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Validation of an automated, end-to-end metagenomic sequencing assay for agnostic detection of respiratory viruses.
Gauthier, Nick P G; Chan, Wilson; Locher, Kerstin; Smailus, Duane; Coope, Robin; Charles, Marthe; Jassem, Agatha; Kopetzky, Jennifer; Chorlton, Samuel D; Manges, Amee R.
Afiliación
  • Gauthier NPG; Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
  • Chan W; School of Population and Public Health, University of British Columbia, Vancouver, British Columbia.
  • Locher K; Division of Medical Microbiology, Vancouver General Hospital, Vancouver, British Columbia, Canada.
  • Smailus D; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
  • Coope R; Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada.
  • Charles M; Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada.
  • Jassem A; Division of Medical Microbiology, Vancouver General Hospital, Vancouver, British Columbia, Canada.
  • Kopetzky J; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
  • Chorlton SD; British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
  • Manges AR; British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
J Infect Dis ; 2024 May 02.
Article en En | MEDLINE | ID: mdl-38696336
ABSTRACT

BACKGROUND:

Current molecular diagnostics are limited in the number and type of detectable pathogens. Metagenomic next generation sequencing (mNGS) is an emerging, and increasingly feasible, pathogen-agnostic diagnostic approach. Translational barriers prohibit the widespread adoption of this technology in clinical laboratories. We validate an end-to-end mNGS assay for detection of respiratory viruses. Our assay is optimized to reduce turnaround time, lower cost-per-sample, increase throughput, and deploy secure and actionable bioinformatic results.

METHODS:

We validated our assay using residual nasopharyngeal swab specimens from Vancouver General Hospital (n = 359), RT-PCR-positive, or negative for Influenza, SARS-CoV-2, and RSV. We quantified sample stability, assay precision, the effect of background nucleic acid levels, and analytical limits of detection. Diagnostic performance metrics were estimated.

RESULTS:

We report that our mNGS assay is highly precise, semi-quantitative, with analytical limits of detection ranging from 103-104 copies/mL. Our assay is highly specific (100%) and sensitive (61.9% Overall 86.8%; RT-PCR Ct < 30). Multiplexing capabilities enable processing of up to 55-specimens simultaneously on an Oxford Nanopore GridION device, with results reported within 12-hours.

CONCLUSIONS:

This study outlines the diagnostic performance and feasibility of mNGS for respiratory viral diagnostics, infection control, and public health surveillance. We addressed translational barriers to widespread mNGS adoption.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: J Infect Dis Año: 2024 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: J Infect Dis Año: 2024 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Estados Unidos