Epidemiology Flashcards
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
What is antigenic shift?
2 or more strains of a virus combine to form a new subtype and cause a large outbreak in the population
What is antigenic drift?
New strains persist and circulate in a population, accumulating mutations within the subtype
What is epidemiology?
The study of infectious disease in populations
What are the 3 key pieces of information that are needed in order to understand epidemiology of an infectious disease?
- transmission biology
- pathogenesis of infection
- host demography and behaviour
What is statistical epidemiology?
Tests of association and measurement of risk factors, includes cohort studies and case control studies
What is mathematical epidemiology?
Representation of epidemiological processes, such as differential equation models and microsimulations
What are microparasites?
Small parasites which multiply rapidly and directly within the definitive host
What is the basic reproduction number R0?
R0 is the average number of secondary cases produced by a single primary case introduced into a large population of previously unexposed individuals
What is the SLIR model?
A compartment model which divides the population into susceptible, latent, infectious and recovered
In which ways does compartment model show us ways of stopping and reducing infection?
- risk averse behaviours, avoiding contact due to illness (S/I)
- quarantine or isolation (I)
- vaccination (S)
What is herd immunity?
The minimum fraction that must be immunologically protected by natural exposure or vaccination to reduce R0 below 1
What is the definition of emerging infectious disease?
Diseases of infectious origin whose incidence in humans has increased within the last 2 decades or threatens to increase in the near future
What is zoonoses?
Diseases which are naturally transmitted between vertebrate animals and humans
What are the 4 stages of the pathogen pyramid and their respective R0 values?
Level 1 - exposure
Level 2 - infection R0=0
Level 3 - transmission 0<R0<1
Level 4 - epidemic spread R0>1
Why are there no level 4 tick borne viruses?
There are no anthropophilic ticks
RNA viruses and anyhropophilic vectors
- 91 human RNA viruses transmitted by vectors, with 18 of these being level 3/4 carried by anthropophilic vectors
