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Updated: Jun 12, 2026
Development of Multiplex Real-Time RT-qPCR Assays for the Detection of SARS-CoV-2, Influenza A/B, and MERS-CoV
Published on: November 10, 2023
An extraction-free multiplex RT-PCR assay for simultaneous detection of six respiratory pathogens using polychromatic
Ya Bian1, Lishan Lu2, Xiaohan Ma3
1Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361005, China; State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China; BioDetect (Xiamen) Biotechnology Co., Ltd., Fujian, China.
Objectives:
Acute respiratory infections commonly result from a spectrum of pathogens, including SARS-CoV-2, influenza A (IAV) and B viruses (IBV), respiratory syncytial virus (RSV), human adenovirus (HAdV), and Mycoplasma pneumoniae (MP). This study aimed to develop and validate a rapid, extraction-free multiplex RT-PCR assay coupled with polychromatic melting curve analysis (RPCR-MC). This assay enables simultaneous detection of all six pathogens in a single tube.
Methods:
Specific primers and TaqMan probes were designed to target conserved regions of each pathogen. An extraction-free workflow was established by direct lysis of throat swab samples. The assay integrated four fluorescence channels (FAM, HEX, ROX, and CY5) with melting curve analysis to differentiate amplicons based on their melting temperatures (Tm). We evaluated analytical performance (sensitivity, specificity, repeatability, and stability) using synthetic plasmids, viral culture supernatants, and clinical samples. The results were further validated by Sanger sequencing.
Results:
The RPCR-MC assay achieved a limit of detection of 1 copy/μL for all six pathogens. No cross-reactivity was observed with 30 potentially interfering substances. In the clinical evaluation of 249 samples, the assay identified 62 SARS-CoV-2, 33 IAV, 62 IBV, 19 RSV, 61 HAdV, and 28 MP cases, including 34 co-infections. The assay achieved an overall accuracy of 99.6% and demonstrated excellent agreement with commercial reference kits. The entire workflow was completed within three hours without the need for nucleic acid extraction. The RPCR-MC assay received China's National Class III Medical Device Registration Certificate, supporting its immediate application in clinical microbiology laboratories. This work has been previously posted as a preprint.
