Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery DOI Creative Commons
Charles Y. Chiu,

Jessica Tan,

Venice Servellita

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: May 31, 2024

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

Language: Английский

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

Jessica Karielle Tan,

Venice Servellita,

Doug Stryke

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 12, 2024

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

Language: Английский

Citations

8
Exploring the changing landscape of medical imaging: insights from highly cited studies before and during the COVID-19 pandemic DOI

Peiling Ou,

Ru Wen, Lihua Deng

et al.

European Radiology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 18, 2024

Language: Английский

Citations

1
Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery DOI Creative Commons
Charles Y. Chiu,

Jessica Tan,

Venice Servellita

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: May 31, 2024

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

Language: Английский

Citations

0