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  1. Article: Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13.

    Arizti-Sanz, Jon / Bradley, A'Doriann / Zhang, Yibin B / Boehm, Chloe K / Freije, Catherine A / Grunberg, Michelle E / Kosoko-Thoroddsen, Tinna-Solveig F / Welch, Nicole L / Pillai, Priya P / Mantena, Sreekar / Kim, Gaeun / Uwanibe, Jessica N / John, Oluwagboadurami G / Eromon, Philomena E / Kocher, Gregory / Gross, Robin / Lee, Justin S / Hensley, Lisa E / Happi, Christian T /
    Johnson, Jeremy / Sabeti, Pardis C / Myhrvold, Cameron

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a ... ...

    Abstract The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a Cas13-based nucleic acid diagnostic that combines quick and ambient temperature sample processing and lyophilized reagents to greatly simplify the test procedure and assay distribution. We benchmarked a SHINEv2 assay for SARS-CoV-2 detection against state-of-the-art antigen-capture tests using 96 patient samples, demonstrating 50-fold greater sensitivity and 100% specificity. We designed SHINEv2 assays for discriminating the Alpha, Beta, Gamma and Delta VOCs, which can be read out visually using lateral flow technology. We further demonstrate that our assays can be performed without any equipment in less than 90 minutes. SHINEv2 represents an important advance towards rapid nucleic acid tests that can be performed in any location.
    Language English
    Publishing date 2021-11-02
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.11.01.21265764
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants.

    Arizti-Sanz, Jon / Bradley, A'Doriann / Zhang, Yibin B / Boehm, Chloe K / Freije, Catherine A / Grunberg, Michelle E / Kosoko-Thoroddsen, Tinna-Solveig F / Welch, Nicole L / Pillai, Priya P / Mantena, Sreekar / Kim, Gaeun / Uwanibe, Jessica N / John, Oluwagboadurami G / Eromon, Philomena E / Kocher, Gregory / Gross, Robin / Lee, Justin S / Hensley, Lisa E / MacInnis, Bronwyn L /
    Johnson, Jeremy / Springer, Michael / Happi, Christian T / Sabeti, Pardis C / Myhrvold, Cameron

    Nature biomedical engineering

    2022  Volume 6, Issue 8, Page(s) 932–943

    Abstract: The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and ... ...

    Abstract The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
    MeSH term(s) COVID-19/diagnosis ; COVID-19/virology ; COVID-19 Testing ; CRISPR-Associated Proteins ; Humans ; Nucleic Acids ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification
    Chemical Substances CRISPR-Associated Proteins ; Nucleic Acids
    Language English
    Publishing date 2022-05-30
    Publishing country England
    Document type Journal Article
    ISSN 2157-846X
    ISSN (online) 2157-846X
    DOI 10.1038/s41551-022-00889-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2.

    Arizti-Sanz, Jon / Freije, Catherine A / Stanton, Alexandra C / Boehm, Chloe K / Petros, Brittany A / Siddiqui, Sameed / Shaw, Bennett M / Adams, Gordon / Kosoko-Thoroddsen, Tinna-Solveig F / Kemball, Molly E / Gross, Robin / Wronka, Loni / Caviness, Katie / Hensley, Lisa E / Bergman, Nicholas H / MacInnis, Bronwyn L / Lemieux, Jacob E / Sabeti, Pardis C / Myhrvold, Cameron

    bioRxiv : the preprint server for biology

    2020  

    Abstract: The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (SHERLOCK and HUDSON Integration to Navigate Epidemics), a sensitive and specific integrated diagnostic tool ...

    Abstract The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (SHERLOCK and HUDSON Integration to Navigate Epidemics), a sensitive and specific integrated diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We combine the steps of SHERLOCK into a single-step reaction and optimize HUDSON to accelerate viral inactivation in nasopharyngeal swabs and saliva. SHINE's results can be visualized with an in-tube fluorescent readout - reducing contamination risk as amplification reaction tubes remain sealed - and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-PCR with a sample-to-answer time of 50 minutes. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.
    Keywords covid19
    Language English
    Publishing date 2020-05-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.05.28.119131
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13

    Arizti-Sanz, Jon / Bradley, A'Doriann / Zhang, Yibin B. / Boehm, Chloe K. / Freije, Catherine A. / Grunberg, Michelle E. / Kosoko-Thoroddsen, Tinna-Solveig F. / Welch, Nicole L. / Pillai, Priya P. / Mantena, Sreekar / Kim, Gaeun / Uwanibe, Jessica N. / John, Oluwagboadurami G. / Eromon, Philomena E. / Kocher, Gregory / Gross, Robin / Lee, Justin S. / Hensley, Lisa E. / Happi, Christian /
    Johnson, Jeremy / Sabeti, Pardis / Myhrvold, Cameron

    medRxiv

    Abstract: The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a ... ...

    Abstract The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a Cas13-based nucleic acid diagnostic that combines quick and ambient temperature sample processing and lyophilized reagents to greatly simplify the test procedure and assay distribution. We benchmarked a SHINEv2 assay for SARS-CoV-2 detection against state-of-the-art antigen-capture tests using 96 patient samples, demonstrating 50-fold greater sensitivity and 100% specificity. We designed SHINEv2 assays for discriminating the Alpha, Beta, Gamma and Delta VOCs, which can be read out visually using lateral flow technology. We further demonstrate that our assays can be performed without any equipment in less than 90 minutes. SHINEv2 represents an important advance towards rapid nucleic acid tests that can be performed in any location.
    Keywords covid19
    Language English
    Publishing date 2021-11-02
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.11.01.21265764
    Database COVID19

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  5. Article ; Online: Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2.

    Arizti-Sanz, Jon / Freije, Catherine A / Stanton, Alexandra C / Petros, Brittany A / Boehm, Chloe K / Siddiqui, Sameed / Shaw, Bennett M / Adams, Gordon / Kosoko-Thoroddsen, Tinna-Solveig F / Kemball, Molly E / Uwanibe, Jessica N / Ajogbasile, Fehintola V / Eromon, Philomena E / Gross, Robin / Wronka, Loni / Caviness, Katie / Hensley, Lisa E / Bergman, Nicholas H / MacInnis, Bronwyn L /
    Happi, Christian T / Lemieux, Jacob E / Sabeti, Pardis C / Myhrvold, Cameron

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 5921

    Abstract: The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool ... ...

    Abstract The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE's results can be visualized with an in-tube fluorescent readout - reducing contamination risk as amplification reaction tubes remain sealed - and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.
    MeSH term(s) Betacoronavirus/isolation & purification ; Biological Assay ; COVID-19 ; CRISPR-Associated Proteins/metabolism ; Coronavirus Infections/diagnosis ; Coronavirus Infections/virology ; Fluorescence ; Humans ; Molecular Diagnostic Techniques/methods ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/virology ; SARS-CoV-2
    Chemical Substances CRISPR-Associated Proteins
    Language English
    Publishing date 2020-11-20
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-19097-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2

    Jon Arizti-Sanz / Catherine A. Freije / Alexandra C. Stanton / Brittany A. Petros / Chloe K. Boehm / Sameed Siddiqui / Bennett M. Shaw / Gordon Adams / Tinna-Solveig F. Kosoko-Thoroddsen / Molly E. Kemball / Jessica N. Uwanibe / Fehintola V. Ajogbasile / Philomena E. Eromon / Robin Gross / Loni Wronka / Katie Caviness / Lisa E. Hensley / Nicholas H. Bergman / Bronwyn L. MacInnis /
    Christian T. Happi / Jacob E. Lemieux / Pardis C. Sabeti / Cameron Myhrvold

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 9

    Abstract: The COVID-19 pandemic has highlighted the need for user-friendly diagnostic techniques. Here, the authors present SHINE, a streamlined and optimised Cas13-based method with accompanying smartphone app for visual diagnosis. ...

    Abstract The COVID-19 pandemic has highlighted the need for user-friendly diagnostic techniques. Here, the authors present SHINE, a streamlined and optimised Cas13-based method with accompanying smartphone app for visual diagnosis.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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