Evidence map›Paper›PMID 39532844›Full record

ArticleNature communications2024

Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery.

Jessica Karielle Tan, Venice Servellita, Doug Stryke, Emily Kelly, Jessica Streithorst, Nanami Sumimoto, Abiodun Foresythe, Hee Jae Huh, Jenny Nguyen, Miriam Oseguera and 16 more

Abstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
43citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

43 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  9. Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

26 authors.

Jessica Karielle Tan *Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID 0009-0003-8527-6726
Venice Servellita *Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Doug Stryke *Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Emily KellyDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Jessica StreithorstDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Nanami SumimotoDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Abiodun ForesytheDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Hee Jae HuhDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Jenny NguyenDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Miriam OsegueraDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID 0009-0004-9621-2848
Noah BrazerDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Jack TangDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Danielle IngebrigtsenDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Becky FungDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Helen ReyesDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Melissa HillbergDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Alice ChenViral and Rickettsial Disease Laboratory, Center for Laboratory Sciences, California Department of Public Health, Richmond, CA, USA.
Hugo GuevaraViral and Rickettsial Disease Laboratory, Center for Laboratory Sciences, California Department of Public Health, Richmond, CA, USA.
Shigeo YagiViral and Rickettsial Disease Laboratory, Center for Laboratory Sciences, California Department of Public Health, Richmond, CA, USA.
Christina MoralesViral and Rickettsial Disease Laboratory, Center for Laboratory Sciences, California Department of Public Health, Richmond, CA, USA.
Debra A WadfordViral and Rickettsial Disease Laboratory, Center for Laboratory Sciences, California Department of Public Health, Richmond, CA, USA.ORCID 0000-0002-8630-427X
Peter M MouraniDepartment of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.ORCID 0000-0002-1829-3775
Charles R LangelierDivision of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0002-6708-4646
Mikael de Lorenzi-TognonDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0002-2969-542X
Patrick BenoitDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
Charles Y ChiuDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. charles.chiu@ucsf.edu.ORCID 0000-0003-2915-2094

Funding

Integrated Host/Microbe (IHM) Metagenomics of the Lower Airway to Diagnose PediatricRespiratory Infections, Identify Etiologic Pathogens, and Predict OutcomesR01AI182308 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Charles Langelier, Peter Michael Mourani · 2025 to 2026
$1.6M
NIAID NIH HHS R01 AI182308
6 · The paper itself

Abstract

Tools for rapid identification of novel and/or emerging viruses are urgently needed for clinical diagnosis of unexplained infections and pandemic preparedness. Here we developed and clinically validated a largely automated metagenomic next-generation sequencing (mNGS) assay for agnostic detection of respiratory viral pathogens from upper respiratory swab and bronchoalveolar lavage samples in <24 h. The mNGS assay achieved mean limits of detection of 543 copies/mL, viral load quantification with 100% linearity, and 93.6% sensitivity, 93.8% specificity, and 93.7% accuracy compared to gold-standard clinical multiplex RT-PCR testing. Performance increased to 97.9% overall predictive agreement after discrepancy testing and clinical adjudication, which was superior to that of RT-PCR (95.0% agreement). To enable discovery of novel, sequence-divergent human viruses with pandemic potential, de novo assembly and translated nucleotide algorithms were incorporated into the automated SURPI+ computational pipeline used by the mNGS assay for pathogen detection. Using in silico analysis, we showed that after removal of all human viral sequences from the reference database, 70 (100%) of 70 representative human viral pathogens could still be identified based on homology to related animal or plant viruses. Our assay, which was granted breakthrough device designation from the US Food and Drug Administration (FDA) in August of 2023, demonstrates the feasibility of routine mNGS testing in clinical and public health laboratories, thus facilitating a robust and rapid response to the next viral pandemic.

Indexed as

High-Throughput Nucleotide SequencingMetagenomicsRespiratory Tract InfectionsVirusesAdolescentAdultAgedBronchoalveolar Lavage FluidChildChild, PreschoolFemaleHumansMaleMiddle AgedSensitivity and SpecificityViral Load

Identifiers

PMID39532844
PMCPMC11558004

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.