1
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Yang Y, Tan J, Wang F, Sun W, Shi H, Cheng Z, Xie Y, Zhou X. Preconcentration and detection of SARS-CoV-2 in wastewater: A comprehensive review. Biosens Bioelectron 2024; 263:116617. [PMID: 39094290 DOI: 10.1016/j.bios.2024.116617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/17/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) affected the health of human beings and the global economy. The patients with SARS-CoV-2 infection had viral RNA or live infectious viruses in feces. Thus, the possible transmission of SARS-CoV-2 through wastewater received great attentions. Moreover, SARS-CoV-2 in wastewater can serve as an early indicator of the infection within communities. We summarized the preconcentration and detection technology of SARS-CoV-2 in wastewater aiming at the complex matrices of wastewater and low virus concentration and compared their performance characteristics. We described the emerging tests that would be possible to realize the rapid detection of SARS-CoV-2 in fields and encourage academics to advance their technologies beyond conception. We concluded with a brief discussion on the outlook for integrating preconcentration and the detection of SARS-CoV-2 with emerging technologies.
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Affiliation(s)
- Yihan Yang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jisui Tan
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Fan Wang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Weiming Sun
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hanchang Shi
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zhao Cheng
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yangcun Xie
- Chinese Academy of Environmental Planning, Beijing, 100043, China.
| | - Xiaohong Zhou
- School of Environment, Tsinghua University, Beijing, 100084, China.
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2
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Fang M, Wang Y, Yang T, Zhang J, Yu H, Luo Z, Su B, Lin X. Nucleic Acid Plate Culture: Label-Free and Naked-Eye-Based Digital Loop-Mediated Isothermal Amplification in Hydrogel with Machine Learning. ACS Sens 2024; 9:2010-2019. [PMID: 38602267 DOI: 10.1021/acssensors.3c02807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Digital nucleic acid amplification enables the absolute quantification of single molecules. However, due to the ultrasmall reaction volume in the digital system (i.e., short light path), most digital systems are limited to fluorescence signals, while label-free and naked-eye readout remain challenging. In this work, we report a digital nucleic acid plate culture method for label-free, ultrasimple, and naked-eye nucleic acid analysis. As simple as the bacteria culture, the nanoconfined digital loop-mediated isothermal amplification was performed by using polyacrylamide (PAM) hydrogel as the amplification matrix. The nanoconfinement of PAM hydrogel with an ionic polymer chain can remarkably accelerate the amplification of target nucleic acids and the growth of inorganic byproducts, namely, magnesium pyrophosphate particles (MPPs). Compared to that in aqueous solutions, MPPs trapped in the hydrogel with enhanced light scattering characteristics are clearly visible to the naked eye, forming white "colony" spots that can be simply counted in a label-free and instrument-free manner. The MPPs can also be photographed by a smartphone and automatically counted by a machine-learning algorithm to realize the absolute quantification of antibiotic-resistant pathogens in diverse real samples.
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Affiliation(s)
- Mei Fang
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
| | - Yiru Wang
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
| | - Tao Yang
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
| | - Jing Zhang
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
| | - Bin Su
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Xingyu Lin
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
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3
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Akter J, Smith WJM, Gebrewold M, Kim I, Simpson SL, Bivins A, Ahmed W. Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167964. [PMID: 37865239 DOI: 10.1016/j.scitotenv.2023.167964] [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: 09/22/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea; CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Metasebia Gebrewold
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea
| | | | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
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4
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Reyes-Morales R, Segundo-Ibañez P, Flores-de Los Ángeles C, Vizcarra-Ramos D, Ibañez-Galeana DI, Salas-Cuevas G, Olvera-Serrano Á, Pérez-Silva NB, Rocha-Rocha VM, El-Kassi EG, Escobedo-Straffon J, Contreras-Mioni L, Rosas-Díaz M, Lopez-Martinez KM, Arias-Matus CE, Bautista-Rodriguez E, Nolasco-Quiroga M. Reverse transcription loop‑mediated isothermal amplification has a high performance in the detection of SARS‑CoV‑2 in saliva samples and nasal swabs from asymptomatic and symptomatic individuals. Exp Ther Med 2023; 26:398. [PMID: 37522063 PMCID: PMC10375439 DOI: 10.3892/etm.2023.12097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/31/2023] [Indexed: 08/01/2023] Open
Abstract
The detection of coronavirus disease 2019 cases represents a significant challenge at the epidemiological level. Limitations exist in effectively detecting asymptomatic cases, achieving good follow-up in hospitals without the infrastructure for reverse transcription-quantitative PCR (RT-qPCR) or in difficult-to-access areas and developing methods with the need for less invasive sampling procedures. Therefore, the present study evaluated the performance of the direct reverse transcription loop-mediated isothermal amplification (RT-LAMP) test for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the saliva and nasal samples of asymptomatic individuals belonging to the university population. In addition, this test was also assessed for effectiveness in symptomatic individuals referred from a hospital with poor infrastructure in molecular biology and located outside the urban area. The RT-LAMP assay was compared with the results obtained from the RT-qPCR nasopharyngeal swab test, where the diagnosis was confirmed by lateral flow immunoassay test for rapid antigen detection. A total of 128 samples were analyzed, of which 43% were symptomatic positive individuals, 25% were asymptomatic positive individuals and 32% were SARS-CoV2-negative control individuals. Among positive individuals, no differences were found between the Cq values determined by RT-qPCR. A sensitivity of 96.5% and a specificity of 97.6% was reported for the detection of SARS-CoV-2 in symptomatic individuals by salivary and nasal RT-LAMP, as well as a sensitivity of 100% and a specificity of 97.6% for the detection of SARS-CoV-2 in asymptomatic individuals. These findings indicated that performance of the direct RT-LAMP test using saliva and nasal samples has high sensitivity and specificity, which in turn suggest that it is a viable and reliable alternative for use in epidemiological monitoring.
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Affiliation(s)
- Rodolfo Reyes-Morales
- Laboratory of Medical and Pharmaceutical Biotechnology, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Patricia Segundo-Ibañez
- Molecular Biology Laboratory, Biotechnology Department, Interamerican University, Puebla 72828, Mexico
| | - César Flores-de Los Ángeles
- Molecular Diagnostic Laboratory, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - David Vizcarra-Ramos
- Molecular Biology Laboratory, Biotechnology Department, Interamerican University, Puebla 72828, Mexico
| | | | - Gabriela Salas-Cuevas
- COVID Area of Hospital Clinic Huauchinango, Institute of Social Security and Services for State Workers, Huauchinango, Puebla 73160, Mexico
| | - Ángel Olvera-Serrano
- COVID Area of Hospital Clinic Huauchinango, Institute of Social Security and Services for State Workers, Huauchinango, Puebla 73160, Mexico
| | - Nancy Bibiana Pérez-Silva
- Molecular Diagnostic Laboratory, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Valeria Magali Rocha-Rocha
- Biological Science Department, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Elie Girgis El-Kassi
- Biological Science Department, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Jorge Escobedo-Straffon
- Biological Science Department, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Laura Contreras-Mioni
- Biological Science Department, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Marisol Rosas-Díaz
- Molecular Biology Laboratory, Multidisciplinary Academic Unit Reynosa-Aztlan Reynosa, Autonomous University of Tamaulipas, Tamaulipas 88740, Mexico
| | - Karla María Lopez-Martinez
- Laboratory of Medical and Pharmaceutical Biotechnology, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Carlos Eduardo Arias-Matus
- Laboratory of Medical and Pharmaceutical Biotechnology, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Elizabeth Bautista-Rodriguez
- Laboratory of Medical and Pharmaceutical Biotechnology, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Manuel Nolasco-Quiroga
- COVID Area of Hospital Clinic Huauchinango, Institute of Social Security and Services for State Workers, Huauchinango, Puebla 73160, Mexico
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5
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Yan Y, Yang T, Luo Z, Li D, Li L, Lin X. Ultrasensitive quantification of pathogens in milliliters of beverage by filtration-based digital LAMP. Food Chem 2023; 408:135226. [PMID: 36549156 DOI: 10.1016/j.foodchem.2022.135226] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The quantitative detection of pathogens in milliliters of beverage sample requires complex preprocessing. To achieve rapid and ultrasensitive quantification of pathogens in large volume food sample, we developed a filtration-based interfacial digital LAMP (idLAMP) system, which consists of a nanoporous membrane for filtration and nanoporous hydrogel for digital amplification. Digital counting of single bacteria at the membrane surface under nanoconfinement could be achieved. The idLAMP successfully accomplished the quantitative detection of Escherichia coli in 100 mL water samples within 30 min, with wide dynamic range from 0.09 to 900 cells/mL. This technique could also be well applied to the quantification of Escherichia coli and Salmonella typhi in real beverage samples (juice, tea drinks, carbonated drinks and alcoholic drinks) without tedious sample pretreatments. With facile operation, higher specificity and sensitivity and better end-point analysis capabilities, the system has great potential in quantitative counting of single bacteria in large-volume food samples.
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Affiliation(s)
- Yuhua Yan
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, China
| | - Tao Yang
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, China; Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China; Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Dong Li
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, China; Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Li Li
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, China; Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Xingyu Lin
- College of Biosystems Engineering and Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, China; Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China; Ningbo Research Institute, Zhejiang University, Ningbo, China.
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6
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Sen P, Zhang Z, Li P, Adhikari BR, Guo T, Gu J, MacIntosh AR, van der Kuur C, Li Y, Soleymani L. Integrating Water Purification with Electrochemical Aptamer Sensing for Detecting SARS-CoV-2 in Wastewater. ACS Sens 2023; 8:1558-1567. [PMID: 36926840 PMCID: PMC10042147 DOI: 10.1021/acssensors.2c02655] [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: 12/04/2022] [Accepted: 03/02/2023] [Indexed: 03/18/2023]
Abstract
Wastewater analysis of pathogens, particularly SARS-CoV-2, is instrumental in tracking and monitoring infectious diseases in a population. This method can be used to generate early warnings regarding the onset of an infectious disease and predict the associated infection trends. Currently, wastewater analysis of SARS-CoV-2 is almost exclusively performed using polymerase chain reaction for the amplification-based detection of viral RNA at centralized laboratories. Despite the development of several biosensing technologies offering point-of-care solutions for analyzing SARS-CoV-2 in clinical samples, these remain elusive for wastewater analysis due to the low levels of the virus and the interference caused by the wastewater matrix. Herein, we integrate an aptamer-based electrochemical chip with a filtration, purification, and extraction (FPE) system for developing an alternate in-field solution for wastewater analysis. The sensing chip employs a dimeric aptamer, which is universally applicable to the wild-type, alpha, delta, and omicron variants of SARS-CoV-2. We demonstrate that the aptamer is stable in the wastewater matrix (diluted to 50%) and its binding affinity is not significantly impacted. The sensing chip demonstrates a limit of detection of 1000 copies/L (1 copy/mL), enabled by the amplification provided by the FPE system. This allows the integrated system to detect trace amounts of the virus in native wastewater and categorize the amount of contamination into trace (<10 copies/mL), medium (10-1000 copies/mL), or high (>1000 copies/mL) levels, providing a viable wastewater analysis solution for in-field use.
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Affiliation(s)
- Payel Sen
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Phoebe Li
- Department of Physics, McMaster
University, Hamilton L8S 4K1, Canada
| | - Bal Ram Adhikari
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Tianyi Guo
- Forsee Instruments, Ltd.,
Hamilton L8P0A1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
| | | | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
- School of Biomedical Engineering, McMaster
University, Hamilton L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease
Research, McMaster University, Hamilton L8S 4K1,
Canada
| | - Leyla Soleymani
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
- School of Biomedical Engineering, McMaster
University, Hamilton L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease
Research, McMaster University, Hamilton L8S 4K1,
Canada
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7
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Sellam AZ, Benlamoudi A, Cid CA, Dobelle L, Slama A, El Hillali Y, Taleb-Ahmed A. Deep Learning Solution for Quantification of Fluorescence Particles on a Membrane. SENSORS (BASEL, SWITZERLAND) 2023; 23:1794. [PMID: 36850392 PMCID: PMC9967937 DOI: 10.3390/s23041794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The detection and quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus particles in ambient waters using a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) method can play an important role in large-scale environmental surveillance for early warning of potential outbreaks. However, counting particles or cells in fluorescence microscopy is an expensive, time-consuming, and tedious task that only highly trained technicians and researchers can perform. Although such objects are generally easy to identify, manually annotating cells is occasionally prone to fatigue errors and arbitrariness due to the operator's interpretation of borderline cases. In this research, we proposed a method to detect and quantify multiscale and shape variant SARS-CoV-2 fluorescent cells generated using a portable (mgLAMP) system and captured using a smartphone camera. The proposed method is based on the YOLOv5 algorithm, which uses CSPnet as its backbone. CSPnet is a recently proposed convolutional neural network (CNN) that duplicates gradient information within the network using a combination of Dense nets and ResNet blocks, and bottleneck convolution layers to reduce computation while at the same time maintaining high accuracy. In addition, we apply the test time augmentation (TTA) algorithm in conjunction with YOLO's one-stage multihead detection heads to detect all cells of varying sizes and shapes. We evaluated the model using a private dataset provided by the Linde + Robinson Laboratory, California Institute of Technology, United States. The model achieved a mAP@0.5 score of 90.3 in the YOLOv5-s6.
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Affiliation(s)
- Abdellah Zakaria Sellam
- Institute of Applied Sciences and Intelligent Systems, National Research Council of Italy, 73100 Lecce, Italy
| | - Azeddine Benlamoudi
- Laboratoire de Génie Électrique, Faculté des Nouvelles Technologies de l’Information et de la Communication, Université Ouargla, Ouargla 30000, Algeria
| | - Clément Antoine Cid
- Linde Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leopold Dobelle
- Linde Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amina Slama
- Faculty of Humanities and Social Sciences, Mohamed Khider University of Biskra, Biskra 07000, Algeria
| | - Yassin El Hillali
- Institut d’Electronique de Microélectronique et de Nanotechnologie (IEMN), UMR 8520, Université Polytechnique Hauts de France, Université de Lille, CNRS, 59313 Valenciennes, France
| | - Abdelmalik Taleb-Ahmed
- Institut d’Electronique de Microélectronique et de Nanotechnologie (IEMN), UMR 8520, Université Polytechnique Hauts de France, Université de Lille, CNRS, 59313 Valenciennes, France
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8
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Yang T, Li D, Yan Y, Ettoumi FE, Wu RA, Luo Z, Yu H, Lin X. Ultrafast and absolute quantification of SARS-CoV-2 on food using hydrogel RT-LAMP without pre-lysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130050. [PMID: 36182888 PMCID: PMC9507997 DOI: 10.1016/j.jhazmat.2022.130050] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 05/13/2023]
Abstract
With rapid growing of environmental contact infection, more and more attentions are focused on the precise and absolute quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus on cold chain foods via point-of-care test (POCT). In this work, we propose a hydrogel-mediated reverse transcription loop-mediated isothermal amplification (RT-LAMP) for ultrafast and absolute quantification of SARS-CoV-2. Cross-linked hydrogel offers opportunities for digital single molecule amplification in nanoconfined spaces, facilitating the virus lysis, RNA reverse transcription and amplification process, which is about 3.4-fold faster than conventional bulk RT-LAMP. Ultrafast quantification of SARS-CoV-2 is accomplished in 15 min without virus pre-lysis and RNA extraction. The sensitivity can accurately quantify SARS-CoV-2 down to 0.5 copy/μL. Furthermore, the integrated system has an excellent specificity, reproducibility and storage stability, which can be also used to test SARS-CoV-2 on various cold chain fruits. The developed ultrafast and simple hydrogel RT-LAMP will be an enormous potential for surveillance of virus or other hazardous microbes in environmental, agricultural and food industry.
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Affiliation(s)
- Tao Yang
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Dong Li
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Yuhua Yan
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Fatima-Ezzahra Ettoumi
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Ricardo A Wu
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China; Ningbo Research Institute, Zhejiang University, 310058, China
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Xingyu Lin
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China; Ningbo Research Institute, Zhejiang University, 310058, China.
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9
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Corpuz MVA, Buonerba A, Zarra T, Hasan SW, Korshin GV, Belgiorno V, Naddeo V. Advances in virus detection methods for wastewater-based epidemiological applications. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100238. [PMID: 37520925 PMCID: PMC9339091 DOI: 10.1016/j.cscee.2022.100238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 06/08/2023]
Abstract
Wastewater-based epidemiology (WBE) is a powerful tool that has the potential to reveal the extent of an ongoing disease outbreak or to predict an emerging one. Recent studies have shown that SARS-CoV-2 concentration in wastewater may be correlated with the number of COVID-19 cases in the corresponding population. Most of the recent studies and applications of wastewater-based surveillance of SARS-CoV-2 applied the "gold standard" real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) detection method. However, this method also has its limitations. The paper aimed to present recent improvements and applications of the PCR-based methods for SARS-CoV-2 monitoring in wastewater. Furthermore, it aimed to review alternative methods utilized and/or proposed for the detection of the virus in wastewater matrices. From the review, it was found that several studies have investigated the use of reverse-transcription digital polymerase reaction (RT-dPCR), which was generally shown to have a lower limit of detection (LOD) over the RT-qPCR. Aside from this, non-PCR-based and non-RNA based methods have also been explored for the detection of SARS-CoV-2 in wastewater, with detailed attention given to the detection of SARS-CoV-2 proteins. The potential methods for protein detection include mass spectrometry, the use of immunosensors, and nanotechnological applications. In addition, the review of recent studies also revealed two types of emerging methods related to the detection of SARS-CoV-2 in wastewater: i) capsid-integrity assays to infer about the infectivity of SARS-CoV-2 present in wastewater, and ii) alternative methods for detection of SARS-CoV-2 variants of concern (VOCs) in wastewater. The recent studies on proposed methods of SARS-CoV-2 detection in wastewater have considered improving this approach in one or more of the following aspects: rapidity, simplicity, cost, sensitivity, and specificity. However, further studies are needed in order to realize the full application of these methods for WBE in the field.
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Affiliation(s)
- Mary Vermi Aizza Corpuz
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines
| | - Antonio Buonerba
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Via Giovanni Paolo II-132, 84084, Fisciano, Italy
| | - Tiziano Zarra
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II-132, 84084, Fisciano, Italy
| | - Shadi W Hasan
- Department of Chemical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Gregory V Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA, 98105-2700, United States
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II-132, 84084, Fisciano, Italy
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II-132, 84084, Fisciano, Italy
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10
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Hoar C, McClary-Gutierrez J, Wolfe MK, Bivins A, Bibby K, Silverman AI, McLellan SL. Looking Forward: The Role of Academic Researchers in Building Sustainable Wastewater Surveillance Programs. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:125002. [PMID: 36580023 PMCID: PMC9799055 DOI: 10.1289/ehp11519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND In just over 2 years, tracking the COVID-19 pandemic through wastewater surveillance advanced from early reports of successful SARS-CoV-2 RNA detection in untreated wastewater to implementation of programs in at least 60 countries. Early wastewater monitoring efforts primarily originated in research laboratories and are now transitioning into more formal surveillance programs run in commercial and public health laboratories. A major challenge in this progression has been to simultaneously optimize methods and build scientific consensus while implementing surveillance programs, particularly during the rapidly changing landscape of the pandemic. Translating wastewater surveillance results for effective use by public health agencies also remains a key objective for the field. OBJECTIVES We examined the evolution of wastewater surveillance to identify model collaborations and effective partnerships that have created rapid and sustained success. We propose needed areas of research and key roles academic researchers can play in the framework of wastewater surveillance to aid in the transition from early monitoring efforts to more formalized programs within the public health system. DISCUSSION Although wastewater surveillance has rapidly developed as a useful public health tool for tracking COVID-19, there remain technical challenges and open scientific questions that academic researchers are equipped to address. This includes validating methodology and backfilling important knowledge gaps, such as fate and transport of surveillance targets and epidemiological links to wastewater concentrations. Our experience in initiating and implementing wastewater surveillance programs in the United States has allowed us to reflect on key barriers and draw useful lessons on how to promote synergy between different areas of expertise. As wastewater surveillance programs are formalized, the working relationships developed between academic researchers, commercial and public health laboratories, and data users should promote knowledge co-development. We believe active involvement of academic researchers will contribute to building robust surveillance programs that will ultimately provide new insights into population health. https://doi.org/10.1289/EHP11519.
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Affiliation(s)
- Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, New York, USA
| | - Jill McClary-Gutierrez
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marlene K. Wolfe
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Indiana, USA
| | - Andrea I. Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, New York, USA
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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11
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Cao H, Mao K, Ran F, Xu P, Zhao Y, Zhang X, Zhou H, Yang Z, Zhang H, Jiang G. Paper Device Combining CRISPR/Cas12a and Reverse-Transcription Loop-Mediated Isothermal Amplification for SARS-CoV-2 Detection in Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13245-13253. [PMID: 36040863 PMCID: PMC9454323 DOI: 10.1021/acs.est.2c04727] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 05/04/2023]
Abstract
Wastewater-based surveillance of the COVID-19 pandemic holds great promise; however, a point-of-use detection method for SARS-CoV-2 in wastewater is lacking. Here, a portable paper device based on CRISPR/Cas12a and reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with excellent sensitivity and specificity was developed for SARS-CoV-2 detection in wastewater. Three primer sets of RT-LAMP and guide RNAs (gRNAs) that could lead Cas12a to recognize target genes via base pairing were used to perform the high-fidelity RT-LAMP to detect the N, E, and S genes of SARS-CoV-2. Due to the trans-cleavage activity of CRISPR/Cas12a after high-fidelity amplicon recognition, carboxyfluorescein-ssDNA-Black Hole Quencher-1 and carboxyfluorescein-ssDNA-biotin probes were adopted to realize different visualization pathways via a fluorescence or lateral flow analysis, respectively. The reactions were integrated into a paper device for simultaneously detecting the N, E, and S genes with limits of detection (LODs) of 25, 310, and 10 copies/mL, respectively. The device achieved a semiquantitative analysis from 0 to 310 copies/mL due to the different LODs of the three genes. Blind experiments demonstrated that the device was suitable for wastewater analysis with 97.7% sensitivity and 82% semiquantitative accuracy. This is the first semiquantitative endpoint detection of SARS-CoV-2 in wastewater via different LODs, demonstrating a promising point-of-use method for wastewater-based surveillance.
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Affiliation(s)
- Haorui Cao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
- University of Chinese Academy of
Sciences, Beijing100049, China
| | - Kang Mao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Fang Ran
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Pengqi Xu
- Precision Medicine Center, The Seventh
Affiliated Hospital, Sun Yat-sen University, Shenzhen518107,
China
| | - Yirong Zhao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
- University of Chinese Academy of
Sciences, Beijing100049, China
| | - Xiangyan Zhang
- Guizhou Provincial People’s
Hospital, Guiyang550002, China
| | - Hourong Zhou
- Guizhou Provincial People’s
Hospital, Guiyang550002, China
- Jiangjunshan Hospital of Guizhou
Province, Guiyang550001, China
| | - Zhugen Yang
- School of Water, Energy, and Environment,
Cranfield University, CranfieldMK43 0AL,
UK
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing100085, China
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12
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Bivins A, Kaya D, Ahmed W, Brown J, Butler C, Greaves J, Leal R, Maas K, Rao G, Sherchan S, Sills D, Sinclair R, Wheeler RT, Mansfeldt C. Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155347. [PMID: 35460780 PMCID: PMC9020839 DOI: 10.1016/j.scitotenv.2022.155347] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 05/09/2023]
Abstract
Much of what is known and theorized concerning passive sampling techniques has been developed considering chemical analytes. Yet, historically, biological analytes, such as Salmonella typhi, have been collected from wastewater via passive sampling with Moore swabs. In response to the COVID-19 pandemic, passive sampling is re-emerging as a promising technique to monitor SARS-CoV-2 RNA in wastewater. Method comparisons and disease surveillance using composite, grab, and passive sampling for SARS-CoV-2 RNA detection have found passive sampling with a variety of materials routinely produced qualitative results superior to grab samples and useful for sub-sewershed surveillance of COVID-19. Among individual studies, SARS-CoV-2 RNA concentrations derived from passive samplers demonstrated heterogeneous correlation with concentrations from paired composite samples ranging from weak (R2 = 0.27, 0.31) to moderate (R2 = 0.59) to strong (R2 = 0.76). Among passive sampler materials, electronegative membranes have shown great promise with linear uptake of SARS-CoV-2 RNA observed for exposure durations of 24 to 48 h and in several cases RNA positivity on par with composite samples. Continuing development of passive sampling methods for the surveillance of infectious diseases via diverse forms of fecal waste should focus on optimizing sampler materials for the efficient uptake and recovery of biological analytes, kit-free extraction, and resource-efficient testing methods capable of rapidly producing qualitative or quantitative data. With such refinements passive sampling could prove to be a fundamental tool for scaling wastewater surveillance of infectious disease, especially among the 1.8 billion persons living in low-resource settings served by non-traditional wastewater collection infrastructure.
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Affiliation(s)
- Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA.
| | - Devrim Kaya
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
| | - Caitlyn Butler
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, 130 Natural Resources Rd., Amherst, MA 01003, USA
| | - Justin Greaves
- School of Environmental Sustainability, Loyola University Chicago, 6364 N. Sheridan Rd, Chicago, IL 60660, USA
| | - Raeann Leal
- Loma Linda University, School of Public Health, 24951 North Circle Drive, Loma Linda, CA 92354, USA
| | - Kendra Maas
- Microbial Analyses, Resources, and Services Facility, University of Connecticut, Storrs, CT 06269, USA
| | - Gouthami Rao
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
| | - Samendra Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA; Center for Climate and Health, Morgan State University, Baltimore, MD 21251, USA
| | - Deborah Sills
- Bucknell University, Department of Civil and Environmental Engineering, Lewisburg, PA 17837, USA
| | - Ryan Sinclair
- Loma Linda University, School of Public Health, 24951 North Circle Drive, Loma Linda, CA 92354, USA
| | - Robert T Wheeler
- Department of Molecular & Biomedical Sciences, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA
| | - Cresten Mansfeldt
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, 1111 Engineering Drive, Boulder, CO 80309, USA; University of Colorado Boulder, Environmental Engineering Program, 4001 Discovery Dr, Boulder, CO 80303, USA
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13
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Sullivan BP, Chou YS, Bender AT, Martin CD, Kaputa ZG, March H, Song M, Posner JD. Quantitative isothermal amplification on paper membranes using amplification nucleation site analysis. LAB ON A CHIP 2022; 22:2352-2363. [PMID: 35548880 PMCID: PMC9202034 DOI: 10.1039/d2lc00007e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and viral RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.
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Affiliation(s)
- Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Yu-Shan Chou
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Coleman D Martin
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Zoe G Kaputa
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Hugh March
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Minyung Song
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
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