Fig 1.
Network structure of the model(s).
Every compartment (except S and E) has a quarantined version, transitions into which occur via testing. New infections are transmitted by individuals of the classes coloured red (with the stage Is2 being less infectious). Classes R and Im (mortalities) are no longer infectious.
Table 1.
Interventions considered in the basic UK model.
Fig 2.
Plot of log-posterior and log-prior.
Models without change in IFR in blue, models with change in IFR in orange.
Table 2.
Summary of MAP results.
Fig 3.
Mean trajectories of weekly cases and deaths for model variants BC0 and BC1.
Deterministic trajectories for the MAP parameters of models BC0 (dashed blue) and BC1 (solid orange), along with data (black).
Fig 4.
Mean trajectories of weekly cases and deaths for further model variants.
Deterministic trajectories for the MAP parameters of the various model variants, along with data (black). Models without change in IFR are shown as dashed, models with change in IFR solid.
Fig 5.
Estimated fraction of infected population conditional on observation.
Mean fraction of people infected (symptomatic and asymptomatic) in the total population, conditional on the observation of cases and deaths in models BC0 (blue), BC1 (orange) and P0 (grey). For comparison, we also show the prevalence of infections reported in the ONS infection survey.
Fig 6.
Logarithm of the posterior distribution along a slice of the parameter space.
Data for model variants BC1 (blue) and C1 (orange) are shown. The computed posterior is shown as points, the Gaussian approximation of Eq (5) is shown as solid lines. We vary the onset time (left) and the factor (right) of the change in IFR around the value of θ*, keeping all other parameters fixed. Values shown for the log-posterior are the difference to the maximal values for models BC1 and C1, respectively.
Fig 7.
We show data for model variants BC0 (blue) and BC1 (orange, time-dependent), for four different age groups (indicated in square brackets). The thick lines represent the IFR determined from the MAP parameters, the thin lines correspond to 100 samples of the parameters for the IFR drawn from the Gaussian approximation of the posterior.