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

и другие.

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Май 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.

Язык: 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

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Ноя. 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.

Язык: Английский

Процитировано

10
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

и другие.

European Radiology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 18, 2024

Язык: Английский

Процитировано

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

и другие.

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Май 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.

Язык: Английский

Процитировано

0