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A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV-2

Brogan, Daniel J. and Chaverra-Rodriguez, Duverney and Lin, Calvin P. and Smidler, Andrea L. and Yang, Ting and Alcantara, Lenissa M. and Antoshechkin, Igor and Liu, Junru and Raban, Robyn R. and Belda-Ferre, Pedro and Knight, Rob and Komives, Elizabeth A. and Akbari, Omar S. (2020) A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV-2. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20201119-093121134

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Abstract

Since its first emergence from China in late 2019, the SARS-CoV-2 virus has spread globally despite unprecedented containment efforts, resulting in a catastrophic worldwide pandemic. Successful identification and isolation of infected individuals can drastically curtail virus spread and limit outbreaks. However, during the early stages of global transmission, point-of-care diagnostics were largely unavailable and continue to remain difficult to procure, greatly inhibiting public health efforts to mitigate spread. Furthermore, the most prevalent testing kits rely on reagent- and time-intensive protocols to detect viral RNA, preventing rapid and cost-effective diagnosis. Therefore the development of an extensive toolkit for point-of-care diagnostics that is expeditiously adaptable to new emerging pathogens is of critical public health importance. Recently, a number of novel CRISPR-based diagnostics have been developed to detect COVID-19. Herein, we outline the development of a CRISPR-based nucleic acid molecular diagnostic utilizing a Cas13d ribonuclease derived from Ruminococcus flavefaciens (CasRx) to detect SARS-CoV-2, an approach we term SENSR (Sensitive Enzymatic Nucleic-acid Sequence Reporter). We demonstrate SENSR robustly detects SARS-CoV-2 sequences in both synthetic and patient-derived samples by lateral flow and fluorescence, thus expanding the available point-of-care diagnostics to combat current and future pandemics.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.10.14.20212795DOIDiscussion Paper
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7587836/PubMed CentralDiscussion Paper
ORCID:
AuthorORCID
Chaverra-Rodriguez, Duverney0000-0001-8068-7436
Smidler, Andrea L.0000-0002-3281-1161
Antoshechkin, Igor0000-0002-9934-3040
Liu, Junru0000-0002-6198-8150
Raban, Robyn R.0000-0002-5648-6770
Belda-Ferre, Pedro0000-0001-6532-1161
Knight, Rob0000-0002-0975-9019
Komives, Elizabeth A.0000-0001-5264-3866
Akbari, Omar S.0000-0002-6853-9884
Additional Information:The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. This version posted October 20, 2020. We thank the SEARCH (San Diego Epidemiology And Research for COVID-19 Health) Alliance for providing clinical samples. This work was supported in part by UCSD Seed Funds for Emergent COVID-19 Related Research a Directors New Innovator award from NIH/NIAID (DP2 AI152071-01) and a DARPA Safe Genes Program Grant (HR0011-17-2-0047) awarded to O.S.A. and a Directors Pioneer award from NCCIH (DP1 AT010885) to R.K. and the UCSD Return to Learn program via the EXCITE (EXpedited COVID-19 IdenTification Environment) lab. Data Availability: All data is available in the manuscript. Competing Interest Statement: S.A. has a patent pending on this technology. All other authors declare no significant competing financial, professional, or personal interests that might have influenced the performance or presentation of the work described. Author Declarations: I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes. The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Human samples from patients were collected under University of California San Diego Human Research Protection Program protocol number 200470 for negatives (PI: Lauge Farnaes) and under a waiver of consent from clinical samples from San Diego County for positives (PI: Kristian Andersen) as part of the SEARCH Alliance activities. Samples were de-identified as required by these protocols prior to testing and analysis under University of California San Diego Biological Use Authorization protocols R1806 and 2401. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes. I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes. I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes.
Group:COVID-19
Funders:
Funding AgencyGrant Number
University of California, San DiegoUNSPECIFIED
NIHDP2 AI152071-01
Defense Advanced Research Projects Agency (DARPA)HR0011-17-2-0047
NIHDP1 AT010885
PubMed Central ID:PMC7587836
Record Number:CaltechAUTHORS:20201119-093121134
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20201119-093121134
Official Citation:A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV-2. Daniel J Brogan, Duverney Chaverra-Rodriguez, Calvin P Lin, Andrea L Smidler, Ting Yang, Lenissa M. Alcantara, Igor Antoshechkin, Junru Liu, Robyn R Raban, Pedro Belda-Ferre, Rob Knight, Elizabeth A Komives, Omar S. Akbari. medRxiv 2020.10.14.20212795; doi: https://doi.org/10.1101/2020.10.14.20212795
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106734
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:19 Nov 2020 19:11
Last Modified:02 Feb 2021 22:39

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