Dataset Information

An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing.

ABSTRACT: The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use-with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses.

SUBMITTER: Ramos-Mandujano G

PROVIDER: S-EPMC10663496 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing.

Ramos-Mandujano Gerardo G Grünberg Raik R Zhang Yingzi Y Bi Chongwei C Guzmán-Vega Francisco J FJ Shuaib Muhammad M Gorchakov Rodion V RV Xu Jinna J Tehseen Muhammad M Takahashi Masateru M Takahashi Etsuko E Dada Ashraf A Ahmad Adeel Nazir AN Hamdan Samir M SM Pain Arnab A Arold Stefan T ST Li Mo M

Scientific reports 20231121 1

The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which h ...[more]

PMID: 37990068

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Project description:BackgroundRemote monitoring of plants using hyperspectral imaging has become an important tool for the study of plant growth, development, and physiology. Many applications are oriented towards use in field environments to enable non-destructive analysis of crop responses due to factors such as drought, nutrient deficiency, and disease, e.g., using tram, drone, or airplane mounted instruments. The field setting introduces a wide range of uncontrolled environmental variables that make validation and interpretation of spectral responses challenging, and as such lab- and greenhouse-deployed systems for plant studies and phenotyping are of increasing interest. In this study, we have designed and developed an open-source, hyperspectral reflectance-based imaging system for lab-based plant experiments: the HyperScanner. The reliability and accuracy of HyperScanner were validated using drought and salt stress experiments with Arabidopsis thaliana.ResultsA robust, scalable, and reliable system was created. The system was built using open-sourced parts, and all custom parts, operational methods, and data have been made publicly available in order to maintain the open-source aim of HyperScanner. The gathered reflectance images showed changes in narrowband red and infrared reflectance spectra for each of the stress tests that was evident prior to other visual physiological responses and exhibited congruence with measurements using full-range contact spectrometers.ConclusionsHyperScanner offers the potential for reliable and inexpensive laboratory hyperspectral imaging systems. HyperScanner was able to quickly collect accurate reflectance curves on a variety of plant stress experiments. The resulting images showed spectral differences in plants shortly after application of a treatment but before visual manifestation. HyperScanner increases the capacity for spectroscopic and imaging-based analytical tools by providing more access to hyperspectral analyses in the laboratory setting.

Dataset Information

An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing.

Publications

An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing.

Similar Datasets

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