1
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Pang B, Reid MS, Wei J, Peng H, Bu L, Li J, Zhang H, Le XC. Protein-Induced DNA Dumbbell Amplification (PINDA) and its applications to food hazards detection. Biosens Bioelectron 2024; 266:116720. [PMID: 39241338 DOI: 10.1016/j.bios.2024.116720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/25/2024] [Accepted: 08/27/2024] [Indexed: 09/09/2024]
Abstract
Quantification of trace amounts of proteins is technically challenging because proteins cannot be directly amplified like nucleic acids. To improve the analytical sensitivity and to complement conventional protein analysis methods, we developed a highly sensitive and homogeneous detection strategy called Protein-Induced DNA Dumbbell Amplification (PINDA). PINDA combines protein recognition with exponential nucleic acid amplification by using protein binding probes made of DNA strands conjugated to protein affinity ligands. When a pair of probes bind to the same target protein, complementary nucleic acid sequences that are conjugated to each probe are brought into close proximity. The increased local concentration of the probes results in the formation of a stable dumbbell structure of the nucleic acids. The DNA dumbbell is readily amplifiable exponentially using techniques such as loop-mediated isothermal amplification. The PINDA assay eliminates the need for washing or separation steps, and is suitable for on-site applications. Detection of the model protein, thrombin, has a linear range of 10 fM-100 pM and detection limit of 10 fM. The PINDA technique is successfully applied to the analysis of dairy samples for the detection of β-lactoglobulin, a common food allergen, and Salmonella enteritidis, a foodborne pathogenic bacterium. The PINDA assay can be easily modified to detect other targets by changing the affinity ligands used to bind to the specific targets.
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Affiliation(s)
- Bo Pang
- School of Public Health, Jilin University, Changchun, 130021, PR China; Division of Analytical and Environmental Toxicology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, Alberta, T6G 2G3, Canada
| | - Michael S Reid
- Division of Analytical and Environmental Toxicology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, Alberta, T6G 2G3, Canada; Alberta Precision Laboratories and Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, T2L 2K8, Canada
| | - Jia Wei
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, 130021, PR China
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, Alberta, T6G 2G3, Canada; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China
| | - Liangyun Bu
- School of Public Health, Jilin University, Changchun, 130021, PR China
| | - Juan Li
- School of Public Health, Jilin University, Changchun, 130021, PR China.
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, Alberta, T6G 2G3, Canada.
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, Alberta, T6G 2G3, Canada.
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2
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Hu T, Ji Q, Ke X, Zhou H, Zhang S, Ma S, Yu C, Ju W, Lu M, Lin Y, Ou Y, Zhou Y, Xiao Y, Xu C, Hu C. Repurposing Type I-A CRISPR-Cas3 for a robust diagnosis of human papillomavirus (HPV). Commun Biol 2024; 7:858. [PMID: 39003402 PMCID: PMC11246428 DOI: 10.1038/s42003-024-06537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
R-loop-triggered collateral single-stranded DNA (ssDNA) nuclease activity within Class 1 Type I CRISPR-Cas systems holds immense potential for nucleic acid detection. However, the hyperactive ssDNase activity of Cas3 introduces unwanted noise and false-positive results. In this study, we identified a novel Type I-A Cas3 variant derived from Thermococcus siculi, which remains in an auto-inhibited state until it is triggered by Cascade complex and R-loop formation. This Type I-A CRISPR-Cas3 system not only exhibits an expanded protospacer adjacent motif (PAM) recognition capability but also demonstrates remarkable intolerance towards mismatched sequences. Furthermore, it exhibits dual activation modes-responding to both DNA and RNA targets. The culmination of our research efforts has led to the development of the Hyper-Active-Verification Establishment (HAVE, ). This innovation enables swift and precise human papillomavirus (HPV) diagnosis in clinical samples, providing a robust molecular diagnostic tool based on the Type I-A CRISPR-Cas3 system. Our findings contribute to understanding type I-A CRISPR-Cas3 system regulation and facilitate the creation of advanced diagnostic solutions with broad clinical applicability.
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Affiliation(s)
- Tao Hu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang University, Hangzhou, Zhejiang, 310052, China
| | - Quanquan Ji
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xinxin Ke
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Zhejiang University, Hangzhou, Zhejiang, 310052, China
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Senfeng Zhang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Shengsheng Ma
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Chenlin Yu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Wenjun Ju
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Meiling Lu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Yu Lin
- International Peace Maternity & Child Health Hospital, Shanghai Municipal Key Clinical Specialty, Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yangjing Ou
- International Peace Maternity & Child Health Hospital, Shanghai Municipal Key Clinical Specialty, Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yingsi Zhou
- HuidaGene Therapeutics Inc., Shanghai, China.
| | - Yibei Xiao
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
| | - Chunlong Xu
- Lingang Laboratory, Shanghai, China.
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, China.
| | - Chunyi Hu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Precision Medicine Translational Research Programme (TRP), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
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3
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Jung JK, Dreyer KS, Dray KE, Muldoon JJ, George J, Shirman S, Cabezas MD, D’Aquino AE, Verosloff MS, Seki K, Rybnicky GA, Alam KK, Bagheri N, Jewett MC, Leonard JN, Mangan NM, Lucks JB. Developing, characterizing and modeling CRISPR-based point-of-use pathogen diagnostics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601853. [PMID: 39005318 PMCID: PMC11244977 DOI: 10.1101/2024.07.03.601853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Recent years have seen intense interest in the development of point-of-care nucleic acid diagnostic technologies to address the scaling limitations of laboratory-based approaches. Chief among these are combinations of isothermal amplification approaches with CRISPR-based detection and readouts of target products. Here, we contribute to the growing body of rapid, programmable point-of-care pathogen tests by developing and optimizing a one-pot NASBA-Cas13a nucleic acid detection assay. This test uses the isothermal amplification technique NASBA to amplify target viral nucleic acids, followed by Cas13a-based detection of amplified sequences. We first demonstrate an in-house formulation of NASBA that enables optimization of individual NASBA components. We then present design rules for NASBA primer sets and LbuCas13a guide RNAs for fast and sensitive detection of SARS-CoV-2 viral RNA fragments, resulting in 20 - 200 aM sensitivity without any specialized equipment. Finally, we explore the combination of high-throughput assay condition screening with mechanistic ordinary differential equation modeling of the reaction scheme to gain a deeper understanding of the NASBA-Cas13a system. This work presents a framework for developing a mechanistic understanding of reaction performance and optimization that uses both experiments and modeling, which we anticipate will be useful in developing future nucleic acid detection technologies.
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Affiliation(s)
- Jaeyoung K. Jung
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Center for Water Research, Northwestern University (Evanston, IL, USA)
| | - Kathleen S. Dreyer
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Kate E. Dray
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Joseph J. Muldoon
- Department of Medicine, University of California, San Francisco (San Francisco, CA, USA)
- Gladstone-UCSF Institute of Genomic Immunology (San Francisco, CA, USA)
| | - Jithin George
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Engineering Sciences and Applied Mathematics, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Sasha Shirman
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Maria D. Cabezas
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Biomedical Engineering, Northwestern University (Evanston, IL, USA)
| | - Anne E. D’Aquino
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Stemloop, Inc. (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Matthew S. Verosloff
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Kosuke Seki
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Grant A. Rybnicky
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
- Chemistry of Life Processes Institute, Northwestern University (Evanston, IL, USA)
| | | | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
- Departments of Biology and Chemical Engineering, University of Washington (Seattle, WA, USA)
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Bioengineering, Stanford University (Stanford, CA)
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Niall M. Mangan
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Engineering Sciences and Applied Mathematics, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Center for Water Research, Northwestern University (Evanston, IL, USA)
- Chemistry of Life Processes Institute, Northwestern University (Evanston, IL, USA)
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4
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Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods 2024; 21:954-966. [PMID: 38689099 DOI: 10.1038/s41592-024-02262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.
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Affiliation(s)
- Daniel P Agustinho
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Vipin K Menon
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
- Senior research project manager, Human Genetics, Genentech, South San Francisco, CA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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5
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Kang S, Choi P, Maile-Moskowitz A, Brown CL, Gonzalez RA, Pruden A, Vikesland PJ. Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance. ACS ES&T WATER 2024; 4:1629-1636. [PMID: 38633369 PMCID: PMC11019537 DOI: 10.1021/acsestwater.3c00690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.
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Affiliation(s)
- Seju Kang
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Petra Choi
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Ayella Maile-Moskowitz
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Connor L. Brown
- Department
of Genetics, Bioinformatics, and Computational Biology, Blacksburg, Virginia 24061, United States
| | - Raul A. Gonzalez
- Hampton
Roads Sanitation District, Virginia Beach ,Virginia23455, United States
| | - Amy Pruden
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Peter J. Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
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6
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Wang F, Ma X, Ye J, Shi C, Chen Y, Yu Z, Li T, Yang D, Li M, Wang P. Precise Detection of Viral RNA by Programming Multiplex Rolling Circle Amplification and Strand Displacement. Anal Chem 2023; 95:17699-17707. [PMID: 37971750 DOI: 10.1021/acs.analchem.3c03548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Detection of viral infections (e.g., SARS-CoV-2) with high precision is critical to disease control and treatment. There is an urgent need to develop point-of-care detection methods to complement the gold standard laboratory-based PCR assay with comparable sensitivity and specificity. Herein, we developed a method termed mCAD to achieve ultraspecific point-of-care detection of SARS-CoV-2 RNA while maintaining high sensitivity by programming multiplex rolling circle amplification and toehold-mediated strand displacement reactions. RCA offers sufficient amplification of RNA targets for subsequent detection. Most importantly, a multilayer of detection specificity is implemented into mCAD via sequence-specific hybridization of nucleic acids across serial steps of this protocol to fully eliminate potential false-positive detections. Using mCAD, we demonstrated a highly specific, sensitive, and convenient visual detection of SARS-CoV-2 RNA from both synthetic and clinical samples, exhibiting performance comparable to qPCR. We envision that mCAD will find its broad applications in clinical prospects for nucleic acid detections readily beyond SARS-CoV-2 RNA.
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Affiliation(s)
- Fukai Wang
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200233, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jing Ye
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yun Chen
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhicai Yu
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Tianming Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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7
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Ren R, Cai S, Fang X, Wang X, Zhang Z, Damiani M, Hudlerova C, Rosa A, Hope J, Cook NJ, Gorelkin P, Erofeev A, Novak P, Badhan A, Crone M, Freemont P, Taylor GP, Tang L, Edwards C, Shevchuk A, Cherepanov P, Luo Z, Tan W, Korchev Y, Ivanov AP, Edel JB. Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes. Nat Commun 2023; 14:7362. [PMID: 37963924 PMCID: PMC10646045 DOI: 10.1038/s41467-023-43004-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.
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Affiliation(s)
- Ren Ren
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Xiaona Fang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Xiaoyi Wang
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Zheng Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Micol Damiani
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Charlotte Hudlerova
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Annachiara Rosa
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Wolfson Education Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Joshua Hope
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Peter Gorelkin
- National University of Science and Technology "MISIS", Leninskiy Prospect 4, 119991, Moscow, Russian Federation
| | - Alexander Erofeev
- National University of Science and Technology "MISIS", Leninskiy Prospect 4, 119991, Moscow, Russian Federation
| | - Pavel Novak
- ICAPPIC Limited, The Fisheries, Mentmore Terrace, London, E8 3PN, UK
| | - Anjna Badhan
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Michael Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Paul Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Graham P Taylor
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, 310027, Hangzhou, China
| | - Christopher Edwards
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- ICAPPIC Limited, The Fisheries, Mentmore Terrace, London, E8 3PN, UK
| | - Andrew Shevchuk
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Peter Cherepanov
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Zhaofeng Luo
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Weihong Tan
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
| | - Yuri Korchev
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
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8
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Luna-Callejas B, Oropeza-Ramos L, Ramón-Gallegos E. Comparative genomic analysis of Mycoplasma related to cell culture for infB gene-based loop-mediated isothermal amplification. World J Microbiol Biotechnol 2023; 39:355. [PMID: 37878143 DOI: 10.1007/s11274-023-03794-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Mycoplasma contamination in cell culture affects the properties of cell lines. Gold standard detection by microbiological culture takes days and requires specialists. The polymerase chain reaction and loop-mediated isothermal amplification (LAMP) are fast molecular options, but LAMP only requires one heating block for DNA amplification. This study presents a comparative genomic analysis of Mycoplasma species to identify common target genes different from the rrsA gene, which encodes 16 S rRNA. The aim is to implement a LAMP assay to detect Mycoplasma species, reducing the time and specialized equipment required for detection. We performed a comparative genomic analysis through Mauve software and the GView server and selected infB and clpB genes as target candidates for designing LAMP primers. We evaluated both genes by multiple sequence alignment (MSA). The infB gene presented the best score MSA assessment with lower odd-log values (5,480,281) than other genes. We selected the infB gene to design LAMP primers specific to Mycoplasma spp. We used these primers to implement LAMP at 63 °C for 30 min, which showed 100% positive amplifications for detecting Mycoplasma spp. In conclusion, we present a methodology utilizing the infB gene-based LAMP assay to detect three of the six most prevalent Mycoplasma species in cell culture.
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Affiliation(s)
- Benjamín Luna-Callejas
- Facultad de Ingeniería, Universidad Nacional Autónoma de México, 04510, Mexico City, México
- Department of Morphology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 07738, Mexico City, México
| | - Laura Oropeza-Ramos
- Facultad de Ingeniería, Universidad Nacional Autónoma de México, 04510, Mexico City, México
| | - Eva Ramón-Gallegos
- Department of Morphology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 07738, Mexico City, México.
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9
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Nguyen T, Vinayaka AC, Huynh VN, Linh QT, Andreasen SZ, Golabi M, Bang DD, Møller JK, Wolff A. PATHPOD - A loop-mediated isothermal amplification (LAMP)-based point-of-care system for rapid clinical detection of SARS-CoV-2 in hospitals in Denmark. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 392:134085. [PMID: 37304211 PMCID: PMC10245468 DOI: 10.1016/j.snb.2023.134085] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/19/2023] [Accepted: 06/03/2023] [Indexed: 06/13/2023]
Abstract
Sensitive and rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a vital goal in the ongoing COVID-19 pandemic. We present in this comprehensive work, for the first time, detailed fabrication and clinical validation of a point of care (PoC) device for rapid, onsite detection of SARS-CoV-2 using a real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) reaction on a polymer cartridge. The PoC system, namely PATHPOD, consisting of a standalone device (weight less than 1.2 kg) and a cartridge, can perform the detection of 10 different samples and two controls in less than 50 min, which is much more rapid than the golden standard real-time reverse-transcription Polymerase Chain Reaction (RT-PCR), typically taking 16-48 h. The novel total internal reflection (TIR) scheme and the reactions inside the cartridge in the PoC device allow monitoring of the diagnostic results in real-time and onsite. The analytical sensitivity and specificity of the PoC test are comparable with the current RT-PCR, with a limit of detection (LOD) down to 30-50 viral genome copies. The robustness of the PATHPOD PoC system has been confirmed by analyzing 398 clinical samples initially examined in two hospitals in Denmark. The clinical sensitivity and specificity of these tests are discussed.
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Affiliation(s)
- Trieu Nguyen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Van Ngoc Huynh
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Quyen Than Linh
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sune Zoëga Andreasen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens Kjølseth Møller
- Department of Clinical Microbiology, University Hospital of Southern Denmark, Vejle Hospital, Beriderbakken 4, DK-7100 Vejle, Denmark
| | - Anders Wolff
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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10
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Cui X, Ngang S, Liu DD, Cheow LF. Rapid Single-Round Pool Testing of Infectious Disease Enabled by Multicolor Digital Melting PCR. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205636. [PMID: 37209020 DOI: 10.1002/smll.202205636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/27/2023] [Indexed: 05/21/2023]
Abstract
Pooled nucleic acid amplification test is a promising strategy to reduce cost and resources for screening large populations for infectious disease. However, the benefit of pooled testing is reversed when disease prevalence is high, because of the need to retest each sample to identify infected individual when a pool is positive. Split, Amplify, and Melt analysis of Pooled Assay (SAMPA) is presented, a multicolor digital melting PCR assay in nanoliter chambers that simultaneously identify infected individuals and quantify their viral loads in a single round of pooled testing. This is achieved by early sample tagging with unique barcodes and pooling, followed by single molecule barcode identification in a digital PCR platform using a highly multiplexed melt curve analysis strategy. The feasibility is demonstrated of SAMPA for quantitative unmixing and variant identification from pools of eight synthetic DNA and RNA samples corresponding to the N1 gene, as well as from heat-inactivated SARS-CoV-2 virus. Single round pooled testing of barcoded samples with SAMPA can be a valuable tool for rapid and scalable population testing of infectious disease.
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Affiliation(s)
- Xu Cui
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Shaun Ngang
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Dong Dong Liu
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
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11
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Chen HC. A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level. Front Mol Biosci 2023; 10:1141534. [PMID: 37496777 PMCID: PMC10366608 DOI: 10.3389/fmolb.2023.1141534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023] Open
Abstract
The outbreak of SARS-CoV-2 has made us more alert to the importance of viral diagnostics at a population level to rapidly control the spread of the disease. The critical question would be how to scale up testing capacity and perform a diagnostic test in a high-throughput manner with robust results and affordable costs. Here, the latest 26 articles using barcoding technology for COVID-19 diagnostics and biologically-relevant studies are reviewed. Barcodes are molecular tags, that allow proceeding an array of samples at once. To date, barcoding technology followed by high-throughput sequencing has been made for molecular diagnostics for SARS-CoV-2 infections because it can synchronously analyze up to tens of thousands of clinical samples within a short diagnostic time. Essentially, this technology can also be used together with different biotechnologies, allowing for investigation with resolution of single molecules. In this Mini-Review, I first explain the general principle of the barcoding strategy and then put forward recent studies using this technology to accomplish COVID-19 diagnostics and basic research. In the meantime, I provide the viewpoint to improve the current COVID-19 diagnostic strategy with potential solutions. Finally, and importantly, two practical ideas about how barcodes can be further applied in studying SARS-CoV-2 to accelerate our understanding of this virus are proposed.
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12
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Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
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13
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Alhamid G, Tombuloglu H, Al-Suhaimi E. Development of loop-mediated isothermal amplification (LAMP) assays using five primers reduces the false-positive rate in COVID-19 diagnosis. Sci Rep 2023; 13:5066. [PMID: 36977756 PMCID: PMC10044074 DOI: 10.1038/s41598-023-31760-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a cheaper and faster testing alternative for detecting SARS-CoV-2. However, a high false-positive rate due to misamplification is one of the major limitations. To overcome misamplifications, we developed colorimetric and fluorometric RT-LAMP assays using five LAMP primers, instead of six. The gold-standard RT-PCR technique verified the assays' performance. Compared to other primer sets with six primers (N, S, and RdRp), the E-ID1 primer set, including five primers, performed superbly on both colorimetric and fluorometric assays. The sensitivity of colorimetric and fluorometric assays was 89.5% and 92.2%, respectively, with a limit of detection of 20 copies/µL. The colorimetric RT-LAMP had a specificity of 97.2% and an accuracy of 94.5%, while the fluorometric RT-LAMP obtained 99% and 96.7%, respectively. No misamplification was evident even after 120 min, which is crucial for the success of this technique. These findings are important to support the use of RT-LAMP in the healthcare systems in fighting COVID-19.
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Affiliation(s)
- Galyah Alhamid
- Master Program of Biotechnology, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia.
| | - Ebtesam Al-Suhaimi
- Biology Department, College of Science and Institute of Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
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14
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A triple-target reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid and accurate detection of SARS-CoV-2 virus. Anal Chim Acta 2023; 1255:341146. [PMID: 37032059 PMCID: PMC10039734 DOI: 10.1016/j.aca.2023.341146] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
The spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across the world has impacted people's health and lives worldwide in recent years. Rapid and accurate diagnosis is crucial for curbing the pandemic of coronavirus disease 2019 (COVID-19). Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has great potential for SARS-CoV-2 detection but fails to completely replace conventional PCR due to the high false-positive rate (FPR). We proposed a triple-target RT-LAMP method for dual-signal, sensitive, and simultaneous detection of conserved genes of SARS-CoV-2. Multiple LAMP primer sets were designed for N, E, and M genes and their amplification efficacy were screened. Then, using artificial plasmids and RNA, the optimal primer set for each gene was examined on specificity, sensitivity, and detection range. The RT-LAMP initiated by these primer sets exhibited better specificity and sensitivity than that of RT-qPCR, and the triple-target RT-LAMP could determine different variants of SARS-CoV-2. By testing 78 artificial RNA samples, the total FPR of triple-target RT-LAMP was eliminated compared with that of mono-target RT-LAMP. The triple-target RT-LAMP method precisely identified throat swab specimens through colorimetry and fluorescent signals within 60 min, and the limit of detection (LOD) was as low as 187 copies/reaction. In the future, the triple-target RT-LAMP can be applied to in-field and on-site diagnosis of symptomatic and asymptomatic virus carriers.
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15
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Khanizadeh S, Malekshahi A, Hanifehpour H, Birjandi M, Fallahi S. Rapid, sensitive, and specific detection of SARS-CoV-2 in nasopharyngeal swab samples of suspected patients using a novel one-step loop-mediated isothermal amplification (one-step LAMP) technique. BMC Microbiol 2023; 23:63. [PMID: 36882699 PMCID: PMC9989590 DOI: 10.1186/s12866-023-02806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND In the absence of effective antiviral drugs or vaccines, early and accurate detection of SARS-CoV-2 infection is essential to the COVID-19 pandemic. This study developed and evaluated a novel rapid One-Step LAMP assay to directly detect the SARS-CoV-2 RNA from nasopharyngeal (NP) swab samples of patients with suspected SARS-CoV-2 infection living in deprived areas in comparison to One-Step Real-time PCR. METHODS Two hundred fifty-four NP swab samples from patients suspected of COVID-19 infection living in deprived western areas of Iran were tested by TaqMan One-Step RT-qPCR and fast One-Step LAMP assays. Tenfold serial dilutions of SARS-CoV-2 RNA standard strain where the viral copy number in each dilution was previously determined using the qPCR and various templates were used to investigate the analytical sensitivity and specificity of the One-Step LAMP assay in triplicate. Also, the efficacy and reliability of the method compared to TaqMan One-Step RT-qPCR were evaluated using SARS-CoV-2 positive and negative clinical samples. RESULTS The results of the One-Step RT-qPCR and One-Step LAMP tests were positive in 131 (51.6%) and 127 (50%) participants, respectively. Based on Cohen's kappa coefficient (κ), the agreement between the two tests was 97%, which was statistically significant (P < 0.001). The detection limit for the One-Step LAMP assay was 1 × 101 copies of standard SARS-CoV-2 RNA per reaction in less than an hour in triplicates. Negative results in all samples with non-SARS-CoV-2 templates represent 100% specificity. CONCLUSIONS The results showed that the One-Step LAMP assay is an efficient consistent technique for detecting SARS-CoV-2 among suspected individuals due to its simplicity, speed, low cost, sensitivity, and specificity. Therefore, it has great potential as a useful diagnostic tool for disease epidemic control, timely treatment, and public health protection, especially in poor and underdeveloped countries.
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Affiliation(s)
- Sayyad Khanizadeh
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.,Department of Virology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Asra Malekshahi
- Department of Virology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Hooman Hanifehpour
- Department of Microbiology, Cancer Biomedical Research Center (CBC), Tehran, Iran
| | - Mehdi Birjandi
- Department of Biostatistics and Epidemiology, School of Health and Nutrition, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Shirzad Fallahi
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran. .,Department of Parasitology and Mycology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
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16
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Szobi A, Buranovská K, Vojtaššáková N, Lovíšek D, Özbaşak HÖ, Szeibeczederová S, Kapustian L, Hudáčová Z, Kováčová V, Drobná D, Putaj P, Bírová S, Čirková I, Čarnecký M, Kilián P, Jurkáček P, Čabanová V, Boršová K, Sláviková M, Vaňová V, Klempa B, Čekan P, Paul ED. Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system. Commun Biol 2023; 6:233. [PMID: 36864129 PMCID: PMC9979146 DOI: 10.1038/s42003-023-04612-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Sensitive and rapid point-of-care assays have been crucial in the global response to SARS-CoV-2. Loop-mediated isothermal amplification (LAMP) has emerged as an important diagnostic tool given its simplicity and minimal equipment requirements, although limitations exist regarding sensitivity and the methods used to detect reaction products. We describe the development of Vivid COVID-19 LAMP, which leverages a metallochromic detection system utilizing zinc ions and a zinc sensor, 5-Br-PAPS, to circumvent the limitations of classic detection systems dependent on pH indicators or magnesium chelators. We make important strides in improving RT-LAMP sensitivity by establishing principles for using LNA-modified LAMP primers, multiplexing, and conducting extensive optimizations of reaction parameters. To enable point-of-care testing, we introduce a rapid sample inactivation procedure without RNA extraction that is compatible with self-collected, non-invasive gargle samples. Our quadruplexed assay (targeting E, N, ORF1a, and RdRP) reliably detects 1 RNA copy/µl of sample (=8 copies/reaction) from extracted RNA and 2 RNA copies/µl of sample (=16 copies/reaction) directly from gargle samples, making it one of the most sensitive RT-LAMP tests and even comparable to RT-qPCR. Additionally, we demonstrate a self-contained, mobile version of our assay in a variety of high-throughput field testing scenarios on nearly 9,000 crude gargle samples. Vivid COVID-19 LAMP can be an important asset for the endemic phase of COVID-19 as well as preparing for future pandemics.
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Affiliation(s)
- Adrián Szobi
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Katarína Buranovská
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Nina Vojtaššáková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Daniel Lovíšek
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Halil Önder Özbaşak
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Sandra Szeibeczederová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Liudmyla Kapustian
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Zuzana Hudáčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- Stanford University, 730 Escondido Rd., Stanford, CA, 94305, USA
| | - Viera Kováčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- University of Cologne, Institute for Biological Physics, Zülpicher Str. 77, 50937, Köln, Germany
| | - Diana Drobná
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Piotr Putaj
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Stanislava Bírová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Ivana Čirková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Martin Čarnecký
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Kilián
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Jurkáček
- AstonITM s.r.o., Račianska 153, 831 54, Bratislava, Slovakia
| | - Viktória Čabanová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Kristína Boršová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Veronika Vaňová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
| | - Evan D Paul
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
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17
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Song M, Hong S, Lee LP. Multiplexed Ultrasensitive Sample-to-Answer RT-LAMP Chip for the Identification of SARS-CoV-2 and Influenza Viruses. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207138. [PMID: 36398425 DOI: 10.1002/adma.202207138] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Prompt on-site diagnosis of SARS-CoV-2 with other respiratory infections will have minimized the global impact of the COVID-19 pandemic through rapid, effective management. However, no such multiplex point-of-care (POC) chip has satisfied a suitable sensitivity of gold-standard nucleic acid amplification tests (NAATs). Here, a rapid multiplexed ultrasensitive sample-to-answer loop-mediated isothermal amplification (MUSAL) chip operated by simple LED-driven photothermal amplification to detect six targets from single-swab sampling is presented. First, the MUSAL chip allows ultrafast on-chip sample preparation with ≈500-fold preconcentration at a rate of 1.2 mL min-1 . Second, the chip enables contamination-free amplification using autonomous target elution into on-chip reagents by photothermal activation. Finally, the chip accomplishes multiplexed on-chip diagnostics of SARS-CoV-2 and influenza viruses with a limit of detection (LoD) of 0.5 copies µL-1 . The rapid, ultrasensitive, cost-effective sample-to-answer chip with a multiplex capability will allow timely management of various pandemics situations that may be faced shortly.
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Affiliation(s)
- Minsun Song
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - SoonGweon Hong
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, Gyeonggi-do, 16419, Republic of Korea
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18
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Li X, Wang J, Geng J, Xiao L, Wang H. Emerging Landscape of SARS-CoV-2 Variants and Detection Technologies. Mol Diagn Ther 2023; 27:159-177. [PMID: 36577887 PMCID: PMC9797111 DOI: 10.1007/s40291-022-00631-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2022] [Indexed: 12/29/2022]
Abstract
In 2019, a new coronavirus was identified that has caused significant morbidity and mortality worldwide. Like all RNA viruses, severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) evolves over time through random mutation resulting in genetic variations in the population. Although the currently approved coronavirus disease 2019 vaccines can be given to those over 5 years of age and older in most countries, strikingly, the number of people diagnosed positive for SARS-Cov-2 is still increasing. Therefore, to prevent and control this epidemic, early diagnosis of infected individuals is of great importance. The current detection of SARS-Cov-2 coronavirus variants are mainly based on reverse transcription-polymerase chain reaction. Although the sensitivity of reverse transcription-polymerase chain reaction is high, it has some disadvantages, for example, multiple temperature changes, long detection time, complicated operation, expensive instruments, and the need for professional personnel, which brings considerable inconvenience to the early diagnosis of this virus. This review comprehensively summarizes the development and application of various current detection technologies for novel coronaviruses, including isothermal amplification, CRISPR-Cas detection, serological detection, biosensor, ensemble, and microfluidic technology, along with next-generation sequencing. Those findings offer us a great potential to replace or combine with reverse transcription-polymerase chain reaction detection to achieve the purpose of allowing predictive diagnostics and targeted prevention of SARS-Cov-2 in the future.
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Affiliation(s)
- Xianghui Li
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China
| | - Jing Wang
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jingping Geng
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China
| | - Liming Xiao
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Hu Wang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China.
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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19
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Abstract
INTRODUCTION The SARS-CoV-2 pandemic, and the subsequent limitations on standard diagnostics, has vastly expanded the user base of Reverse Transcription Loop-mediated isothermal Amplification (RT-LAMP) in fundamental research and development. RT-LAMP has also penetrated commercial markets, with emergency use authorizations for clinical diagnosis. AREAS COVERED This review discusses the role of RT-LAMP within the context of other technologies like RT-qPCR and rapid antigen tests, progress in sample preparation strategies to enable simplified workflow for RT-LAMP directly from clinical specimens, new challenges with primer and assay design for the evolving pandemic, prominent detection modalities including colorimetric and CRISPR-mediated methods, and translational research and commercial development of RT-LAMP for clinical applications. EXPERT OPINION RT-LAMP occupies a middle ground between RT-qPCR and rapid antigen tests. The simplicity approaches that of rapid antigen tests, making it suitable for point-of-care use, but the sensitivity nears that of RT-qPCR. RT-LAMP still lags RT-qPCR in fundamental understanding of the mechanism, and the interplay between sample preparation and assay performance. Industry is now beginning to address issues around scalability and usability, which could finally enable LAMP and RT-LAMP to find future widespread application as a diagnostic for other conditions, including other pathogens with pandemic potential.
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Affiliation(s)
- Gihoon Choi
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Taylor J Moehling
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Robert J Meagher
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
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20
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Ki J, Na HK, Yoon SW, Le VP, Lee TG, Lim EK. CRISPR/Cas-Assisted Colorimetric Biosensor for Point-of-Use Testing for African Swine Fever Virus. ACS Sens 2022; 7:3940-3946. [PMID: 36399393 PMCID: PMC9791683 DOI: 10.1021/acssensors.2c02007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
African swine fever virus (ASFV) causes a highly contagious and fatal disease affecting both domesticated and wild pigs. Substandard therapies and inadequate vaccinations cause severe economic damages from pig culling and removal of infected carcasses. Therefore, there is an urgent need to develop a rapid point-of-use approach that assists in avoiding the spread of ASFV and reducing economic loss. In this study, we developed a colorimetric sensing platform based on dual enzymatic amplification that combined the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a) system and the enzyme urease for accurate and sensitive detection of ASFV. The mechanism of the sensing platform involves a magnetic bead-anchored urease-conjugated single-stranded oligodeoxynucleotide (MB@urODN), which in the presence of ASFV dsDNA is cleaved by activated CRISPR/Cas12a. After magnetically separating the free urease, the presence of virus can be confirmed by measuring the colorimetric change in the solution. The advantage of this method is that it can detect the presence of virus without undergoing a complex target gene duplication process. The established method detected ASFV from three clinical specimens collected from porcine clinical tissue samples. The proposed platform is designed to provide an adequate, simple, robust, highly sensitive and selective analytical technique for rapid zoonotic disease diagnosis while eliminating the need for vast or specialized tools.
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Affiliation(s)
- Jisun Ki
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hee-Kyung Na
- Center
for Nano-Bio Measurement, Korea Research
Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Sun Woo Yoon
- Department
of Biological Sciences and Biotechnology, Andong National University, Andong 36729, Republic of Korea
| | - Van Phan Le
- Department
of Microbiology and Infectious Disease, College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 100000, Vietnam
| | - Tae Geol Lee
- Center
for Nano-Bio Measurement, Korea Research
Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea,Department
of Nano Science, University of Science and
Technology (UST), Daejeon 34113, Republic of Korea,
| | - Eun-Kyung Lim
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea,Department
of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea,School
of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea,. Phone: +82-42-879-8456
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21
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Kang J, Jang H, Kim TH, Cho U, Bang H, Jang J, Lee W, Joo H, Noh J, Lee GY, Shin DH, Kang CK, Choe PG, Kim NJ, Oh MD, Song M, Kwon S, Veas F, Park WB. Accurate Diagnosis of COVID-19 from Self-Collectable Biospecimens Using Synthetic Apolipoprotein H Peptide-Coated Nanoparticle Assay. Anal Chem 2022; 94:17186-17194. [PMID: 36399654 PMCID: PMC9718094 DOI: 10.1021/acs.analchem.2c03813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A high-throughput, accurate screening is crucial for the prevention and control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Current methods, which involve sampling from the nasopharyngeal (NP) area by medical staffs, constitute a fundamental bottleneck in expanding the testing capacity. To meet the scales required for population-level surveillance, self-collectable specimens can be used; however, its low viral load has hindered its clinical adoption. Here, we describe a magnetic nanoparticle functionalized with synthetic apolipoprotein H (ApoH) peptides to capture, concentrate, and purify viruses. The ApoH assay demonstrates a viral enrichment efficiency of >90% for both SARS-CoV-2 and its variants, leading to an order of magnitude improvement in analytical sensitivity. For validation, we apply the assay to a total of 84 clinical specimens including nasal, oral, and mouth gargles obtained from COVID-19 patients. As a result, a 100% positivity rate is achieved from the patient-collected nasal and gargle samples, which exceeds that of the traditional NP swab method. The simple 12 min pre-enrichment assay enabling the use of self-collectable samples will be a practical solution to overcome the overwhelming diagnostic capacity. Furthermore, the methodology can easily be built on various clinical protocols, allowing its broad applicability to various disease diagnoses.
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Affiliation(s)
- Junwon Kang
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Korea
- Integrated Major in Innovative Medical Science, Seoul National University, Seoul03080, Korea
| | - Haewook Jang
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Korea
| | - Tae Hyun Kim
- Bio-MAX Institute, Seoul National University, Seoul08826, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
| | - Untack Cho
- QuantaMatrix Inc., Seoul08506, Korea
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul03080, Korea
| | | | | | - Wooseok Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
| | - Hyelyn Joo
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Korea
| | - Jinsung Noh
- Bio-MAX Institute, Seoul National University, Seoul08826, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
| | - Gi Yoon Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
| | - Dong Hoon Shin
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
| | - Manki Song
- International Vaccine Institute, Seoul08826, Korea
| | - Sunghoon Kwon
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul08826, Korea
- Bio-MAX Institute, Seoul National University, Seoul08826, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul08826, Korea
- QuantaMatrix Inc., Seoul08506, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul03080, Korea
| | - Francisco Veas
- Copernicus Integrated Solutions for Biosafety Risks (CISBR), Mauguio34130, France
- ApoH-Technologies, 94 Allée des Fauvettes, La Grande Motte34280, France
- UMR5151/French Research Institute for Development (IRD), University of Montpellier (UM), Montpellier 34093, France
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul03080, Korea
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22
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Zhu Y, Zhang M, Jie Z, Tao S. Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects. Front Microbiol 2022; 13:1074289. [PMID: 36569096 PMCID: PMC9780671 DOI: 10.3389/fmicb.2022.1074289] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has brought a huge threat to public health and the global economy. Rapid identification and isolation of SARS-CoV-2-infected individuals are regarded as one of the most effective measures to control the pandemic. Because of its high sensitivity and specificity, nucleic acid testing has become the major method of SARS-CoV-2 detection. A deep understanding of different diagnosis methods for COVID-19 could help researchers make an optimal choice in detecting COVID-19 at different symptom stages. In this review, we summarize and evaluate the latest developments in current nucleic acid detection methods for SARS-CoV-2. In particular, we discuss biosensors and CRISPR-based diagnostic systems and their characteristics and challenges. Furthermore, the emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis are systematically introduced and discussed. Considering the disease dynamics, we also recommend optional diagnostic tests for different symptom stages. From sample preparation to results readout, we conclude by pointing out the pain points and future directions of COVID-19 detection.
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Affiliation(s)
- Yuanshou Zhu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China,Center of Community-Based Health Research, Fudan University, Shanghai, China,*Correspondence: Zhijun Jie,
| | - Shengce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China,Shengce Tao,
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23
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Perera GS, Rahman MA, Blazevski A, Wood A, Walia S, Bhaskaran M, Sriram S. Rapid Conductometric Detection of SARS-CoV-2 Proteins and Its Variants Using Molecularly Imprinted Polymer Nanoparticles. ADVANCED MATERIALS TECHNOLOGIES 2022; 8:2200965. [PMID: 36718387 PMCID: PMC9877662 DOI: 10.1002/admt.202200965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/20/2022] [Indexed: 06/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) biosensors have captured more attention than the conventional methodologies for SARS-CoV-2 detection due to having cost-effective platforms and fast detection. However, these reported SARS-CoV-2 biosensors suffer from drawbacks including issues in detection sensitivity, degradation of biomaterials on the sensor's surface, and incapability to reuse the biosensors. To overcome these shortcomings, molecularly imprinted polymer nanoparticles (nanoMIPs) incorporated conductometric biosensor for highly accurate, rapid, and selective detection of two model SARS-CoV-2 proteins: (i) receptor binding domain (RBD) of the spike (S) glycoprotein and (ii) full length trimeric spike protein are introduced. In addition, these biosensors successfully responded to several other SARS-CoV-2 RBD spike protein variants including Alpha, Beta, Gamma, and Delta. Our conductometric biosensor selectively detects the two model proteins and SARS-CoV-2 RBD spike protein variant samples in real-time with sensitivity to a detection limit of 7 pg mL-1 within 10 min of sample incubation. A battery-free, wireless near-field communication (NFC) interface is incorporated with the biosensor for fast and contactless detection of SARS-CoV-2 variants. The smartphone enabled real-time detection and on-screen rapid result for SARS-CoV-2 variants can curve the outbreak due to its ability to alert the user to infection in real time.
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Affiliation(s)
- Ganganath S. Perera
- Functional Materials and Microsystems Research Group and the Micro Nano Research FacilityRMIT UniversityMelbourneVIC3001Australia
| | - Md. Ataur Rahman
- Functional Materials and Microsystems Research Group and the Micro Nano Research FacilityRMIT UniversityMelbourneVIC3001Australia
| | - April Blazevski
- Functional Materials and Microsystems Research Group and the Micro Nano Research FacilityRMIT UniversityMelbourneVIC3001Australia
| | | | - Sumeet Walia
- Functional Materials and Microsystems Research Group and the Micro Nano Research FacilityRMIT UniversityMelbourneVIC3001Australia
| | - Madhu Bhaskaran
- Functional Materials and Microsystems Research Group and the Micro Nano Research FacilityRMIT UniversityMelbourneVIC3001Australia
| | - Sharath Sriram
- Functional Materials and Microsystems Research Group and the Micro Nano Research FacilityRMIT UniversityMelbourneVIC3001Australia
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24
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Detection of SARS-CoV-2 Virus by Triplex Enhanced Nucleic Acid Detection Assay (TENADA). Int J Mol Sci 2022; 23:ijms232315258. [PMID: 36499587 PMCID: PMC9740288 DOI: 10.3390/ijms232315258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2, a positive-strand RNA virus has caused devastating effects. The standard method for COVID diagnosis is based on polymerase chain reaction (PCR). The method needs expensive reagents and equipment and well-trained personnel and takes a few hours to be completed. The search for faster solutions has led to the development of immunological assays based on antibodies that recognize the viral proteins that are faster and do not require any special equipment. Here, we explore an innovative analytical approach based on the sandwich oligonucleotide hybridization which can be adapted to several biosensing devices including thermal lateral flow and electrochemical devices, as well as fluorescent microarrays. Polypurine reverse-Hoogsteen hairpins (PPRHs) oligonucleotides that form high-affinity triplexes with the polypyrimidine target sequences are used for the efficient capture of the viral genome. Then, a second labeled oligonucleotide is used to detect the formation of a trimolecular complex in a similar way to antigen tests. The reached limit of detection is around 0.01 nM (a few femtomoles) without the use of any amplification steps. The triplex enhanced nucleic acid detection assay (TENADA) can be readily adapted for the detection of any pathogen requiring only the knowledge of the pathogen genome sequence.
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25
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Das D, Lin CW, Chuang HS. LAMP-Based Point-of-Care Biosensors for Rapid Pathogen Detection. BIOSENSORS 2022; 12:bios12121068. [PMID: 36551035 PMCID: PMC9775414 DOI: 10.3390/bios12121068] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Seeking optimized infectious pathogen detection tools is of primary importance to lessen the spread of infections, allowing prompt medical attention for the infected. Among nucleic-acid-based sensing techniques, loop-mediated isothermal amplification is a promising method, as it provides rapid, sensitive, and specific detection of microbial and viral pathogens and has enormous potential to transform current point-of-care molecular diagnostics. In this review, the advances in LAMP-based point-of-care diagnostics assays developed during the past few years for rapid and sensitive detection of infectious pathogens are outlined. The numerous detection methods of LAMP-based biosensors are discussed in an end-point and real-time manner with ideal examples. We also summarize the trends in LAMP-on-a-chip modalities, such as classical microfluidic, paper-based, and digital LAMP, with their merits and limitations. Finally, we provide our opinion on the future improvement of on-chip LAMP methods. This review serves as an overview of recent breakthroughs in the LAMP approach and their potential for use in the diagnosis of existing and emerging diseases.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung 413, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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26
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Siavash Moakhar R, del Real Mata C, Jalali M, Shafique H, Sanati A, de Vries J, Strauss J, AbdElFatah T, Ghasemi F, McLean M, I. Hosseini I, Lu Y, Yedire SG, Mahshid SS, Tabatabaiefar MA, Liang C, Mahshid S. A Versatile Biomimic Nanotemplating Fluidic Assay for Multiplex Quantitative Monitoring of Viral Respiratory Infections and Immune Responses in Saliva and Blood. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2204246. [PMID: 36253095 PMCID: PMC9685479 DOI: 10.1002/advs.202204246] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 05/17/2023]
Abstract
The last pandemic exposed critical gaps in monitoring and mitigating the spread of viral respiratory infections at the point-of-need. A cost-effective multiplexed fluidic device (NFluidEX), as a home-test kit analogous to a glucometer, that uses saliva and blood for parallel quantitative detection of viral infection and body's immune response in an automated manner within 11 min is proposed. The technology integrates a versatile biomimetic receptor based on molecularly imprinted polymers in a core-shell structure with nano gold electrodes, a multiplexed fluidic-impedimetric readout, built-in saliva collection/preparation, and smartphone-enabled data acquisition and interpretation. NFluidEX is validated with Influenza A H1N1 and SARS-CoV-2 (original strain and variants of concern), and achieves low detection limit in saliva and blood for the viral proteins and the anti-receptor binding domain (RBD) Immunoglobulin G (IgG) and Immunoglobulin M (IgM), respectively. It is demonstrated that nanoprotrusions of gold electrodes are essential for the fine templating of antibodies and spike proteins during molecular imprinting, and differentiation of IgG and IgM in whole blood. In the clinical setting, NFluidEX achieves 100% sensitivity and 100% specificity by testing 44 COVID-positive and 25 COVID-negative saliva and blood samples on par with the real-time quantitative polymerase chain reaction (p < 0.001, 95% confidence) and the enzyme-linked immunosorbent assay.
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Affiliation(s)
| | | | - Mahsa Jalali
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Houda Shafique
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Alireza Sanati
- Biosensor Research CenterIsfahan University of Medical SciencesIsfahan81746‐73461Iran
| | - Justin de Vries
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Julia Strauss
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Tamer AbdElFatah
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Fahimeh Ghasemi
- Biosensor Research CenterIsfahan University of Medical SciencesIsfahan81746‐73461Iran
| | - Myles McLean
- Department of MedicineMcGill UniversityMontrealQuebecH4A 3J1Canada
- Lady Davis Institute for Medical Research and McGill AIDS CentreJewish General HospitalMontrealQCH3T 1E2Canada
| | - Imman I. Hosseini
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | - Yao Lu
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
| | | | - Sahar Sadat Mahshid
- Biological SciencesSunnybrook Research InstituteSunnybrook Health Sciences CentreTorontoONM4N 3M5Canada
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular BiologySchool of MedicineIsfahan University of Medical SciencesIsfahan81746‐73461Iran
| | - Chen Liang
- Department of MedicineMcGill UniversityMontrealQuebecH4A 3J1Canada
- Lady Davis Institute for Medical Research and McGill AIDS CentreJewish General HospitalMontrealQCH3T 1E2Canada
| | - Sara Mahshid
- Department of BioengineeringMcGill UniversityMontrealQuebecH3A 0E9Canada
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27
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Park JW. Principles and Applications of Loop-Mediated Isothermal Amplification to Point-of-Care Tests. BIOSENSORS 2022; 12:bios12100857. [PMID: 36290994 PMCID: PMC9599884 DOI: 10.3390/bios12100857] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 05/03/2023]
Abstract
For the identification of nucleic acids, which are important biomarkers of pathogen-mediated diseases and viruses, the gold standard for NA-based diagnostic applications is polymerase chain reaction (PCR). However, the requirements of PCR limit its application as a rapid point-of-care diagnostic technique. To address the challenges associated with regular PCR, many isothermal amplification methods have been developed to accurately detect NAs. Isothermal amplification methods enable NA amplification without changes in temperature with simple devices, as well as faster amplification times compared with regular PCR. Of the isothermal amplifications, loop-mediated isothermal amplification (LAMP) is the most studied because it amplifies NAs rapidly and specifically. This review describes the principles of LAMP, the methods used to monitor the process of LAMP, and examples of biosensors that detect the amplicons of LAMP. In addition, current trends in the application of LAMP to smartphones and self-diagnosis systems for point-of-care tests are also discussed.
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Affiliation(s)
- Jee-Woong Park
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Korea
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28
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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29
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Santiago-Frangos A, Nemudryi A, Nemudraia A, Wiegand T, Nichols JE, Krishna P, Scherffius AM, Zahl TR, Wilkinson RA, Wiedenheft B. CRISPR-Cas, Argonaute proteins and the emerging landscape of amplification-free diagnostics. Methods 2022; 205:1-10. [PMID: 35690249 PMCID: PMC9181078 DOI: 10.1016/j.ymeth.2022.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/06/2022] [Accepted: 06/04/2022] [Indexed: 01/04/2023] Open
Abstract
Polymerase Chain Reaction (PCR) is the reigning gold standard for molecular diagnostics. However, the SARS-CoV-2 pandemic reveals an urgent need for new diagnostics that provide users with immediate results without complex procedures or sophisticated equipment. These new demands have stimulated a tsunami of innovations that improve turnaround times without compromising the specificity and sensitivity that has established PCR as the paragon of diagnostics. Here we briefly introduce the origins of PCR and isothermal amplification, before turning to the emergence of CRISPR-Cas and Argonaute proteins, which are being coupled to fluorimeters, spectrometers, microfluidic devices, field-effect transistors, and amperometric biosensors, for a new generation of nucleic acid-based diagnostics.
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Affiliation(s)
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Anna Nemudraia
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Joseph E Nichols
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Pushya Krishna
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Andrew M Scherffius
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Trevor R Zahl
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Royce A Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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30
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Jabs JM, Schwabe A, Wollkopf AD, Gebel B, Stadelmaier J, Erdmann S, Radicke F, Grundmann H, Kramer A, Monsef I, Rücker G, Rupp J, Scheithauer S, Schmucker C, Simon A, Mutters NT. The role of routine SARS-CoV-2 screening of healthcare-workers in acute care hospitals in 2020: a systematic review and meta-analysis. BMC Infect Dis 2022; 22:587. [PMID: 35780088 PMCID: PMC9250183 DOI: 10.1186/s12879-022-07554-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/08/2022] [Indexed: 02/08/2023] Open
Abstract
Background Healthcare workers (HCW) are at increased risk of infection with SARS-CoV-2. Vulnerable patient populations in particular must be protected, and clinics should not become transmission hotspots to avoid delaying medical treatments independent of COVID. Because asymptomatic transmission has been described, routine screening of asymptomatic HCW would potentially be able to interrupt chains of infection through early detection. Methods A systematic search was conducted in the Cochrane COVID-19 Study Register, Web of Science and WHO COVID‐19 Global literature on coronavirus with regard to non-incident related testing of healthcare workers using polymerase chain reaction on May 4th 2021. Studies since January 2020 were included. An assessment of risk of bias and representativeness was performed. Results The search identified 39 studies with heterogeneous designs. Data collection of the included studies took place from January to August 2020. The studies were conducted worldwide and the sample size of the included HCW ranged from 70 to 9449 participants. In total, 1000 of 51,700 (1.9%) asymptomatic HCW were tested positive for SARS-CoV-2 using PCR testing. The proportion of positive test results ranged between 0 and 14.3%. No study reported on HCW-screening related reductions in infected person-days. Discussion and conclusions The heterogeneous proportions might be explained by different regional incidences, lock-downs, and pre-analytical pitfalls that reduce the sensitivity of the nasopharyngeal swab. The very high prevalence in some studies indicates that screening HCW for SARS-CoV-2 may be important particularly in geographical regions and pandemic periods with a high-incidence. With low numbers and an increasing rate of vaccinated HCW, a strict cost–benefit consideration must be made, especially in times of low incidences. Since we found no studies that reported on HCW-screening related reductions in infected person-days, re-evaluation should be done when these are available. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07554-5.
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Affiliation(s)
- J M Jabs
- Institute for Hygiene and Public Health, Bonn University Hospital, Venusberg-Campus 1, 53127, Bonn, Germany
| | - A Schwabe
- Institute for Hygiene and Public Health, Bonn University Hospital, Venusberg-Campus 1, 53127, Bonn, Germany
| | - A D Wollkopf
- Institute for Hygiene and Public Health, Bonn University Hospital, Venusberg-Campus 1, 53127, Bonn, Germany
| | - B Gebel
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - J Stadelmaier
- Institute for Evidence in Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Breisacher Str. 86, 79110, Freiburg, Germany
| | - S Erdmann
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17475, Greifswald, Germany
| | - F Radicke
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17475, Greifswald, Germany
| | - H Grundmann
- Institute for Infection Prevention and Hospital Hygiene, Faculty of Medicine and Medical Center, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - A Kramer
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17475, Greifswald, Germany
| | - I Monsef
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Cochrane Haematology, University Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - G Rücker
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Zinkmattenstraße 6a, 79108, Freiburg, Germany
| | - J Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - S Scheithauer
- Institute of Infection Control and Infectious Diseases, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - C Schmucker
- Institute for Evidence in Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Breisacher Str. 86, 79110, Freiburg, Germany
| | - A Simon
- Clinic for Pediatric Oncology and Hematology, Saarland University Hospital, Kirrberger Straße, 66421, Homburg, Saar, Germany
| | - Nico T Mutters
- Institute for Hygiene and Public Health, Bonn University Hospital, Venusberg-Campus 1, 53127, Bonn, Germany.
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31
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Lee H, Marco Salas S, Gyllborg D, Nilsson M. Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue. Sci Rep 2022; 12:7976. [PMID: 35562352 PMCID: PMC9106737 DOI: 10.1038/s41598-022-11534-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/26/2022] [Indexed: 11/25/2022] Open
Abstract
Highly multiplexed spatial mapping of transcripts within tissues allows for investigation of the transcriptomic and cellular diversity of mammalian organs previously unseen. Here we explore a direct RNA (dRNA) detection approach incorporating the use of padlock probes and rolling circle amplification in combination with hybridization-based in situ sequencing chemistry. We benchmark a High Sensitivity Library Preparation Kit from CARTANA that circumvents the reverse transcription needed for cDNA-based in situ sequencing (ISS) via direct RNA detection. We found a fivefold increase in transcript detection efficiency when compared to cDNA-based ISS and also validated its multiplexing capability by targeting a curated panel of 50 genes from previous publications on mouse brain sections, leading to additional data interpretation such as de novo cell clustering. With this increased efficiency, we also found to maintain specificity, multiplexing capabilities and ease of implementation. Overall, the dRNA chemistry shows significant improvements in target detection efficiency, closing the gap to other fluorescent in situ hybridization-based technologies and opens up possibilities to explore new biological questions previously not possible with cDNA-based ISS.
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Affiliation(s)
- Hower Lee
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65, Solna, Sweden
| | - Sergio Marco Salas
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65, Solna, Sweden
| | - Daniel Gyllborg
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65, Solna, Sweden.
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65, Solna, Sweden.
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32
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Warneford-Thomson R, Shah PP, Lundgren P, Lerner J, Morgan J, Davila A, Abella BS, Zaret K, Schug J, Jain R, Thaiss CA, Bonasio R. A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva. eLife 2022; 11:69949. [PMID: 35532013 PMCID: PMC9084890 DOI: 10.7554/elife.69949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/24/2022] [Indexed: 12/02/2022] Open
Abstract
The COVID-19 pandemic has created an urgent need for rapid, effective, and low-cost SARS-CoV-2 diagnostic testing. Here, we describe COV-ID, an approach that combines RT-LAMP with deep sequencing to detect SARS-CoV-2 in unprocessed human saliva with a low limit of detection (5–10 virions). Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here, we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS calibration standard. The approach was validated on clinical saliva samples, where it showed excellent agreement with RT-qPCR. COV-ID can also be performed directly on saliva absorbed on filter paper, simplifying collection logistics and sample handling.
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Affiliation(s)
- Robert Warneford-Thomson
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Parisha P Shah
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Patrick Lundgren
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jonathan Lerner
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jason Morgan
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Antonio Davila
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,University of Pennsylvania School of Nursing, Philadelphia, United States
| | - Benjamin S Abella
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Kenneth Zaret
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jonathan Schug
- Next-Generation Sequencing Core, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Rajan Jain
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Christoph A Thaiss
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
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33
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Yermanos A, Hong KL, Agrafiotis A, Han J, Nadeau S, Valenzuela C, Azizoglu A, Ehling R, Gao B, Spahr M, Neumeier D, Chang CH, Dounas A, Petrillo E, Nissen I, Burcklen E, Feldkamp M, Beisel C, Oxenius A, Savic M, Stadler T, Rudolf F, Reddy ST. DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. BMC Genomics 2022; 23:289. [PMID: 35410128 PMCID: PMC8995413 DOI: 10.1186/s12864-022-08403-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. RESULTS Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. CONCLUSIONS DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com .
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Affiliation(s)
- Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Botnar Research Centre for Child Health, Basel, Switzerland.
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Botnar Research Centre for Child Health, Basel, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Botnar Research Centre for Child Health, Basel, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Botnar Research Centre for Child Health, Basel, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cecilia Valenzuela
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Asli Azizoglu
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Roy Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Michael Spahr
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Andreas Dounas
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
| | - Ezequiel Petrillo
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ina Nissen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Elodie Burcklen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Mirjam Feldkamp
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Miodrag Savic
- Department of Health, Economics and Health Directorate Canton Basel-Landschaft, Liestal, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Botnar Research Centre for Child Health, Basel, Switzerland.
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34
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
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35
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Palmieri D, Javorina A, Siddiqui J, Gardner A, Fries A, Chapleau RR, Starr C, Fishel R, Miles WO. Mass COVID-19 patient screening using UvsX and UvsY mediated DNA recombination and high throughput parallel sequencing. Sci Rep 2022; 12:4082. [PMID: 35260723 PMCID: PMC8902726 DOI: 10.1038/s41598-022-08034-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 03/01/2022] [Indexed: 01/08/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV), is a highly infectious RNA virus. A percentage of patients develop coronavirus disease 2019 (COVID-19) after infection, whose symptoms include fever, cough, shortness of breath and fatigue. Acute and life-threatening respiratory symptoms are experienced by 10-20% of symptomatic patients, particularly those with underlying medical conditions. One of the main challenges in the containment of COVID-19 is the identification and isolation of asymptomatic/pre-symptomatic individuals. A number of molecular assays are currently used to detect SARS-CoV-2. Many of them can accurately test hundreds or even thousands of patients every day. However, there are presently no testing platforms that enable more than 10,000 tests per day. Here, we describe the foundation for the REcombinase Mediated BaRcoding and AmplificatioN Diagnostic Tool (REMBRANDT), a high-throughput Next Generation Sequencing-based approach for the simultaneous screening of over 100,000 samples per day. The REMBRANDT protocol includes direct two-barcoded amplification of SARS-CoV-2 and control amplicons using an isothermal reaction, and the downstream library preparation for Illumina sequencing and bioinformatics analysis. This protocol represents a potentially powerful approach for community screening of COVID-19 that may be modified for application to any infectious or non-infectious genome.
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Affiliation(s)
- Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Amanda Javorina
- Public Health and Preventive Medicine Department, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Jalal Siddiqui
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Anne Gardner
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Anthony Fries
- Public Health and Preventive Medicine Department, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Richard R Chapleau
- Public Health and Preventive Medicine Department, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Clarise Starr
- Public Health and Preventive Medicine Department, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Wayne O Miles
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
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36
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Zhuang X, Lu X, Lee Yu HL, Hsing IM. Unique Barcoded Primer-Assisted Sample-Specific Pooled Testing (Uni-Pool) for Large-Scale Screening of Viral Pathogens. Anal Chem 2022; 94:4021-4029. [PMID: 35199524 DOI: 10.1021/acs.analchem.1c05204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pooled testing has been widely adopted recently to facilitate large-scale community testing during the COVID-19 pandemic. This strategy allows to collect and screen multiple specimen samples in a single test, thus immensely saving the assay time and consumable expenses. Nevertheless, when the outcome of a pooled testing is positive, it necessitates repetitive retesting steps for each sample which can pose a serious challenge during a rising infection wave of increasing prevalence. In this work, we develop a unique barcoded primer-assisted sample-specific pooled testing strategy (Uni-Pool) where the key genetic sequences of the viral pathogen in a crude sample are extracted and amplified with concurrent tagging of sample-specific identifiers. This new process improves the existing pooled testing by eliminating the need for retesting and allowing the test results-positive or negative-for all samples in the pool to be revealed by multiplex melting curve analysis right after real-time polymerase chain reaction. It significantly reduces the total assay time for large-scale screening without compromising the specificity and detection sensitivity caused by the sample dilution of pooling. Our method was able to successfully differentiate five samples, positive and negative, in one pool with negligible cross-reactivity among the positive and negative samples. A pooling of 40 simulated samples containing severe acute respiratory syndrome coronavirus-2 pseudovirus of different loads (min: 10 copies/μL; max: 103 copies/μL) spiked into artificial saliva was demonstrated in eight randomized pools. The outcome of five samples in one pool with a hypothetical infection prevalence of 15% in 40 samples was successfully tested and validated by a typical Dorman-based pooling.
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Affiliation(s)
- Xinyu Zhuang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Xiao Lu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Henson L Lee Yu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
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37
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Park GS, Maeng JS. A novel isothermal method for amplification of long specific amplicon from linear template. Sci Rep 2022; 12:2756. [PMID: 35177762 PMCID: PMC8854607 DOI: 10.1038/s41598-022-06785-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/31/2022] [Indexed: 11/09/2022] Open
Abstract
Isothermal nucleic acid amplification methods have been successfully developed and applied for diagnostic purpose, especially for detection of pathogens. However, amplicon size of such methods is relatively short (< 500 bp) to limit their application for long amplicon production that can be used for various downstream applications including genomic surveillance of pathogens. To fill the gap, we developed a method for specific amplification of kilobases-long target sequence from RNA templates. This method, named CREA, utilizes sequence specific recombination of Cre recombinase to generate circular intermediate template for subsequent RCA reaction. CREA with SARS-CoV-2 spike template could amplify ~ 2.9 kb target and up to ~ 1.9 kb amplicon was able to produce in sufficient amount for general cloning. Each step of CREA procedure was thoroughly analyzed to provide directions for further optimizations. Furthermore, we evaluated a variation of CREA which utilized DNA ligase.
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Affiliation(s)
- Gun-Soo Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Research Division of Food Convergence, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
| | - Jin-Soo Maeng
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Research Division of Food Convergence, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
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38
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Heithoff DM, Barnes L, Mahan SP, Fox GN, Arn KE, Ettinger SJ, Bishop AM, Fitzgibbons LN, Fried JC, Low DA, Samuel CE, Mahan MJ. Assessment of a Smartphone-Based Loop-Mediated Isothermal Amplification Assay for Detection of SARS-CoV-2 and Influenza Viruses. JAMA Netw Open 2022; 5:e2145669. [PMID: 35089353 PMCID: PMC8800074 DOI: 10.1001/jamanetworkopen.2021.45669] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Importance A critical need exists in low-income and middle-income countries for low-cost, low-tech, yet highly reliable and scalable testing for SARS-CoV-2 virus that is robust against circulating variants. Objective To assess whether a smartphone-based assay is suitable for SARS-CoV-2 and influenza virus testing without requiring specialized equipment, accessory devices, or custom reagents. Design, Setting, and Participants This cohort study enrolled 2 subgroups of participants (symptomatic and asymptomatic) at Santa Barbara Cottage Hospital. The symptomatic group consisted of 20 recruited patients who tested positive for SARS-CoV-2 with symptoms; 30 asymptomatic patients were recruited from the same community, through negative admission screening tests for SARS-CoV-2. The smartphone-based real-time loop-mediated isothermal amplification (smaRT-LAMP) was first optimized for analysis of human saliva samples spiked with either SARS-CoV-2 or influenza A or B virus; these results then were compared with those obtained by side-by-side analysis of spiked samples using the Centers for Disease Control and Prevention (CDC) criterion-standard reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) assay. Next, both assays were used to test for SARS-CoV-2 and influenza viruses present in blinded clinical saliva samples obtained from 50 hospitalized patients. Statistical analysis was performed from May to June 2021. Exposures Testing for SARS-CoV-2 and influenza A and B viruses. Main Outcomes and Measures SARS-CoV-2 and influenza infection status and quantitative viral load were determined. Results Among the 50 eligible participants with no prior SARS-CoV-2 infection included in the study, 29 were men. The mean age was 57 years (range, 21 to 93 years). SmaRT-LAMP exhibited 100% concordance (50 of 50 patient samples) with the CDC criterion-standard diagnostic for SARS-CoV-2 sensitivity (20 of 20 positive and 30 of 30 negative) and for quantitative detection of viral load. This platform also met the CDC criterion standard for detection of clinically similar influenza A and B viruses in spiked saliva samples (n = 20), and in saliva samples from hospitalized patients (50 of 50 negative). The smartphone-based LAMP assay was rapid (25 minutes), sensitive (1000 copies/mL), low-cost (<$7/test), and scalable (96 samples/phone). Conclusions and Relevance In this cohort study of saliva samples from patients, the smartphone-based LAMP assay detected SARS-CoV-2 infection and exhibited concordance with RT-qPCR tests. These findings suggest that this tool could be adapted in response to novel CoV-2 variants and other pathogens with pandemic potential including influenza and may be useful in settings with limited resources.
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Affiliation(s)
- Douglas M Heithoff
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara
| | - Lucien Barnes
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara
| | - Scott P Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis
| | - Gary N Fox
- Department of Materials and Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara
| | - Katherine E Arn
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Sarah J Ettinger
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Andrew M Bishop
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Lynn N Fitzgibbons
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, California
- Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Jeffrey C Fried
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, California
- Department of Pulmonary and Critical Care Medicine, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - David A Low
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara
| | - Charles E Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara
| | - Michael J Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara
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39
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Zhao Y, Fang X, Yu H, Fu Y, Zhao Y. Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus. Anal Chem 2022; 94:927-933. [PMID: 34983181 DOI: 10.1021/acs.analchem.1c03702] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
| | - Xiaoxing Fang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
| | - Huahang Yu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
| | - Youlan Fu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
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40
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Kaymaz SV, Ergenç AF, Aytekin AÖ, Lucas SJ, Elitas M. A low-cost, portable, and practical LAMP device for point-of-diagnosis in the field. Biotechnol Bioeng 2021; 119:994-1003. [PMID: 34953069 DOI: 10.1002/bit.28025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/07/2022]
Abstract
Transition of rapid, ready-to-use, and low-cost nucleic acid-based detection technologies from laboratories to points of sample collection has drastically accelerated. However, most of these approaches are still incapable of diagnosis starting from sampling, through nucleic acid isolation and detection in the field. Here, we developed a simple, portable, low-cost, colorimetric, and remotely controllable platform for reliable, high-throughput, and rapid diagnosis using loop mediated isothermal amplification (LAMP) assays. It consists of a thermally isolated cup, low-cost electronic components, a polydimethylsiloxane sample well, and a fast prototyped case that covers electronic components. The steady-state temperature error of the system is less than 1%. We performed LAMP, Colony-LAMP, and Colony PCR reactions using the yaiO2 primer set for Escherichia coli and Pseudomonas aeruginosa samples at 65˚C and 30 min. We detected the end-point colorimetric readouts by the naked eye under day light. We confirmed the specificity and sensitivity of our approach using pure genomic DNA and crude bacterial colonies. We benchmarked our Colony-LAMP detection against Colony PCR. The number of samples tested can easily be modified for higher throughput in our system. We strongly believe that our platform can greatly contribute rapid and reliable diagnosis in versatile operational environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sümeyra Vural Kaymaz
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ali Fuat Ergenç
- Faculty of Electrical and Electronics Engineering, Department of Control and Automation Eng., Istanbul Technical University, Istanbul, Turkey
| | - Ali Özhan Aytekin
- Faculty of Engineering, Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Center, Istanbul, Turkey
| | - Meltem Elitas
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.,Sabanci University Nanotechnology Research and Application Center, Istanbul, Turkey
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41
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Chappleboim A, Joseph-Strauss D, Rahat A, Sharkia I, Adam M, Kitsberg D, Fialkoff G, Lotem M, Gershon O, Schmidtner AK, Oiknine-Djian E, Klochendler A, Sadeh R, Dor Y, Wolf D, Habib N, Friedman N. Early sample tagging and pooling enables simultaneous SARS-CoV-2 detection and variant sequencing. Sci Transl Med 2021; 13:eabj2266. [PMID: 34591660 PMCID: PMC9928115 DOI: 10.1126/scitranslmed.abj2266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests have relied on RNA extraction followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays. Whereas automation improved logistics and different pooling strategies increased testing capacity, highly multiplexed next-generation sequencing (NGS) diagnostics remain a largely untapped resource. NGS tests have the potential to markedly increase throughput while providing crucial SARS-CoV-2 variant information. Current NGS-based detection and genotyping assays for SARS-CoV-2 are costly, mostly due to parallel sample processing through multiple steps. Here, we have established ApharSeq, in which samples are barcoded in the lysis buffer and pooled before reverse transcription. We validated this assay by applying ApharSeq to more than 500 clinical samples from the Clinical Virology Laboratory at Hadassah hospital in a robotic workflow. The assay was linear across five orders of magnitude, and the limit of detection was Ct 33 (~1000 copies/ml, 95% sensitivity) with >99.5% specificity. ApharSeq provided targeted high-confidence genotype information due to unique molecular identifiers incorporated into this method. Because of early pooling, we were able to estimate a 10- to 100-fold reduction in labor, automated liquid handling, and reagent requirements in high-throughput settings compared to current testing methods. The protocol can be tailored to assay other host or pathogen RNA targets simultaneously. These results suggest that ApharSeq can be a promising tool for current and future mass diagnostic challenges.
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Affiliation(s)
- Alon Chappleboim
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ayelet Rahat
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Israa Sharkia
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Miriam Adam
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daniel Kitsberg
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Gavriel Fialkoff
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Matan Lotem
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Gershon
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Anna-Kristina Schmidtner
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Esther Oiknine-Djian
- Hadassah Hebrew University Medical Center, Jerusalem 9112001, Israel.,Lautenberg Centre for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ronen Sadeh
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Dana Wolf
- Hadassah Hebrew University Medical Center, Jerusalem 9112001, Israel.,Lautenberg Centre for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Naomi Habib
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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