Early detection intervals for epidemics caused by SARS-CoV-2 Omicron variant in multiple countries

This dataset contains the estimated early detection intervals for the emergence of the Omicron variant of SARS-CoV-2 in 117 countries based on genomic evidence and reported COVID-19 cases. The early detection interval is defined as the time between the date of introduction of an infectious agent into a country and the date at which an increase is detectable in traditional indicator-based surveillance data. This dataset can be served as reference data to reproducibly and quantitatively evaluate the performance of event-based surveillance systems in the early detection of disease outbreaks.

In this dataset of early detection intervals for the Omicron variant, the date of introduction of the Omicron variant (BA.1 and BA.2) (i.e., the beginning of the early detection interval) was determined by linking genomic evidence from published papers and two online genome databases: GenBank and GISAID (Global Initiative on Sharing All Influenza Data). The end of the interval was the earliest alert detected from the reported COVID-19 case counts using a Bayesian online change point detection (BOCP) model and the second derivative of the generalized additive model (GAM). In addition to the early detection intervals, this dataset also contains variables indicating data quality, such as discordance between interval start dates using phylogenetic estimation and data from genomic sample collection & submission.