Clinical and Operational Outcomes Associated With Targeted and Multiplex Viral PCR Testing

Polymerase chain reaction (PCR) testing enables rapid viral pathogen diagnosis for patients with upper respiratory complaints, potentially reducing unnecessary imaging and antibiotic use. However, whether multiplex PCR panels (five or more pathogens) confer benefits over more targeted approaches remains unclear. We compared clinical and operational outcomes between these testing strategies.

We conducted a retrospective cohort analysis of adult patients with chief complaints suggestive of a viral respiratory illness (e.g., “cough” or “congestion”) who had PCR testing during visits to 9 EDs (academic, urban, and rural), with >500,000 annual visits between 2015-2025. Since multiplex panels were restricted to patients with chronic lung disease or immunodeficiency, propensity score matching was used to compare patients across testing strategies. Outcomes included rates of viral detection and diagnosis, antibiotic use, CT chest imaging, and length of stay, analyzed via chi-square and t-tests, with p<0.001 for multiple comparisons.

During the study period, 11​​,739 patients had multiplex testing and were matched to 11,739 with targeted testing, with no significant post-matching differences in age, self-identified race/ethnicity, or medical comorbidities. Multiplex testing yielded higher viral detection (0.38 [95% CI 0.36-0.38] vs 0.20 [95% CI 0.19-0.21]), and specific viral diagnoses (0.19 [0.18-0.20] vs 0.16 [0.16-0.17]). However, multiplex patients had higher antibiotic rates (0.27 [0.25-0.29] vs 0.21 [0.20-0.22]), chest CT rates (0.18 [0.17-0.19] vs 0.11 [0.10-0.12]), and longer length of stay (12.8h [12.5-13.1] vs. 8.3h [8.1-8.4]). Notably, 98% of multiplex tests resulted after imaging and antibiotics when ordered.

Despite higher viral detection rates, multiplex PCR testing was associated with increased length of stay, imaging, and antibiotic use. Earlier test initiation may mitigate these paradoxical outcomes.