order
What is the order of substitution models from simplest to most complex?
Jukes-cantor, Kimura-2-parameter, HKY, TN93, GTR
What is the Jukes-cantor model?
Base frequencies are equal and all substitutions are equally likely
What is the kimura-2-parameter model?
Base frequencies are equal and transversions occur at different rates
What is the HKY model?
Unequal base frequencies and transitions and transversions occur at different rates
What is the TN93 model?
Unequal base frequencies, transitions and transversions occur at different rates, and different rates for different transition types
What is the GTR model?
Unequal base frequencies and all substitution types occur at different rates
What is a clustering algorithm and an example?
A simple and fast method that progressively joins the 2 closest sequences or ancestral sequences
Eg. Neighbouring joining algorithm
What is an optimisation algorithm and an example?
Defines an explicit score/goodness for each tree, trying to find the one tree which optimises inferion by swapping parts
Eg. Maximum likelihood
What are generic clusters and why are they useful?
- Sequences from samples which are genetically similar
- Can determine who infected who
- Genetically similar samples have recent time to most recent common ancestor (TMRCA)
What are clusters and why are they useful?
- are sequences from samples which are genetically similar
- genetically similar sequences have recent time to most recent common ancestor
- can be used to tell who infected who
What are clusters and why are they useful?
- are sequences from samples which are genetically similar
- genetically similar sequences have recent time to most recent common ancestor
- can be used to tell who infected who
What is the degree of an individual? What is degree distribution?
The number of links an individual has. Degree distribution describes how connected individuals are in the network fragmentation
Scale free network influence in epidemics?
Scale free network consists of long range interactions between few highly connected nodes (hubs), meaning epidemic can spread quickly
