Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning

Lei, Zhengyang; Lian, Lijin; Zhang, Likun; Wei, Jiazhang; Liu, Changyue; Liu, Hong; Liu, Ying; Zhai, Shiyao; Zhong, Xiaoyun; Gul, Ijaz; Yuan, Xi; Dong, Yuhan; Zhang, Haihui; Wang, Chuhui; Zhang, Can Yang; Xing, Xin‐Hui; Yu, Dongmei; He, Qian; Qin, Peiwu

doi:10.1101/2022.08.22.504785

Cited by 3 publications

(3 citation statements)

References 85 publications

(87 reference statements)

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“…The sequences of synthetic DNA, oligos, crRNAs, and single‐stranded DNA (ssDNA) reporter (Table 1) were synthesized by Sangon Biotech, Shanghai Co., Ltd. EnGen® Lba ( Lachnospiraceae bacterium ) Cas12a (Cpf1) (cat‐M0653T) was obtained from New England Biolabs. UvsX (M105) and T4 GP32 (M104) were obtained from ATG Biotechnology Co., Ltd., while UvsY and Bsu were purified in our lab as described earlier 24 (for details, see Supporting Information Section 2.1). TwistAmp TM Basic Kit was procured from Morey Biosciences.…”

Section: Methodsmentioning

confidence: 99%

CRISPR–Cas12‐based field‐deployable system for rapid detection of synthetic DNA sequence of the monkeypox virus genome

Chen

Gul

Liu

et al. 2022

Journal of Medical Virology

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The global outbreak of the monkeypox virus (MPXV) highlights the need for rapid and cost‐effective MPXV detection tools to effectively monitor and control the monkeypox disease. Herein, we demonstrated a portable CRISPR–Cas‐based system for naked‐eye detection of MPXV. The system harnesses the high selectivity of CRISPR–Cas12 and the isothermal nucleic acid amplification potential of recombinase polymerase amplification. It can detect both the current circulating MPXV clade and the original clades. We reached a limit of detection (LoD) of 22.4 aM (13.5 copies/µl) using a microtiter plate reader, while the visual LoD of the system is 75 aM (45 copies/µl) in a two‐step assay, which is further reduced to 25 aM (15 copies/µl) in a one‐pot system. We compared our results with quantitative polymerase chain reaction and obtained satisfactory consistency. For clinical application, we demonstrated a sensitive and precise visual detection method with attomolar sensitivity and a sample‐to‐answer time of 35 min.

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Section: Methodsmentioning

confidence: 99%

CRISPR–Cas12‐based field‐deployable system for rapid detection of synthetic DNA sequence of the monkeypox virus genome

Chen

Gul

Liu

et al. 2022

Journal of Medical Virology

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“…Rapid and accurate detection of SARS-CoV-2 plays an important role in pandemic surveillance (Alexandersen et al, 2020). CRISPR-based diagnostics have been reported to have great potential for accurate and timely detection of various types of viruses, including Zika virus, human immunodeficiency virus, hepatitis C virus, Frog virus 3, and Ebola virus (Asboe et al, 2012;Pardee et al, 2016;Qin et al, 2019;Kham-Kjing et al, 2022;Lei et al, 2022). The CRISPR/Cas system is an innate bacterial adaptive immune system capable of degrading foreign nucleic acids that enter the host cell (Horvath and Barrangou 2010;Terns and Terns 2011).…”

mentioning

confidence: 99%

AI-boosted CRISPR-Cas13a and total internal reflection fluorescence microscopy system for SARS-CoV-2 detection

Zhang

Lei²,

Xiao³

et al. 2022

Front. Sens.

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Integrating artificial intelligence with SARS-CoV-2 diagnostics can help in the timely execution of pandemic control and monitoring plans. To improve the efficiency of the diagnostic process, this study aims to classify fluorescent images via traditional machine learning and deep learning-based transfer learning. A previous study reported a CRISPR-Cas13a system combined with total internal reflection fluorescence microscopy (TIRFM) to detect the existence and concentrations of SARS-CoV-2 by fluorescent images. However, the lack of professional software and excessive manual labor hinder the practicability of the system. Here, we construct a fluorescent image dataset and develop an AI-boosted CRISPR-Cas13a and total internal reflection fluorescence microscopy system for the rapid diagnosis of SARS-CoV-2. Our study proposes Fluorescent Images Classification Transfer learning based on DenseNet-121 (FICTransDense), an approach that uses TIRF images (before and after sample introduction, respectively) for preprocessing, including outlier exclusion and setting and division preprocessing (i.e., SDP). Classification results indicate that the FICTransDense and Decision Tree algorithms outperform other approaches on the SDP dataset. Most of the algorithms benefit from the proposed SDP technique in terms of Accuracy, Recall, F1 Score, and Precision. The use of AI-boosted CRISPR-Cas13a and TIRFM systems facilitates rapid monitoring and diagnosis of SARS-CoV-2.

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“…It is anticipated that the ACE2-based sensing modalities can be instrumental in developing point-of-care sensors to meet ASSURED criteria, and could be helpful in combating COVID-19 pandemic [ 165 , 166 ]. The detection approaches discussed in this manuscript have potential to be extended for diagnosis of other viruses such as the recently re-emerged monkeypox virus [ 167 ] and amphibian viruses [ 168 ].…”

Section: Discussionmentioning

confidence: 99%

Angiotensin-Converting Enzyme 2-Based Biosensing Modalities and Devices for Coronavirus Detection

et al. 2022

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Rapid and cost-effective diagnostic tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are a critical and valuable weapon for the coronavirus disease 2019 (COVID-19) pandemic response. SARS-CoV-2 invasion is primarily mediated by human angiotensin-converting enzyme 2 (hACE2). Recent developments in ACE2-based SARS-CoV-2 detection modalities accentuate the potential of this natural host-virus interaction for developing point-of-care (POC) COVID-19 diagnostic systems. Although research on harnessing ACE2 for SARS-CoV-2 detection is in its infancy, some interesting biosensing devices have been developed, showing the commercial viability of this intriguing new approach. The exquisite performance of the reported ACE2-based COVID-19 biosensors provides opportunities for researchers to develop rapid detection tools suitable for virus detection at points of entry, workplaces, or congregate scenarios in order to effectively implement pandemic control and management plans. However, to be considered as an emerging approach, the rationale for ACE2-based biosensing needs to be critically and comprehensively surveyed and discussed. Herein, we review the recent status of ACE2-based detection methods, the signal transduction principles in ACE2 biosensors and the development trend in the future. We discuss the challenges to development of ACE2-biosensors and delineate prospects for their use, along with recommended solutions and suggestions.

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Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning

Cited by 3 publications

References 85 publications

CRISPR–Cas12‐based field‐deployable system for rapid detection of synthetic DNA sequence of the monkeypox virus genome

CRISPR–Cas12‐based field‐deployable system for rapid detection of synthetic DNA sequence of the monkeypox virus genome

AI-boosted CRISPR-Cas13a and total internal reflection fluorescence microscopy system for SARS-CoV-2 detection

Angiotensin-Converting Enzyme 2-Based Biosensing Modalities and Devices for Coronavirus Detection

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