Early detection of variants of concern via funnel plots of regional reproduction numbers

Abstract

Tools to early detect the emergence of a new variant of concern are essential to develop strategies that contain epidemic outbreaks and their health-economic-social consequences. For example, knowing in which region a variant of concern appears or starts spreading enables prompt actions to circumscribe the diffusion area. This paper presents ‘funnel plots’ as a statistical process control method that can quickly identify regions of a country where the reproduction number is anomalous with respect to the national one, while keeping false alarms under control. Unlike tools whose purpose is to identify rises of Rt, the proposed method detects when a regional Rt behaves differently from the national average and thus represents an abnormal situation that needs to be investigated through cross-cutting research. The method is validated on public COVID-19 data demonstrating its efficacy in the early detection of SARS-CoV-2 variants in India, South Africa, England, and Italy, as well as of a malfunctioning episode of the diagnostic infrastructure in England.