A rapid, accurate, scalable, and portable testing system for COVID-19 diagnosis.
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ABSTRACT:
SUBMITTER: Xun G
PROVIDER: S-EPMC8131735 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Combating the ongoing coronavirus disease 2019 (COVID-19) pandemic demands accurate, rapid, and point-of-care testing with fast results to triage cases for isolation and treatment. The current testing relies on reverse transcriptase PCR (RT-PCR), which is routinely performed in well-equipped laboratories by trained professionals at specific locations. However, during busy periods, high numbers of samples queued for testing can delay the test results, impacting efforts to reduce the infection risk. Besides, the absence of well-established laboratories at remote sites and low-resourced environments can contribute to a silent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These reasons compel the need to accommodate point-of-care testing for COVID-19 that meets the ASSURED criteria (affordable, sensitive, specific, user-friendly, rapid and robust, equipment-free, and deliverable). This study assessed the agreement and accuracy of the portable Biomeme SARS-CoV-2 system against the gold standard tests. Nasopharyngeal and nasal swabs were used. Of the 192 samples tested using the Biomeme SARS-CoV-2 system, the results from 189 samples (98.4%) were in agreement with the reference standard-of-care RT-PCR testing for SARS-CoV-2. The portable system generated simultaneous results for nine samples in 80 min with high positive and negative percent agreements of 99.0% and 97.8%, respectively. We performed separate testing in a sealed glove box, offering complete biosafety containment. Thus, the Biomeme SARS-CoV-2 system can help decentralize COVID-19 testing and offer rapid test results for patients in remote and low-resourced settings.
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Project description:Rapid and sensitive detection of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for early diagnosis and effective treatment. Nucleic acid testing has been considered the gold standard method for the diagnosis of COVID-19 for its high sensitivity and specificity. However, the polymerase chain reaction (PCR)-based method in the central lab requires expensive equipment and well-trained personnel, which makes it difficult to be used in resource-limited settings. It highlights the need for a sensitive and simple assay that allows potential patients to detect SARS-CoV-2 by themselves. Here, we developed an electricity-free self-testing system based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) that allows for rapid and accurate detection of SARS-CoV-2. Our system employs a heating bag as the heat source, and a 3D-printed box filled with phase change material (PCM) that successfully regulates the temperature for the RT-LAMP. The colorimetric method could be completed in 40 min and the results could be read out by the naked eye. A ratiometric measurement for exact readout was also incorporated to improve the detection accuracy of the system. This self-testing system is a promising tool for point-of-care testing (POCT) that enables rapid and sensitive diagnosis of SARS-CoV-2 in the real world and will improve the current COVID-19 screening efforts for control and mitigation of the pandemic.
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Project description:Prompt diagnosis, patient isolation, and contact tracing are key measures to contain the coronavirus disease 2019 (COVID-19). Molecular tests are the current gold standard for COVID-19 detection, but are carried out at central laboratories, delaying treatment and control decisions. Here we describe a portable assay system for rapid, onsite COVID-19 diagnosis. Termed CODA (CRISPR Optical Detection of Anisotropy), the method combined isothermal nucleic acid amplification, activation of CRISPR/Cas12a, and signal generation in a single assay, eliminating extra manual steps. Importantly, signal detection was based on the ratiometric measurement of fluorescent anisotropy, which allowed CODA to achieve a high signal-to-noise ratio. For point-of-care operation, we built a compact, standalone CODA device integrating optoelectronics, an embedded heater, and a microcontroller for data processing. The developed system completed SARS-CoV-2 RNA detection within 20 min of sample loading; the limit of detection reached 3 copy/μL. When applied to clinical samples (10 confirmed COVID-19 patients; 10 controls), the rapid CODA test accurately classified COVID-19 status, in concordance with gold-standard clinical diagnostics.
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Project description:We herein describe rapid and accurate clinical testing for COVID-19 by nicking and extension chain reaction system-based amplification (NESBA), an ultrasensitive version of NASBA. The primers to identify SARS-CoV-2 viral RNA were designed to additionally contain the nicking recognition sequence at the 5'-end of conventional NASBA primers, which would enable nicking enzyme-aided exponential amplification of T7 RNA promoter-containing double-stranded DNA (T7DNA). As a consequence of this substantially enhanced amplification power, the NESBA technique was able to ultrasensitively detect SARS-CoV-2 genomic RNA (gRNA) down to 0.5 copies/μL (= 10 copies/reaction) for both envelope (E) and nucleocapsid (N) genes within 30 min under isothermal temperature (41 °C). When the NESBA was applied to test a large cohort of clinical samples (n = 98), the results fully agreed with those from qRT-PCR and showed the excellent accuracy by yielding 100% clinical sensitivity and specificity. By employing multiple molecular beacons with different fluorophore labels, the NESBA was further modulated to achieve multiplex molecular diagnostics, so that the E and N genes of SARS-CoV-2 gRNA were simultaneously assayed in one-pot. By offering the superior analytical performances over the current qRT-PCR, the isothermal NESBA technique could serve as very powerful platform technology to realize the point-of-care (POC) diagnosis for COVID-19.
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Project description:Rapid detection of DNA/RNA pathogenic sequences or variants through point-of-care diagnostics is valuable for accelerated clinical prognosis, as witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are tough to implement with limited resources, necessitating the development of accurate and robust alternative strategies. Here, we report FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that utilizes a direct Cas9 based enzymatic readout for detecting nucleobase and nucleotide sequences without trans-cleavage of reporter molecules. We also demonstrate that FELUDA is 100% accurate in detecting single nucleotide variants (SNVs), including heterozygous carriers, and present a simple web-tool JATAYU to aid end-users. FELUDA is semi-quantitative, can adapt to multiple signal detection platforms, and deploy for versatile applications such as molecular diagnosis during infectious disease outbreaks like COVID-19. Employing a lateral flow readout, FELUDA shows 100% sensitivity and 97% specificity across all ranges of viral loads in clinical samples within 1hr. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection closer to home.
| S-EPMC8020606 | biostudies-literature
Project description:Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread and caused a severe global pandemic. Because no specific drugs are available for COVID-19 and few vaccines are available for SARS-CoV-2, accurate and rapid diagnosis of COVID-19 has been the most crucial measure to control this pandemic. Here, we developed a portable bifunctional electrical detector based on graphene fieldeffect transistors for SARS-CoV-2 through either nucleic acid hybridization or antigen-antibody protein interaction, with ultra-low limits of detection of ~0.1 and ~1 fg mL-1 in phosphate buffer saline, respectively. We validated our method by assessment of RNA extracts from the oropharyngeal swabs of ten COVID-19 patients and eight healthy subjects, and the IgM/IgG antibodies from serum specimens of six COVID-19 patients and three healthy subjects. Here we show that the diagnostic results are in excellent agreement with the findings of polymerase chain reaction-based optical methods; they also exhibit rapid detection speed (~10 min for nucleic acid detection and ~5 min for immunoassay). Therefore, our assay provides an efficient, accurate tool for high-throughput point-of-care testing.Electronic supplementary materialSupplementary material is available in the online version of this article at 10.1007/s40843-020-1577-y.
| S-EPMC7852050 | biostudies-literature
Project description:Sensitive detection of SARS-CoV-2 is of great importance for inhibiting the current pandemic of COVID-19. Here, we report a simple yet efficient platform integrating a portable and low-cost custom-made detector and a novel microwell array biochip for rapid and accurate detection of SARS-CoV-2. The instrument exhibits expedited amplification speed that enables colorimetric read-out within 25 minutes. A polymeric chip with a laser-engraved microwell array was developed to process the reaction between the primers and the respiratory swab RNA extracts, based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP). To achieve clinically acceptable performance, we synthesized a group of six primers to identify the conserved regions of the ORF1ab gene of SARS-CoV-2. Clinical trials were conducted with 87 PCR-positive and 43 PCR-negative patient samples. The platform demonstrated both high sensitivity (95.40%) and high specificity (95.35%), showing potentials for rapid and user-friendly diagnosis of COVID-19 among many other infectious pathogens.
| S-EPMC7982056 | biostudies-literature
Project description:Effective containment of the COVID-19 pandemic requires rapid and accurate detection of the pathogen. Polymerase chain reaction (PCR) remains the gold standard for COVID-19 confirmation. In this article, we report the performance of a cost-effective modular microfluidic reverse transcription (RT)-PCR and RT-loop mediated isothermal amplification (RT-LAMP) platform, Epidax®, for the point-of-care testing and confirmation of SARS-CoV-2. This platform is versatile and can be reconfigured either for screening using endpoint RT-PCR or RT-LAMP tests or for confirmatory tests using real-time RT-PCR. Epidax® is highly sensitive and detects as little as 1 RNA copy per µL for real-time and endpoint RT-PCR, while using only half of the reagents. We achieved comparable results with those of a commercial platform when detecting SARS-CoV-2 viruses from 81 clinical RNA extracts. Epidax® can also detect SARS-CoV-2 from 44 nasopharyngeal samples without RNA extraction by using a direct RT-PCR assay, which shortens the sample-to-answer time to an hour with minimal user steps. Furthermore, we validated the technology using an RT-LAMP assay on 54 clinical RNA extracts. Overall, our platform provides a sensitive, cost-effective, and accurate diagnostic solution for low-resource settings.
| S-EPMC9294789 | biostudies-literature
Project description:The transmission of coronavirus disease 2019 (COVID-19) in workplaces has been a persistent issue throughout the pandemic. In response, a not-for-profit initiative emerged to mitigate COVID-19 workplace transmission in Canada. We report the process for establishing a workplace frequent rapid antigen test (RAT) program. The screening program identified 473 asymptomatic individuals who tested positive on the RAT and confirmed positive by a nasopharyngeal polymerase chain reaction (PCR) diagnostic test. One in 4300 RATs was presumptive positive but later tested PCR negative, and thus, false positives did not meaningfully disrupt workplace operations. Most employers rated the program highly and felt strongly that the program contributed to workplace and community safety. The findings describe a sustained and scalable implementation plan for establishing a frequent workplace testing program. High-frequency testing programs offer the potential to break chains of transmission and act as an extra layer of protection in a comprehensive public health response.
| S-EPMC8880770 | biostudies-literature
Project description:Objectives:In this pandemic situation caused by a novel coronavirus disease in 2019 (COVID-19), an electronic support system that can rapidly and accurately perform epidemic investigations, is needed. It would systematically secure and analyze patients' data (who have been confirmed to have the infection), location information, and credit card usage. Methods:The "Infectious Disease Prevention and Control Act" in South Korea, established a legal basis for the securement, handling procedure, and disclosure of information required for epidemic investigations. The Epidemic Investigation Support System (EISS) was developed as an application platform on the Smart City data platform. Results:The EISS performed the function of inter-institutional communication which reduced the processing period of patients' data in comparison to other methods. This system automatically marked confirmed cases' tracking data on a map and hot-spot analysis which lead to the prediction of areas where people may be vulnerable to infection. Conclusion:The EISS was designed and implemented for use during an epidemic investigation to prevent the spread of an infectious disease, by specifically tracking confirmed cases of infection.
| S-EPMC7282422 | biostudies-literature