Rapid detection of novel coronavirus SARS-CoV-2 by RT-LAMP coupled solid-state nanopores

Tang, Zifan; Nouri, Reza; Dong, Ming; Yang, Jianbo; Greene, Wallace; Zhu, Yusheng; Yon, Michele; Nair, Meera Surendran; Kuchipudi, Suresh V.; Guan, Weihua

doi:10.1016/j.bios.2021.113759

Cited by 24 publications

(24 citation statements)

References 36 publications

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“…Comparing our results on sensitivity, specificity, PPV and NPV with those obtained in previous studies, we found that the specificity and PPV values of the RT-LAMP-CRISPR-Cas13a technology were higher than those from 7 out of 10 RT-LAMP papers reviewed [19][20][21][22][23][24][25] and in one case the sensitivity of the novel technique was even higher [18]. Moreover, this technique showed higher sensitivity and NPV values than those from 2 out of 10 RT-LAMP-CRISPR papers reviewed which applied RNA extraction kit on the clinical samples [33,35].…”

Section: Discussionsupporting

confidence: 74%

“…First, we conducted a search in PubMed with "qPCR diagnosis COVID19" as keywords and compared the output with the number of publications on RT-LAMP and RT-LAMP-CRISPR strategies for COVID-19 diagnosis [15]. Finally, we collected data on the different sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) from 10 papers related to RT-LAMP and 10 papers on the RT-LAMP-CRISPR-Cas COVID19 diagnostic technique [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35]. We used the results to calculate the parameters needed for the comparison.…”

Section: Study Of the State Of The Artmentioning

confidence: 99%

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RT-LAMP-CRISPR-Cas13a technology as a promising diagnostic tool for the SARS-CoV-2 virus

Ortiz-Cartagena

Fernández‐García

Blasco

et al. 2022

Preprint

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At the end of 2019, the new coronavirus, SARS-CoV-2, began a pandemic that persists to date and which has caused more than 6.2 million deaths. In the last couple of years, researchers have made great efforts to develop a diagnostic technique that maintains high levels of sensitivity and specificity, since an accurate and early diagnosis is required to minimize the prevalence of SARS-CoV-2 infection. In this context, CRISPR-Cas systems are proposed as promising tools for development in diagnostic techniques due to their high specificity, highlighting that Cas13 endonuclease discriminates single nucleotide changes and displays a collateral activity against single stranded RNA molecules. With the aim of improve the sensitivity of the diagnosis, this technology is usually combined with isothermal pre-amplification reactions (SHERLOCK, DETECTR). Basing on this, we have developed an RT-LAMP-CRISPR-Cas13a for SARS-CoV-2 virus detection in nasopharyngeal samples without using RNA extraction kit that exhibited 100 % specificity and 83 % sensitivity, as well as a positive predictive value of 100 % and a negative predictive value of 100%, 81%, 79.1% and 66.7 % in <20 Ct, 20-30 Ct, >30 Ct and total Ct values, respectively.

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Section: Discussionsupporting

confidence: 74%

Section: Study Of the State Of The Artmentioning

confidence: 99%

RT-LAMP-CRISPR-Cas13a technology as a promising diagnostic tool for the SARS-CoV-2 virus

Ortiz-Cartagena

Fernández‐García

Blasco

et al. 2022

Preprint

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“…The integration of the CRISPR-Cas12a and nucleic acid amplification techniques has been proved by several works. 22,60,63–65 These results demonstrated that our nanopore sensor using a DNA tetrahedron as a signal transducer based on the CRISPR-Cas12a conversion mechanism could detect targets specifically, which we believe could become a promising alternative to biomolecular detection.…”

Section: Resultsmentioning

confidence: 74%

Detection of small-sized DNA fragments in a glassy nanopore by utilization of CRISPR-Cas12a as a converter system

Zhang

Liu

Cui

et al. 2022

Analyst

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“…After dispensing the sample, the real-time RT-LAMP reaction starts at a constant temperature of ∼64 °C. 41 The acquired fluorescence data are transmitted to the smartphone app every 5 s. The threshold to distinguish the positive from the negative was set at 50 RFU based on the no template control (NTC) samples tested ( Supporting Information Figure S5 ). We classify a sample as positive only when two out of three reactions have a higher RFU than the threshold value in 30 min.…”

Section: Resultsmentioning

confidence: 99%

“…After validating all of the subsystems and system integration, we went out to test the performance of the SLIDE. Here, we used our previously validated SARS-CoV-2 RT-LAMP primer set 41 ( Supporting Information Table S1 ) against the highly conserved N region with a modified fluorescent concentration of SYTO9 ( Supporting Information Table S2 ). We formed mock SARS-CoV-2 positive samples by spiking the healthy saliva with different concentrations of heat-inactivated SARS-CoV-2 virus particles.…”

Section: Resultsmentioning

confidence: 99%

SLIDE: Saliva-Based SARS-CoV-2 Self-Testing with RT-LAMP in a Mobile Device

et al. 2022

Self Cite

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Regular, accurate, rapid, and inexpensive self-testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is urgently needed to quell pandemic propagation. The existing at-home nucleic acid testing (NAT) test has high sensitivity and specificity, but it requires users to mail the sample to the central lab, which often takes 3–5 days to obtain the results. On the other hand, rapid antigen tests for the SARS-CoV-2 antigen provide a fast sample to answer the test (15 min). However, the sensitivity of antigen tests is 30 to 40% lower than nucleic acid testing, which could miss a significant portion of infected patients. Here, we developed a fully integrated SARS-CoV-2 reverse transcription loop-mediated isothermal amplification (RT-LAMP) device using a self-collected saliva sample. This platform can automatically handle the complexity and can perform the functions, including (1) virus particles’ thermal lysis preparation, (2) sample dispensing, (3) target sequence RT-LAMP amplification, (4) real-time detection, and (5) result report and communication. With a turnaround time of less than 45 min, our device achieved the limit of detection (LoD) of 5 copies/μL of the saliva sample, which is comparable with the LoD (6 copies/μL) using FDA-approved quantitative real-time polymerase chain reaction (qRT-PCR) assays with the same heat-lysis saliva sample preparation method. With clinical samples, our platform showed a good agreement with the results from the gold-standard RT-PCR method. These results show that our platform can perform self-administrated SARS-CoV-2 nucleic acid testing by laypersons with noninvasive saliva samples. We believe that our self-testing platform will have an ongoing benefit for COVID-19 control and fighting future pandemics.

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Rapid detection of novel coronavirus SARS-CoV-2 by RT-LAMP coupled solid-state nanopores

Cited by 24 publications

References 36 publications

RT-LAMP-CRISPR-Cas13a technology as a promising diagnostic tool for the SARS-CoV-2 virus

RT-LAMP-CRISPR-Cas13a technology as a promising diagnostic tool for the SARS-CoV-2 virus

Detection of small-sized DNA fragments in a glassy nanopore by utilization of CRISPR-Cas12a as a converter system

SLIDE: Saliva-Based SARS-CoV-2 Self-Testing with RT-LAMP in a Mobile Device

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