Abstract

Background Multiplex nucleic acid amplification tests (NAATs) are essential for managing respiratory viral infections. To robustly confirm the capability of laboratories for multiplex respiratory viral detection, a well-designed, large-scale external quality assessment study incorporating in-depth analysis was conducted. Methods Laboratories performing multiplex viral NAATs in China were publicly recruited and provided with a reference panel to assess their testing performance. Multivariate analysis was performed on the collected results and detailed methodological data to identify potential sources of errors. Results Among 914 participating laboratories, overall concordance was 81.6% (746/914). False-positives (FPs) were concentrated in 13 laboratories, suggesting the occurrence of laboratory contamination. False-negatives (FNs) were more prevalent, primarily occurring in samples with low viral loads. Multivariate analysis identified capillary electrophoresis-based multiplex PCR assay (aOR=2.1, 95% CI: 1.1-3.8), certain commercial kit (Flu/RSV kit [Autobio], aOR=102.2, 95% CI:13.4-776.0), and laboratory-developed tests (aOR=6.59, 95% CI:2.2-19.8) as independent risk factors for FNs. Suboptimal laboratory performance also increased the odds of FNs. Conclusions This study demonstrates the advances and limitations of multiplex viral NAATs: high adoption and acceptable concordance reflect the technology's maturity, yet the occurrence of FNs and FPs highlights a need for continued assay optimization, strengthened laboratory quality management, and increased clinician awareness of testing limitations.