Evidence claim

Evidence summary: RNA pathogen detection workflows

Summary of Select an RNA pathogen-detection workflow for diagnostic testing

The single-assay results are a UCSF respiratory RNA metagenomic assay at 93.6% (103 of 110) sensitivity against original clinical respiratory panel testing, as reported by its developers, and the developers' own prospective validation of an Oxford nanopore workflow on 344 nasopharyngeal swabs (preprint). With thresholds fixed on a separate derivation set, the nanopore workflow detected 51% (133 of 260) of PCR-positive targets in the samples passing quality control, from 85% for RSV to 19% for rhinovirus/enterovirus, and 99.8% of PCR-negative targets were not detected; criteria chosen after the validation raised sensitivity to 58%, and the authors attributed all nine false positives to barcode crossover. Its swabs were selected mostly as PCR-positive at Ct 30 or below, with about one negative per eight positives, and reads were matched only to the 23 panel pathogens, so it does not test detection outside the panel. Three comparisons of several workflows add proxy evidence. On 88 nasal washings scored against 1144 respiratory virus PCR results (Carbo et al. 2022), all five classifiers detected 22 or 23 of the 24 PCR-positive results at species level at a read-count cut-off chosen on the same data, but 31% to 58% of their positive calls were PCR-negative. When 13 European clinical virology laboratories each ran their own pipeline on the same 13 clinical datasets (de Vries et al. 2021, preprint), 10 to 13 samples were correctly called positive, and the three pipelines that found every sample reported 6, 2 and 0 additional PCR-negative viruses. In the CAMI II blood metagenome challenge (Meyer et al. 2022), 4 of 10 submissions listed the causal virus. In a developer benchmark of five virus profilers on one shared database (Tisza et al. 2026, preprint), the model-estimated probability of reporting the correct family for reads from seven divergent viruses at 10 read pairs was 0.974 for EsViritu and 0.9998 for Metabuli but 0.045 for Kraken2, 0.012 for Centrifuger and 0.0009 for Sylph at the authors' headline settings, and Metabuli reported a median of 18 false species in seven pathogen-free libraries against 0 for EsViritu. None of this is clinical validation: the cohorts are small or single-site, reference databases and reporting rules differ, and the benchmark data are mostly synthetic.

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Claimed field summary Context-only references	Tan et al., Nature Communications 15, 9016 (2024) Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Tan et al., Nature Communications 15, 9016 (2024) Retrieved: 2026-10-07T12:24:59.206377+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `4b701cdeaf16c948591a34576390dbaed033a123ea9c8bace661b6822889abf6` Hash scope: Hash scope not separately documented; inspect source record
Claimed field summary Context-only references	Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML Retrieved: 2026-10-09T20:06:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `e6683855ad278a555598295fdc4166e54ddb0e39e3d971878b898b20bc8ddf95` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx Retrieved: 2026-10-09T20:16:56Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `cd3a80d785b78377e79960d0280667f98cba3305d68426fdfaf8efeecd4542d7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2021.05.04.21256618 version 1 (2021-05-08), JATS XML; published as J Clin Virol 141:104908 (doi:10.1016/j.jcv.2021.104908) Retrieved: 2026-10-09T20:15:27Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `735ce2e42ae5fe6f5a198bdc14fd2e92ef27fc1d3734d2137a3c86d24480c718` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4) Retrieved: 2026-10-09T20:15:56Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `be0ea61fcffe8ea580077467ca19ef1ac39e88bbc82d916bc65b58a6683214f6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Critical Assessment of Metagenome Interpretation: the second round of challenges Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Methods 19(4):429, published 2022-04-08; PMC9007738 full-text XML Retrieved: 2026-10-09T20:21:44Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `2532db9c9abd1f040047afdcc859cb83739a9cceb4dbd998cd550017da9bd7ba` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Meyer et al. 2022, Supplementary Tables 1-40 Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41592_2022_1431_MOESM3_ESM.xlsx (Supplementary Tables), as linked from the article XML <supplementary-material id="MOESM3"> Retrieved: 2026-10-09T20:18:45Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `9a5ebd2364bb2660ea841227b9d04848b9c60b4d3c2a9f4939fc5994efc851ce` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv 10.64898/2026.02.06.26345651 v2, posted 2026-02-26; JATS XML Retrieved: 2026-10-11T21:38:13Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `c0bc5c035742f53fe291e08b9d956102e102fd743a55de503f00bcaead36a7e2` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1, posted 2026-09-30; JATS XML Retrieved: 2026-10-11T21:39:50Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `fd92099655ddefdec31d35e273b80c4b233eed395c1cfc137eaddaa4efee232b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field summary Context-only references	Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) Original source ↗ amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx) Retrieved: 2026-10-11T21:45:51Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `0559022a3ff5ef5b2682e3c451eda51835c4c8d9be9dfdb1ebc9cd9295fb7701` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

10 source records and release history

Tan et al., Nature Communications 15, 9016 (2024) · Original source · Tan et al., Nature Communications 15, 9016 (2024)
Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort · Original source · Pathogens 11(3):340, published 2022-03-11; PMC8953373 full-text XML
Carbo et al. medRxiv preprint v1, Supplementary Tables 1 and 2 · Original source · medRxiv 2022.01.21.22269647 version 1 (2022-01-21), supplementary file media-1.xlsx
Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples · Original source · medRxiv 2021.05.04.21256618 version 1 (2021-05-08), JATS XML; published as J Clin Virol 141:104908 (doi:10.1016/j.jcv.2021.104908)
de Vries et al. medRxiv preprint v1, Supplementary Tables 2-4 · Original source · medRxiv 2021.05.04.21256618 version 1, supplementary file media-1.xlsx (sheets SuppS2, SuppS3, SuppS4)
Critical Assessment of Metagenome Interpretation: the second round of challenges · Original source · Nature Methods 19(4):429, published 2022-04-08; PMC9007738 full-text XML
Meyer et al. 2022, Supplementary Tables 1-40 · Original source · 41592_2022_1431_MOESM3_ESM.xlsx (Supplementary Tables), as linked from the article XML <supplementary-material id="MOESM3">
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
EsViritu is a sensitive and specific profiler for viral pathogen detection and genome recovery in metagenomes · Original source · bioRxiv 10.64898/2026.09.29.755457 v1, posted 2026-09-30; JATS XML
Tisza et al. 2026 Supplemental Tables S1-S25 (bioRxiv media-1.xlsx) · Original source · bioRxiv 10.64898/2026.09.29.755457 v1 supplementary file DC1 (755457_file02.xlsx)

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Stable ID: use-case-summary-diagnostic-rna-pathogen-detection

field: summary
value: The single-assay results are a UCSF respiratory RNA metagenomic assay at 93.6% (103 of 110) sensitivity against original clinical respiratory panel testing, as reported by its developers, and the developers' own prospective validation of an Oxford nanopore workflow on 344 nasopharyngeal swabs (preprint). With thresholds fixed on a separate derivation set, the nanopore workflow detected 51% (133 of 260) of PCR-positive targets in the samples passing quality control, from 85% for RSV to 19% for rhinovirus/enterovirus, and 99.8% of PCR-negative targets were not detected; criteria chosen after the validation raised sensitivity to 58%, and the authors attributed all nine false positives to barcode crossover. Its swabs were selected mostly as PCR-positive at Ct 30 or below, with about one negative per eight positives, and reads were matched only to the 23 panel pathogens, so it does not test detection outside the panel. Three comparisons of several workflows add proxy evidence. On 88 nasal washings scored against 1144 respiratory virus PCR results (Carbo et al. 2022), all five classifiers detected 22 or 23 of the 24 PCR-positive results at species level at a read-count cut-off chosen on the same data, but 31% to 58% of their positive calls were PCR-negative. When 13 European clinical virology laboratories each ran their own pipeline on the same 13 clinical datasets (de Vries et al. 2021, preprint), 10 to 13 samples were correctly called positive, and the three pipelines that found every sample reported 6, 2 and 0 additional PCR-negative viruses. In the CAMI II blood metagenome challenge (Meyer et al. 2022), 4 of 10 submissions listed the causal virus. In a developer benchmark of five virus profilers on one shared database (Tisza et al. 2026, preprint), the model-estimated probability of reporting the correct family for reads from seven divergent viruses at 10 read pairs was 0.974 for EsViritu and 0.9998 for Metabuli but 0.045 for Kraken2, 0.012 for Centrifuger and 0.0009 for Sylph at the authors' headline settings, and Metabuli reported a median of 18 false species in seven pathogen-free libraries against 0 for EsViritu. None of this is clinical validation: the cohorts are small or single-site, reference databases and reporting rules differ, and the benchmark data are mostly synthetic.
source locator: amp-20261007-rna-pathogens-source: result amp-20261007-rna-pathogens-result; rna-pathogen-20261009-source-carbo2022-supp: Supplementary Table 1; rna-pathogen-20261009-source-devries2021-supp: Supplementary Tables 2 and 4; rna-pathogen-20261009-source-meyer2022-supp: Supplementary Table 39; articles: Methods and Results; rna-pathogen-20261011-sanderson2026-source: Results 'Validation Set: Diagnostic performance', 'Performance by pathogen'; rna-pathogen-20261011-tisza2026-source-supp: Supplemental Tables S2 and S6
review: method: source-hash-verification; independent-cell-check; automated-source-review; reviewer: claude; reviewer note: Separate Claude review agent (reviewer-path), independent of the collector who drafted the summary proposal; the reviewer corrected the text; no human review claimed; reviewed at: 2026-10-11T23:45:00Z; note: Drafted by the collector (data/omics/lit-search-20261011-uc-pathogens/report.md) and corrected by the reviewer; every number traced to stored results. Descriptive summary only; no execution, human scientific review or clinical validation. See docs/reviews/use-cases/pathogen-use-cases-2026-10-11.md.
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