Fig 1.
Comparison of simulation recovery for With COP and No COP models with observational error (0.1).
(A, B) Individual-level antibody kinetics for a subset of individuals, showing observed data points (grey dots), and individual-level posterior medians (red lines) for With COP data and No COP data. (C, D) Model error (mean with 95% credible intervals) in recovering infection times, represented as the difference between simulated and model-predicted infection days for infected individuals With COP data and No COP data. (E, F) Distribution of infection times, comparing simulated infection times with recovered infection times.
Fig 2.
Evaluation of model performance under varying levels of observational uncertainty.
(A) Accuracy in recovering antibody kinetics over various simulated observational errors, measured as the mean CRPS across all individuals of the observational model (B) Accuracy in recovering the epidemic curve over various simulated observational errors, assessed using the mean CRPS across all infection times (C, D) ROC curves for infection status predictions under simulated data with COP (C) and without COP (D) under different observational error (colour) (E) F1-scores for recovering infection status across different observational errors and model types (No COP and With COP). (F, G) Posterior means of the COP curves across various observational uncertainty values (blue colours) compared to the simulated function (dashed red line) (H) Accuracy in recovering the functional form for the COP, measured by Mean CRPS, across various levels of observational uncertainty for both model types (With COP and No COP).
Fig 3.
Sensitivity of serological detection heuristics in identifying infection status for 99 PCR-positive individuals using serological data only.
Posterior probabilities of recovery for individuals using five detection methods: (A) Four-fold spike rise, (B) Four-fold NCP rise, (C) Seropositive threshold spike, (D) Seropositive threshold NCP, and (E) serojump. Green bars represent individuals inferred as true positives, while red points indicate false negatives.
Fig 4.
Antibody kinetics, recovery of infection timings, and correlates of protection from empirical data with PCR information.
(A) Fitted antibody kinetic trajectories for individuals with infection prior to the Delta variant (left), infection during the Delta variant wave (center), and following vaccination (right), showing fold-rise in antibody titre over time for NCP (blue) and spike (orange) biomarkers. Shaded regions represent 95% credible intervals. (B) Inferred epidemic wave during the Delta wave, illustrating the temporal distribution of PCR-confirmed cases (black bars) and total inferred infections (pink shaded curve), with shaded uncertainty. (C) The estimated attack rate during the Delta wave, partitioned into PCR-confirmed cases (dark grey) and total inferred infections (pink). Error bars indicate 95% credible intervals. (D) The fitted logistic curve to the infection risk, showing the posterior probability of infection as a function of antibody titre at infection for NCP (blue) and spike (orange) biomarkers, with shaded regions representing 95% credible intervals. (E) The CPC from the fitted infection risk curve and (F) shows the relative risk for the same biomarkers.