Single-strand RPA for rapid and sensitive detection of SARS-CoV-2 RNA

Kim, Youngeun; Yaseen, Adam; Kishi, Jocelyn Y.; Fan, Hong; Saka, Sinem K.; Sheng, Kuanwei; Gopalkrishnan, Nikhil; Schaus, Thomas E.; Yin, Peng

doi:10.1101/2020.08.17.20177006

Cited by 28 publications

(36 citation statements)

References 43 publications

(31 reference statements)

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“…Isothermal NAAT technologies include transcription-mediated amplification (TMA), nicking enzyme-assisted reaction (NEAR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and systems using clustered regularly interspaced short palindromic repeat (CRISPR)–CRISPR-associated (Cas) (CRISPR-Cas) systems. While most IAT methods have been applied to DNA, they can often be adapted to RNA amplification by adding an RT step (e.g., RT-LAMP and RT-RPA) ( 244 , 271 , 327 , 328 ). Other IATs were designed for the intent of RNA amplification (e.g., TMA).…”

Section: Laboratory Methods For the Detection Of Sars-cov-2mentioning

confidence: 99%

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

et al. 2021

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SUMMARY The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.

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Section: Laboratory Methods For the Detection Of Sars-cov-2mentioning

confidence: 99%

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

et al. 2021

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“…Single-strand recombinase polymerase amplification (ssRPA) allows rapid amplification of double-stranded DNA (dsDNA), conversion to single-stranded DNA (ssDNA), and sequence-specific, hybridization-based readout with a lateral flow dipstick. Initial experimentation of the proof of concept seems to be associated with a very high sensitivity in viral detection (Kim, Yaseen, et al 2020). Finally, Raman spectroscopy, a technology that is based on the principle of inelastic scattering of light, has been tested for the detection of SARS-CoV-2 viral RNA after it yielded interesting findings for other viral infections (92.5% sensitivity and 88.8% specificity) (Desai et al 2020).…”

Section: Point-of-care Technology For Salivary Diagnosis Of Covid-19mentioning

confidence: 99%

Diagnostic Salivary Tests for SARS-CoV-2

et al. 2020

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The diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection relies on the detection of viral RNA by real-time reverse transcription polymerase chain reaction (rRT-PCR) performed with respiratory specimens, especially nasopharyngeal swabs. However, this procedure requires specialized medical personnel, centralized laboratory facilities, and time to provide results (from several hours up to 1 d). In addition, there is a non-negligible risk of viral transmission for the operator who performs the procedure. For these reasons, several studies have suggested the use of other body fluids, including saliva, for the detection of SARS-CoV-2. The use of saliva as a diagnostic specimen has numerous advantages: it is easily self-collected by the patient with almost no discomfort, it does not require specialized health care personnel for its management, and it reduces the risks for the operator. In the past few months, several scientific papers, media, and companies have announced the development of new salivary tests to detect SARS-CoV-2 infection. Posterior oropharyngeal saliva should be distinguished from oral saliva, since the former is a part of respiratory secretions, while the latter is produced by the salivary glands, which are outside the respiratory tract. Saliva can be analyzed through standard (rRT-PCR) or rapid molecular biology tests (direct rRT-PCR without extraction), although, in a hospital setting, these procedures may be performed only in addition to nasopharyngeal swabs to minimize the incidence of false-negative results. Conversely, the promising role of saliva in the diagnosis of SARS-CoV-2 infection is highlighted by the emergence of point-of-care technologies and, most important, point-of-need devices. Indeed, these devices can be directly used in workplaces, airports, schools, cinemas, and shopping centers. An example is the recently described Rapid Salivary Test, an antigen test based on the lateral flow assay, which detects the presence of the virus by identifying the spike protein in the saliva within a few minutes.

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“…Examples of commercially available qRT-PCR test kits are the Xpert Xpress SARS-CoV-2 test 9 , CDC 2019-novel coronavirus Real-Time RT-PCR Diagnostic Panel 10 , ExProbeTM SARS-CoV-2 Testing Kit 11 , Abbott RealTime SARS-CoV-2 RT-PCR Kit 12 , PerkinElmer® New Coronavirus Nucleic Acid Detection Kit 13 , and TaqPath COVID-19 Combo Kit 14 . However, there are disadvantages with these methods as they are time-consuming, requiring a specialized laboratory setting with expensive instruments and trained personnel 15 .To overcome these drawbacks, various isothermal nucleic acid amplification assays such as recombinase polymerase amplification (RPA) 16 and loop-mediated isothermal amplification (LAMP) [17][18][19][20] , deoxyribonucleic acid (DNA) nanoscaffoldbased hybrid chain reaction 21 , and nucleic acid sequence-based amplification 22 , have been developed to overcome the need for sophisticated thermal cycling equipment associated with qRT-PCR.…”

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confidence: 99%

Rapid electrochemical detection of coronavirus SARS-CoV-2

et al. 2021

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Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-consuming and requires expensive instrumentation. Here, we report an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification (RCA) for rapid detection of SARS-CoV-2. The assay involves the hybridization of the RCA amplicons with probes that were functionalized with redox active labels that are detectable by an electrochemical biosensor. The one-step sandwich hybridization assay could detect as low as 1 copy/μL of N and S genes, in less than 2 h. Sensor evaluation with 106 clinical samples, including 41 SARS-CoV-2 positive and 9 samples positive for other respiratory viruses, gave a 100% concordance result with qRT-PCR, with complete correlation between the biosensor current signals and quantitation cycle (Cq) values. In summary, this biosensor could be used as an on-site, real-time diagnostic test for COVID-19.

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Single-strand RPA for rapid and sensitive detection of SARS-CoV-2 RNA

Cited by 28 publications

References 43 publications

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

Diagnostic Salivary Tests for SARS-CoV-2

Rapid electrochemical detection of coronavirus SARS-CoV-2

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