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explodecomputer / covid-uob-pooling

Simulations for pooling covid tests
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Transmission should be a function of density, viral shedding and viral load #3

Open explodecomputer opened 4 years ago

explodecomputer commented 4 years ago

This might be somewhat arbitrary but could make the initial infecteds have some viral load and some uncorrelated viral shedding parameter. So how many people they infect will be a function of

  1. How many people they are in contact with
  2. Their viral load
  3. Their viral shedding

Incorporate duration? 10 hours a day amongst circle - pois(nl) people 5 hours in building - pois(5) people 2 hours everyone else - pois(5) people

explodecomputer commented 3 years ago

To generate heterogeneity of viral load between individuals:

  1. For each infected individual generate a course of infection like in this figure https://www.nejm.org/doi/full/10.1056/NEJMp2025631 such that viral load changes over time. Also allow the peak viral load to differ between individuals.

  2. Sample a random time points over the course of infection for each infected individual

To link the sampled viral load to test sensitivity use this model https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983103/

To generate clustered infections use a 2 time point model

  1. Random people infected and given the above viral load distributions. Infectivity of an individual = peak viral load X individual viral dispersion, where individual viral dispersion is a random variable that represents stuff like how much they spit when they talk, or how much social distancing they do or something like that
  2. Choose people they are in contact with based on living circles and buildings and allow one round of transmission similar as before but also weighting probability based on infectivity

Because there are pre- and post-infectious periods of the infection, in one of the outputs we could evaluate if e.g. a higher level of pooling will have more specificity for capturing infectious individuals (as opposed to higher sensitivity = capturing more post-infectious individuals)