Fig. 2: Performance of current guidance on number of positive specimens to sequence for variant detection with testing rate at 27 tests per 100,000 persons per day.

First day of detection since variant introduction at 95% confidence and the corresponding circulating variant proportion using guidance from the World Health Organization (WHO)/European Centre for Disease Prevention and Control (ECDC)^7,8, Brito et al.⁵ and Wohl et al.⁶ (Table 1) under different genomic surveillance strategies with varying sampling coverage (that is, all collected specimens from all healthcare facilities are sent to one facility to be sampled for sequencing (population-wide strategy); or only one tertiary facility or 10, 25, 50 or 100% of tertiary sentinel facilities would sample the specimens they collected for sequencing). Turnaround time (that is, time from specimen collection to acquisition of sequencing data) was assumed to be negligible. We performed 1,000 random independent simulations for each guidance/surveillance strategy. a,b, We simulated epidemics for wild-type SARS-CoV-2/Alpha (a) and Delta/Omicron (b). Gray regions denote that we could not reliably detect the variant virus with 95% confidence using the guidance in question under the assumed genomic surveillance strategy.