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Pre-specified detection criteria (Sanderson et al. 2026)

The nanopore CMg workflow with the pre-specified detection criteria.

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Evaluations and results

1 evaluation · 8 results. Different protocols are not a single leaderboard.

Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) · Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)

Sorted by False negatives (all PCR targets; target level; reference: routine multiplex PCR) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	False negatives (all PCR targets; target level; reference: routine multiplex PCR)	False positives (all PCR targets; target level; reference: routine multiplex PCR)	Recall (all PCR targets; target level; reference: routine multiplex PCR)	Recall (pathogen target: influenza A; target level; reference: routine multiplex PCR)	Recall (pathogen target: rhinovirus/enterovirus; target level; reference: routine multiplex PCR)	Recall (pathogen target: RSV; target level; reference: routine multiplex PCR)	Recall (pathogen target: SARS-CoV-2; target level; reference: routine multiplex PCR)	Specificity (all PCR targets; target level; reference: routine multiplex PCR)
Pre-specified detection criteria (Sanderson et al. 2026)Evaluation	127	nine	51%	58%	19%	85%	65%	99.8%

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Pre-specified detection criteria (Sanderson et al. 2026)	Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)	127 False negatives (all PCR targets; target level; reference: routine multiplex PCR) count · lower Uncertainty: Not reported by the source: No interval printed with this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pre-specified detection criteria on the validation set (Sanderson et al. 2026) rna-pathogen-20261011-sanderson2026-protocol-validation Aggregation: Not reported Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Results 'Validation Set: Diagnostic performance' paragraph 4: "There were 127 false-negative results"
Configuration: Pre-specified detection criteria (Sanderson et al. 2026)	Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)	nine False positives (all PCR targets; target level; reference: routine multiplex PCR) count · lower Uncertainty: Not reported by the source: No interval printed with this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pre-specified detection criteria on the validation set (Sanderson et al. 2026) rna-pathogen-20261011-sanderson2026-protocol-validation Aggregation: Not reported Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Results 'Validation Set: Diagnostic performance' paragraph 5: "There were nine false-positive pathogen detections by sequencing"
Configuration: Pre-specified detection criteria (Sanderson et al. 2026)	Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)	51% Recall (all PCR targets; target level; reference: routine multiplex PCR) percent · higher Uncertainty: 95% CI 45 to 57 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pre-specified detection criteria on the validation set (Sanderson et al. 2026) rna-pathogen-20261011-sanderson2026-protocol-validation Aggregation: Not reported Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Results 'Validation Set: Diagnostic performance' paragraph 4: "133/260 (51%, 95%CI: 45-57%) PCR-positive results (i.e. gold-standard positives) were also detected by sequencing"
Configuration: Pre-specified detection criteria (Sanderson et al. 2026)	Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)	58% Recall (pathogen target: influenza A; target level; reference: routine multiplex PCR) percent · higher Uncertainty: 95% CI 40 to 75 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pre-specified detection criteria on the validation set (Sanderson et al. 2026) rna-pathogen-20261011-sanderson2026-protocol-validation Aggregation: Not reported Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Results 'Performance by pathogen' paragraph 1: "influenza A 58% (95% CI: 40-75%)"
Configuration: Pre-specified detection criteria (Sanderson et al. 2026)	Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)	19% Recall (pathogen target: rhinovirus/enterovirus; target level; reference: routine multiplex PCR) percent · higher Uncertainty: 95% CI 8 to 29 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pre-specified detection criteria on the validation set (Sanderson et al. 2026) rna-pathogen-20261011-sanderson2026-protocol-validation Aggregation: Not reported Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Results 'Performance by pathogen' paragraph 1: "rhinovirus/enterovirus 19% (95% CI: 8-29%)"
Configuration: Pre-specified detection criteria (Sanderson et al. 2026)	Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)	85% Recall (pathogen target: RSV; target level; reference: routine multiplex PCR) percent · higher Uncertainty: 95% CI 75 to 95 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pre-specified detection criteria on the validation set (Sanderson et al. 2026) rna-pathogen-20261011-sanderson2026-protocol-validation Aggregation: Not reported Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Results 'Performance by pathogen' paragraph 1: "RSV 85% (95% CI: 75-95%)"
Configuration: Pre-specified detection criteria (Sanderson et al. 2026)	Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)	65% Recall (pathogen target: SARS-CoV-2; target level; reference: routine multiplex PCR) percent · higher Uncertainty: 95% CI 53 to 78 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pre-specified detection criteria on the validation set (Sanderson et al. 2026) rna-pathogen-20261011-sanderson2026-protocol-validation Aggregation: Not reported Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Results 'Performance by pathogen' paragraph 1: "SARS-CoV-2 65% (95% CI: 53-78%)"
Configuration: Pre-specified detection criteria (Sanderson et al. 2026)	Protocol: Target-level detection of respiratory pathogens against routine multiplex PCR, validation set (Sanderson et al. 2026) Dataset: Validation set: 344 prospectively collected nasopharyngeal swabs (Sanderson et al. 2026)	99.8% Specificity (all PCR targets; target level; reference: routine multiplex PCR) percent · higher Uncertainty: Not reported by the source: No interval printed with this value Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pre-specified detection criteria on the validation set (Sanderson et al. 2026) rna-pathogen-20261011-sanderson2026-protocol-validation Aggregation: Not reported Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Results 'Validation Set: Diagnostic performance' paragraph 5: "3901/3910 (99.8%) targets negative by PCR (as tested in the original assays) were also not detected from sequencing"

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Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study · Original source · medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML

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Technical metadata and extraction receipts

Stable ID: rna-pathogen-20261011-sanderson2026-config-prespecified

areas: microbes-communities
contexts: clinical_research
method types: conventional_pipeline
reported name: Pre-specified detection criteria
parameters: Thresholds fixed on the derivation set: (genome coverage >= 1 read > 0.25% OR area under the genome > 0.003 OR reads mapping to the reference > 0.006%) AND >= 2 target reads AND ratio criterion > 0.1; super-accuracy basecalling
source locator: Results 'Derivation Set: Defining bioinformatic thresholds for pathogen detection' paragraph 4; Table 2 (image, not transcribed)
foundation model eligible: false
access reuse: Laboratory workflow described in the preprint; not a released product
missing metadata: version: reason: unreported; note: minimap2 and basecaller versions are not given in the inspected text

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