Multi Strain Dynamics Flashcards
Define cross immunity
protection against a given pathogen thanks to immunity acquired from past exposure to a related pathogen
In the multi strain dynamics lab, what did Parameter γ (gamma) represent?
the extent of cross immunity
What do these values mean
𝛾 = 0
0 < 𝛾 < 1
𝛾 = 1
𝛾 = 0: no cross-immunity
0 < 𝛾 < 1: partial cross-immunity
𝛾 = 1: full cross-immunity
In this lab, how do we define a strain?
instead of defining a strain by its entire genome, a strain is defined by the genetic loci that encode antigens against which the immune responses act
1.1 & 1.2
What is the dynamic behavior of each strain in the model?
The dynamic behavior of each strain in the model is SIR-like, showing a series of epidemics followed by an equilibrium state.
1.1 & 1.2
Why are the dynamics of each strain SIR-like in the model?
because the model contains a set of independently transmitting strains (strains do not interfere with each others dynamics), each with the same transmission rate and recovery rate parameters.
1.1 & 1.2
Why do strains behave similarly in the model?
because the transmission rate and recovery rate parameters for each strain are the same. Any differences only arise due to different initial conditions for each strain.
1.1 & 1.2
What is the compartmental model used to produce this plot?
top of page three
dZAX/dt - proportion protected to a particular strain
dWAX/dt - proportion partially protected to a particular strain
dYAX/dt - proportion infected by a particular strain
cross immunity parameter set to 0
1.1 & 1.2
There are six strains in this model but we cannot see them all in the plot, why?
Their transmission dynamics are so similar that they are plotted on top of each other
1.2b
What did running this instruction do?
extractYFinalConditions(simdata)
showed allelic sequences of each of the strains in the simulation
showed that all strains have the same prevalence at the end
What is meant by prevalence?
proportion infected
Define beta
transmission rate
1.3
What are the dynamic consequences of making one strain more transmissible?
The change in beta should translate to a
change in R0.
Strain 2 now causes higher and more frequent epidemics at the start.
Strain 2 ends up with higher prevalence at
equilibrium.
Quantitatively the behaviours
are different, but qualitatively the same.
1.4
Explain the dynamics of strain diversity
Least diverse ecosystem composition = one strain (S=0)
Most diverse = multiple strains all with the same maximal abundance (Smax)
maximum diversity is achieved regardless of total prevalence. Hence if at some point all strains have abundance 0.01 or 0.1 it does not make any difference to S, which will take value Smax in both cases.
Transient times - strains are still adjusting and will display recurrent epidemics. At this point diversity is less than Smax because soe strains are more abundant than others.
Late times - strains are equally abundant and diversity plateaus as the strains become constant at equilibrium
What does Shannon Diversity Index Plot?
the amount of diversity in an ecosystem’s composition at a point in time
2.1
What does this graph show?
Transmission Rates (beta) are set the same - 292
Cross immunity is very high - set to 0.95 (nearly 1 which would mean full cross immunity)
2.1
The three strains have the sam R0 but show different levels of prevalence (proportion infected). What are these levels?
High prevalence (dominant strain)
Intermediate prevalence (subdominant strains)
Low prevalence (strains are excluded and run the risk of becoming extinct)
2.1
If all strains have the same epidemiological parameters (beta, sigma and mu), what does this mean in terms of fitness?
None of the strains have an explicit fitness advantage over the other
x
Once strain X (strain 6) becomes dominant, any strain sharing alleles at the same locus suffers from the high levels of herd immunity to X.
In the presence of a dominant strain, why might some strains be driven to extinction?
x
What happens to strains that don’t share alleles with the dominant strain?
they manage to co-circulate with the dominant strain
Why might one of two strains co-circulating with a third dominant strain, never outdo (or dominate the present dominating strain)?
the two co-circulating strains share alleles and thus are busy comepting directly with each other for susceptible individuals.
What might explain two strains appearing on a plot at an intermediat prevalence (horizontal line in middle of graph)
the two strains do not share alleles with the dominant straina nd thus do not suffer from herd immunity generated by the dominant strain, however the two strains share alleles with each other and therefore compete for susceptible individuals. This means one of the two strains will never outdo the present most dominant strain.
2.5
Why is strain diversity where there is high cross immunity generally smaller than observed under no cross-immunity(Q1)?
Diversity is lower at equilibrium compared to the scenario with no cross-immunity because 3 of the strains are actually “extinct”.