During the coronavirus disease 2019 (COVID-19) pandemic, emergency departments (EDs) faced unprecedented operational stress compounded by mandatory testing requirements that directly influenced patient flow and length-of-stay (LOS). Two testing modalities were central to pandemic ED operations: (1) rapid point-of-care lateral flow assays (LFAs), which return results in minutes but depend on frontline ED personnel and space, and (2) laboratory-based polymerase chain reaction (PCR), which requires sample transport and centralized processing but functions independently of ED capacity. Whether the relative performance of these modalities remains robust under varying ED operational pressures is unclear.

This retrospective observational study analyzed 31,737 COVID-19 testing encounters (11,098 LFA; 20,639 PCR) during the 11-month dual-testing period (May 2022–March 2023) at a high-volume tertiary ED, when both modalities were concurrently deployed. Propensity score matching (PSM; 1:1 nearest-neighbor, caliper 0.5 SD) generated 8,492 well-balanced LFA–PCR pairs. Turnaround time (TAT) was evaluated as an operational stress indicator modifying the association between testing modality and ED LOS. Variability analyses assessed performance stability under differing capacity levels.

Overall, LFA was associated with longer LOS than PCR (median 8.3 versus 5.8 hours; P < 0.001). Under low-stress conditions (TAT ≤30 minutes), this difference was modest (median difference 1.5 hours; 95% CI, 0.80 to 2.07). As TAT increased, modality performance diverged substantially. At TAT >90 minutes, LOS difference increased to 3.6 hours (95% CI, 2.85 to 4.42). Threshold inflection occurred between 60–90 minutes. Lateral flow assays exhibited higher operational variability (CV ratio 2.09; 95% CI, 1.25 to 3.12), with the greatest instability during high-volume periods, while PCR performance remained comparatively stable across stress levels. Stratified analyses were exploratory; confidence intervals were not adjusted for multiplicity.

Turnaround time and its variability serve as actionable, real-time indicators of ED system capacity. Lateral flow assay performance degrades progressively under operational strain due to its reliance on frontline ED resources, whereas PCR—supported by external laboratory infrastructure—maintains more stable throughput. Capacity-contingent, adaptive testing strategies that shift toward PCR as TAT rises may enhance ED resilience, reduce LOS, and support more predictable patient flow during future outbreaks and surge conditions.