tetano
Editor, Senior Moderator
Nat Med
. 2022 Feb 7.
doi: 10.1038/s41591-022-01734-1. Online ahead of print.
Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
Nicole L Welch[SUP] 1 2 [/SUP], Meilin Zhu[SUP] 3 4 [/SUP], Catherine Hua[SUP] 3 5 [/SUP], Juliane Weller[SUP] 3 6 [/SUP], Marzieh Ezzaty Mirhashemi[SUP] 3 [/SUP], Tien G Nguyen[SUP] 3 [/SUP], Sreekar Mantena[SUP] 3 [/SUP], Matthew R Bauer[SUP] 3 7 [/SUP], Bennett M Shaw[SUP] 3 5 [/SUP], Cheri M Ackerman[SUP] 3 4 [/SUP], Sri Gowtham Thakku[SUP] 3 8 [/SUP], Megan W Tse[SUP] 3 4 [/SUP], Jared Kehe[SUP] 3 4 [/SUP], Marie-Martine Uwera[SUP] 3 [/SUP], Jacqueline S Eversley[SUP] 5 [/SUP], Derek A Bielwaski[SUP] 5 [/SUP], Graham McGrath[SUP] 5 [/SUP], Joseph Braidt[SUP] 5 [/SUP], Jeremy Johnson[SUP] 3 [/SUP], Felecia Cerrato[SUP] 3 [/SUP], Gage K Moreno[SUP] 3 [/SUP], Lydia A Krasilnikova[SUP] 3 9 [/SUP], Brittany A Petros[SUP] 3 8 10 11 [/SUP], Gabrielle L Gionet[SUP] 3 [/SUP], Ewa King[SUP] 11 [/SUP], Richard C Huard[SUP] 11 [/SUP], Samantha K Jalbert[SUP] 12 [/SUP], Michael L Cleary[SUP] 12 [/SUP], Nicholas A Fitzgerald[SUP] 3 [/SUP], Stacey B Gabriel[SUP] 3 [/SUP], Glen R Gallagher[SUP] 13 [/SUP], Sandra C Smole[SUP] 13 [/SUP], Lawrence C Madoff[SUP] 13 [/SUP], Catherine M Brown[SUP] 13 [/SUP], Matthew W Keller[SUP] 14 [/SUP], Malania M Wilson[SUP] 14 [/SUP], Marie K Kirby[SUP] 14 [/SUP], John R Barnes[SUP] 14 [/SUP], Daniel J Park[SUP] 3 [/SUP], Katherine J Siddle[SUP] 3 9 [/SUP], Christian T Happi[SUP] 3 15 16 [/SUP], Deborah T Hung[SUP] 3 17 [/SUP], Michael Springer[SUP] 10 12 [/SUP], Bronwyn L MacInnis[SUP] 3 18 [/SUP], Jacob E Lemieux[SUP] 3 5 [/SUP], Eric Rosenberg[SUP] 5 19 [/SUP], John A Branda[SUP] 19 [/SUP], Paul C Blainey[SUP] 3 4 20 [/SUP], Pardis C Sabeti[SUP] 21 22 23 24 25 [/SUP], Cameron Myhrvold[SUP] 26 [/SUP]
Affiliations
Abstract
The COVID-19 pandemic has demonstrated a clear need for high-throughput, multiplexed, and sensitive assays for detecting SARS-CoV-2 and other respiratory viruses as well as their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic CARMEN (mCARMEN), that combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel (RVP) to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens, with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.
. 2022 Feb 7.
doi: 10.1038/s41591-022-01734-1. Online ahead of print.
Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
Nicole L Welch[SUP] 1 2 [/SUP], Meilin Zhu[SUP] 3 4 [/SUP], Catherine Hua[SUP] 3 5 [/SUP], Juliane Weller[SUP] 3 6 [/SUP], Marzieh Ezzaty Mirhashemi[SUP] 3 [/SUP], Tien G Nguyen[SUP] 3 [/SUP], Sreekar Mantena[SUP] 3 [/SUP], Matthew R Bauer[SUP] 3 7 [/SUP], Bennett M Shaw[SUP] 3 5 [/SUP], Cheri M Ackerman[SUP] 3 4 [/SUP], Sri Gowtham Thakku[SUP] 3 8 [/SUP], Megan W Tse[SUP] 3 4 [/SUP], Jared Kehe[SUP] 3 4 [/SUP], Marie-Martine Uwera[SUP] 3 [/SUP], Jacqueline S Eversley[SUP] 5 [/SUP], Derek A Bielwaski[SUP] 5 [/SUP], Graham McGrath[SUP] 5 [/SUP], Joseph Braidt[SUP] 5 [/SUP], Jeremy Johnson[SUP] 3 [/SUP], Felecia Cerrato[SUP] 3 [/SUP], Gage K Moreno[SUP] 3 [/SUP], Lydia A Krasilnikova[SUP] 3 9 [/SUP], Brittany A Petros[SUP] 3 8 10 11 [/SUP], Gabrielle L Gionet[SUP] 3 [/SUP], Ewa King[SUP] 11 [/SUP], Richard C Huard[SUP] 11 [/SUP], Samantha K Jalbert[SUP] 12 [/SUP], Michael L Cleary[SUP] 12 [/SUP], Nicholas A Fitzgerald[SUP] 3 [/SUP], Stacey B Gabriel[SUP] 3 [/SUP], Glen R Gallagher[SUP] 13 [/SUP], Sandra C Smole[SUP] 13 [/SUP], Lawrence C Madoff[SUP] 13 [/SUP], Catherine M Brown[SUP] 13 [/SUP], Matthew W Keller[SUP] 14 [/SUP], Malania M Wilson[SUP] 14 [/SUP], Marie K Kirby[SUP] 14 [/SUP], John R Barnes[SUP] 14 [/SUP], Daniel J Park[SUP] 3 [/SUP], Katherine J Siddle[SUP] 3 9 [/SUP], Christian T Happi[SUP] 3 15 16 [/SUP], Deborah T Hung[SUP] 3 17 [/SUP], Michael Springer[SUP] 10 12 [/SUP], Bronwyn L MacInnis[SUP] 3 18 [/SUP], Jacob E Lemieux[SUP] 3 5 [/SUP], Eric Rosenberg[SUP] 5 19 [/SUP], John A Branda[SUP] 19 [/SUP], Paul C Blainey[SUP] 3 4 20 [/SUP], Pardis C Sabeti[SUP] 21 22 23 24 25 [/SUP], Cameron Myhrvold[SUP] 26 [/SUP]
Affiliations
- PMID: 35130561
- DOI: 10.1038/s41591-022-01734-1
Abstract
The COVID-19 pandemic has demonstrated a clear need for high-throughput, multiplexed, and sensitive assays for detecting SARS-CoV-2 and other respiratory viruses as well as their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic CARMEN (mCARMEN), that combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel (RVP) to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens, with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.