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A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness

The lack of preparedness for detecting and responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen (i.e., COVID-19) has caused enormous harm to public health and the economy. Testing strategies deployed on a population scale at day zero, i.e., the time of the first re...

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Autores principales: Chan, Agnes P., Siddique, Azeem, Desplat, Yvain, Choi, Yongwook, Ranganathan, Sridhar, Choudhary, Kumari Sonal, Khalid, M. Faizan, Diaz, Josh, Bezney, Jon, DeAscanis, Dante, George, Zenas, Wong, Shukmei, Selleck, William, Bowers, Jolene, Zismann, Victoria, Reining, Lauren, Highlander, Sarah, Brown, Keith, Armstrong, Jon R., Hakak, Yaron, Schork, Nicholas J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10110940/
https://www.ncbi.nlm.nih.gov/pubmed/37323571
http://dx.doi.org/10.1016/j.crmeth.2023.100463
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author Chan, Agnes P.
Siddique, Azeem
Desplat, Yvain
Choi, Yongwook
Ranganathan, Sridhar
Choudhary, Kumari Sonal
Khalid, M. Faizan
Diaz, Josh
Bezney, Jon
DeAscanis, Dante
George, Zenas
Wong, Shukmei
Selleck, William
Bowers, Jolene
Zismann, Victoria
Reining, Lauren
Highlander, Sarah
Brown, Keith
Armstrong, Jon R.
Hakak, Yaron
Schork, Nicholas J.
author_facet Chan, Agnes P.
Siddique, Azeem
Desplat, Yvain
Choi, Yongwook
Ranganathan, Sridhar
Choudhary, Kumari Sonal
Khalid, M. Faizan
Diaz, Josh
Bezney, Jon
DeAscanis, Dante
George, Zenas
Wong, Shukmei
Selleck, William
Bowers, Jolene
Zismann, Victoria
Reining, Lauren
Highlander, Sarah
Brown, Keith
Armstrong, Jon R.
Hakak, Yaron
Schork, Nicholas J.
author_sort Chan, Agnes P.
collection PubMed
description The lack of preparedness for detecting and responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen (i.e., COVID-19) has caused enormous harm to public health and the economy. Testing strategies deployed on a population scale at day zero, i.e., the time of the first reported case, would be of significant value. Next-generation sequencing (NGS) has such capabilities; however, it has limited detection sensitivity for low-copy-number pathogens. Here, we leverage the CRISPR-Cas9 system to effectively remove abundant sequences not contributing to pathogen detection and show that NGS detection sensitivity of SARS-CoV-2 approaches that of RT-qPCR. The resulting sequence data can also be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single molecular and analysis workflow. This NGS work flow is pathogen agnostic and, therefore, has the potential to transform how large-scale pandemic response and focused clinical infectious disease testing are pursued in the future.
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spelling pubmed-101109402023-04-18 A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness Chan, Agnes P. Siddique, Azeem Desplat, Yvain Choi, Yongwook Ranganathan, Sridhar Choudhary, Kumari Sonal Khalid, M. Faizan Diaz, Josh Bezney, Jon DeAscanis, Dante George, Zenas Wong, Shukmei Selleck, William Bowers, Jolene Zismann, Victoria Reining, Lauren Highlander, Sarah Brown, Keith Armstrong, Jon R. Hakak, Yaron Schork, Nicholas J. Cell Rep Methods Article The lack of preparedness for detecting and responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen (i.e., COVID-19) has caused enormous harm to public health and the economy. Testing strategies deployed on a population scale at day zero, i.e., the time of the first reported case, would be of significant value. Next-generation sequencing (NGS) has such capabilities; however, it has limited detection sensitivity for low-copy-number pathogens. Here, we leverage the CRISPR-Cas9 system to effectively remove abundant sequences not contributing to pathogen detection and show that NGS detection sensitivity of SARS-CoV-2 approaches that of RT-qPCR. The resulting sequence data can also be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single molecular and analysis workflow. This NGS work flow is pathogen agnostic and, therefore, has the potential to transform how large-scale pandemic response and focused clinical infectious disease testing are pursued in the future. Elsevier 2023-04-18 /pmc/articles/PMC10110940/ /pubmed/37323571 http://dx.doi.org/10.1016/j.crmeth.2023.100463 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Chan, Agnes P.
Siddique, Azeem
Desplat, Yvain
Choi, Yongwook
Ranganathan, Sridhar
Choudhary, Kumari Sonal
Khalid, M. Faizan
Diaz, Josh
Bezney, Jon
DeAscanis, Dante
George, Zenas
Wong, Shukmei
Selleck, William
Bowers, Jolene
Zismann, Victoria
Reining, Lauren
Highlander, Sarah
Brown, Keith
Armstrong, Jon R.
Hakak, Yaron
Schork, Nicholas J.
A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness
title A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness
title_full A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness
title_fullStr A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness
title_full_unstemmed A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness
title_short A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness
title_sort crispr-enhanced metagenomic ngs test to improve pandemic preparedness
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10110940/
https://www.ncbi.nlm.nih.gov/pubmed/37323571
http://dx.doi.org/10.1016/j.crmeth.2023.100463
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