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. 2021 Dec 10;40(28):6277-6294.
doi: 10.1002/sim.9182. Epub 2021 Sep 7.

Geographically weighted generalized Farrington algorithm for rapid outbreak detection over short data accumulation periods

Daisuke Yoneoka  1   2   3 , Takayuki Kawashima  2   4   5 , Koji Makiyama  6 , Yuta Tanoue  2   4 , Shuhei Nomura  2 , Akifumi Eguchi  2   4   7
Affiliations

Geographically weighted generalized Farrington algorithm for rapid outbreak detection over short data accumulation periods

Daisuke Yoneoka et al. Stat Med. .

Abstract

The demand for rapid surveillance and early detection of local outbreaks has been growing recently. The rapid surveillance can select timely and appropriate interventions toward controlling the spread of emerging infectious diseases, such as the coronavirus disease 2019 (COVID-19). The Farrington algorithm was originally proposed by Farrington et al (1996), extended by Noufaily et al (2012), and is commonly used to estimate excess death. However, one of the major challenges in implementing this algorithm is the lack of historical information required to train it, especially for emerging diseases. Without sufficient training data the estimation/prediction accuracy of this algorithm can suffer leading to poor outbreak detection. We propose a new statistical algorithm-the geographically weighted generalized Farrington (GWGF) algorithm-by incorporating both geographically varying and geographically invariant covariates, as well as geographical information to analyze time series count data sampled from a spatially correlated process for estimating excess death. The algorithm is a type of local quasi-likelihood-based regression with geographical weights and is designed to achieve a stable detection of outbreaks even when the number of time points is small. We validate the outbreak detection performance by using extensive numerical experiments and real-data analysis in Japan during COVID-19 pandemic. We show that the GWGF algorithm succeeds in improving recall without reducing the level of precision compared with the conventional Farrington algorithm.

Keywords: emerging infectious disease; geographically weighted quasi-Poisson regression; outbreak detection; statistical surveillance.

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Conflict of interest statement

The authors declare no potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Numerical experiments blueprint: 260 weeks for each of 50 locations (outbreak area colored in orange and the outside of the area colored in blue) [Colour figure can be viewed at wileyonlinelibrary.com]
FIGURE 2
FIGURE 2
Excess death during January to September 2020, under COVID‐19 pandemic in Japan, A, B, and the time‐series death count and the detected outbreak in the 22th prefecture, C: Green is Noufaily method, red is GWGF method, dagger (“+”) is outbreak week, solid line is expected number of deaths, and dashed line is 95% upper bound of prediction interval [Colour figure can be viewed at wileyonlinelibrary.com]
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