ArticleBMC infectious diseases2025
Multiplex metagenomic sequencing for rapid viral pathogen identification and surveillance in clinical specimens.
Article in BMC infectious diseases, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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17 authors.
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Abstract
backgroundRapid and accurate viral detection is essential for clinical diagnosis and effective outbreak surveillance. Traditional methods, including culture-based isolation and antigen tests, are time-consuming and limited by tissue tropism. Multiplex PCR panels, although faster, are constrained by predefined targets, limiting their ability to detect novel or unexpected viral strains.
methodsWe applied Oxford Nanopore Technology sequencing (ONT-Seq), a long-read, real-time, and multiplex metagenomic platform, to 85 clinical specimens using a sequence-independent, single-primer amplification (SISPA) workflow. Sequencing results were compared with routine clinical diagnostics for concordance and for identification of co-infections
resultsONT-Seq achieved 80% concordance with clinical diagnostics and identified co-infections in 7% of cases missed by routine testing, including influenza C virus (ICV), and Sapporovirus. Among 58 adenovirus-positive cases, 31 samples with over 80% genome coverage at 20× depth were used for phylogenetic analysis, revealing adenovirus B3 as the predominant circulating strain.
conclusionsONT-based metagenomic sequencing enhances the detection of both known and emerging viruses in clinical specimens. Its ability to provide real-time, unbiased data supports its utility in improving diagnostic accuracy and viral surveillance. CLINICAL TRIAL: Not applicable.
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