Fig 1.
Schematic of the DIOS framework for optimizing surveillance of infections caused by multiple pathogen subtypes, with example design parameters and objective functions presented in green boxes.
Fig 2.
Temporal and spatial variations in HFMD incidence rate (A,B) and laboratory serotyping (C,D). (A) HFMD incidence rate for Sichuan 2009–2015; (B) annual mean HFMD incidence rate for each prefecture; (C) number of serotyped HFMD cases by year; (D) proportion of all serotyped cases drawn from each prefecture from 2009–2015. The boundaries of the prefectures were obtained from https://gadm.org/download_country.html.
Fig 3.
Comparison between Existing, IncRate, and Optimal subtyping allocation strategies across locations.
Treemaps show the proportion of typing efforts allocated to each location in the (A) Existing, (B) IncRate, and Optimal designs that minimize the error in estimated serotype-specific incidence rate of (C) all HFMD cases and (D) only severe HFMD cases. Tiles represent study locations, with the area of the tile representing the proportion of all typing efforts allocated to the location, and the color of the tile representing the location’s annual mean HFMD incidence rate. Tiles are ordered by decreasing annual mean incidence rate from top to bottom, then left to right. Scatterplots show the correlation between annual mean incidence rate of the optimal proportion of total typing resources allocated to each location to minimize error in estimated serotype-specific incidence rate of (E) all HMFD cases and (F) only severe HFMD cases. Black dots represent the archetypal design IncRate (see definition in section 2.2.7), blue triangles in (E) and squares in (F) represent the optimal allocation strategy for minimizing error in estimating serotype-specific incidence rate for all cases and only severe cases, respectively. The blue lines represent the best fit relating annual mean incidence rates to typing allocations across the Optimal designs. Vertical arrows represent changes from IncRate to Optimal: red arrows represent increases in typing efforts from IncRate to Optimal; green arrows represent reductions in typing efforts from IncRate to Optimal. Inset figures show data for all prefectures, showing the range (red dashed rectangle) displayed in the main panel.
Fig 4.
Impact of the proportion of severe cases serotyped on mean absolute error (MAE) of the estimated serotype-specific incidence rate of (A) all HFMD cases and (B) severe HFMD cases. Colored lines are smoothed by Gaussian process models. Black dot and triangle represent the probabilities of severe cases being serotyped that lead to the lowest error in estimating serotype-specific incidence rate of all (dot) and only severe (triangle) HFMD cases; blue dot and triangle represent the optimal designs from GA.
Fig 5.
Surveillance performance of the optimal design and the seven archetypal designs evaluated with data from 2009–2014 and 2015 over 1000 realizations of the disease system model.
Violin plots and boxplots for different designs (shades of color) show the distribution of mean absolute error (MAE) in estimating serotype-specific incidence rates of (A) all cases and (B) only severe cases using 2009–2014 data; and (C) all cases and (D) only severe cases using 2015 data, which was not used in the optimization procedure. The horizontal dashed lines show the median MAEs of the optimal designs.
Fig 6.
Scatterplots of annual mean incidence rate and the proportion of typing resources allocating to each location under the archetypal design IncRate (black dots) and the Optimal designs for minimizing the MAE of estimated serotype-incidence rate of all HFMD cases (blue triangles) when the available typing resources is (A) halved, (B) doubled, and (C) quintupled; and the Optimal designs for minimizing the MAE of estimated serotype-incidence rate of severe HFMD cases (blue squares) when the available typing resources is (D) halved, (E) doubled, and (F) quintupled.
Fig 7.
Optimal proportion of severe cases to be subjected to serotyping as the availability of typing resources changes, when seeking to minimize error serotype-specific incidence rates of (A) all HFMD cases and (B) only severe HFMD cases.