The diagnostic role of SARS-CoV-2 in routine respiratory testing after policy adjustment: a real-world laboratory study integrating longitudinal PCR and respiratory pathogen testing workflow data

Abstract

Since COVID-19 entered long-term management, SARS-CoV-2 has become increasingly integrated into routine respiratory diagnostics. However, longitudinal laboratory trends and its relative position within multiplex respiratory pathogen testing remain incompletely described in real-world hospital practice. We characterized SARS-CoV-2 in two complementary diagnostic contexts: longitudinal SARS-CoV-2 PCR testing (Phase A) and multiplex respiratory pathogen testing (Phase B). We analyzed routine laboratory data from January 2024 to January 2026 to summarize monthly SARS-CoV-2 PCR testing volume and positivity (Phase A). We also analyzed data from the 11-target respiratory PCR testing workflow from January 2025 to January 2026 (Phase B; de-duplicated overall cohort, N = 3,941), with additional analyses in a hospitalized-only subset ( n = 3,461). Detection rates were calculated using tested denominators, with multiple pathogens allowed per sample. Under the primary definition, weakly positive results were classified as positive. In Phase A, 19,207 SARS-CoV-2 PCR tests were performed, with an overall positivity rate of 10.43%. Monthly positivity showed recurrent temporal fluctuations, and increases in testing volume did not consistently correspond to higher positivity. In Phase B (overall cohort), human rhinovirus (21.02%) and respiratory syncytial virus (13.71%) were the most frequently detected pathogens, followed by influenza A virus (7.59%). In the hospitalized-only subset, SARS-CoV-2 was detected in 3.90% of samples, ranking fifth among 11 targets. Co-detection of ≥ 2 pathogens occurred in 318/3,941 samples (8.1%); the most frequent pairs were HRV + RSV (2.31%), HRV+adenovirus (1.42%), and HRV+influenza A virus (0.96%). Under post-adjustment routine clinical practice, SARS-CoV-2 showed recurrent fluctuations in longitudinal PCR testing and remained a non-dominant component of the Phase B respiratory pathogen testing workflow. A phase-structured laboratory framework may improve interpretation of routine respiratory diagnostic outputs and support context-aware hospital respiratory pathogen surveillance.