Surveillance strategies for the detection of new pathogen variants across epidemiological contexts

Surveillance systems that monitor pathogen genome sequences are critical for rapidly detecting the introduction and emergence of pathogen variants. To evaluate how interactions between surveillance capacity, variant properties, and the epidemiological context influence the timeliness of pathogen variant detection, we developed a geographically explicit stochastic compartmental model to simulate the transmission of a novel SARS-CoV-2 variant in New York City. We measured the impact of (1) testing and sequencing volume, (2) geographic targeting of testing, (3) the timing and location of variant emergence, and (4) the relative variant transmissibility on detection speed and on the undetected disease burden. Improvements in detection times and reduction of undetected infections were driven primarily by increases in the number of sequenced samples. The relative transmissibility of the new variant and the epidemic context of variant emergence also influenced detection times, showing that individual surveillance strategies can result in a wide range of detection outcomes, depending on the underlying dynamics of the circulating variants. These findings help contextualize the design, interpretation, and trade-offs of genomic surveillance strategies of pandemic respiratory pathogens.