1
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Lin TT, Wang JW, Shi QN, Wang HF, Pan JZ, Fang Q. An automated, fully-integrated nucleic acid analyzer based on microfluidic liquid handling robot technique. Anal Chim Acta 2023; 1239:340698. [PMID: 36628766 DOI: 10.1016/j.aca.2022.340698] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 10/29/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022]
Abstract
On-site nucleic acid testing (NAT) plays an important role for disease monitoring and pathogen diagnosis. In this work, we developed an automated and fully-integrated nucleic acid analyzer by combining the automated liquid handling robot technique with the microfluidic droplet-based real-time PCR assay technique. The present analyzer could achieve multiple operations including sample introduction, nucleic acid extraction based on magnetic solid-phase extraction, reverse transcription and, sample droplet generation, PCR amplification, real-time and dual fluorescence detection of droplet array. A strategy of constructing an integrated compact and low-cost system was adopted to minimize the analyzer size to 50 × 45 × 45 cm (length × width × height), and reduce the instrument cost to ca. $900 with a single analysis cost less than $5. A simple chip was also designed to pre-load reagents and carry oil-covered PCR reaction droplets. We applied the analyzer to identify eight types of influenza pathogens in human throat swabs, and the results were consistent with the colloidal gold method.
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Affiliation(s)
- Tong-Tong Lin
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Wei Wang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Nuan Shi
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Feng Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China.
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China; Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou, 310007, China; College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.
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2
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Relich RF, Abbott AN. Syndromic and Point-of-Care Molecular Testing. Clin Lab Med 2022; 42:507-531. [PMID: 36368779 DOI: 10.1016/j.cll.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan F Relich
- Division of Clinical Microbiology, Indiana University Health Pathology Laboratory, Indiana University Health and Indiana University School of Medicine, Suite 6027E, 350 West 11th Street, Indianapolis, IN 46202, USA.
| | - April N Abbott
- Department of Laboratory Medicine, Deaconess Hospital, 600 Mary Street, Evansville, IN 47747, USA
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3
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Clinical performance of SARS-CoV-2 detection on the cobas Liat using water gargle samples. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100108. [PMID: 36117531 PMCID: PMC9468300 DOI: 10.1016/j.jcvp.2022.100108] [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: 08/04/2022] [Revised: 09/04/2022] [Accepted: 09/12/2022] [Indexed: 11/22/2022] Open
Abstract
Spring water gargle (SWG) is a suitable, non-invasive, alternative specimen for SARS-CoV-2 detection by RT-PCR. This study sought to evaluate the performance of the cobas Liat point-of-care system for the detection of SARS-CoV-2 in SWG samples. SWG samples and standard oral and nasopharyngeal swab (ONPS) were collected simultaneously from participants in a COVID-19 screening clinic, in November and December 2020. Both sample types were analyzed in parallel on the cobas Liat platform and with the Seegene Allplex 2019-nCoV assay. Among the 110 participants, 53% had compatible symptoms and 71% had a contact with a confirmed COVID-19 case. Only two (1.8%) individuals had neither symptoms nor contact. Amongst 110 paired samples, 25 (23%) were positive for SARS-CoV-2 on the cobas Liat for a least one sample type, with a kappa coefficient of 0.92. Agreement between the cobas Liat platform and the Seegene assay was also excellent (kappa coefficient values of 0.94 and 0.95). Two SWG samples failed to provide a positive result when their ONPS pair was positive, but their cycle threshold (Ct) values were >35 on the Seegene assay, reflecting a low viral load. Overall, the performance of the cobas Liat platform is excellent for the detection of SARS-CoV-2 in SWG samples in a high pre-test probability population.
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4
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Cong H, Zhang N. Perspectives in translating microfluidic devices from laboratory prototyping into scale-up production. BIOMICROFLUIDICS 2022; 16:021301. [PMID: 35350441 PMCID: PMC8933055 DOI: 10.1063/5.0079045] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/23/2022] [Indexed: 05/05/2023]
Abstract
Transforming lab research into a sustainable business is becoming a trend in the microfluidic field. However, there are various challenges during the translation process due to the gaps between academia and industry, especially from laboratory prototyping to industrial scale-up production, which is critical for potential commercialization. In this Perspective, based on our experience in collaboration with stakeholders, e.g., biologists, microfluidic engineers, diagnostic specialists, and manufacturers, we aim to share our understanding of the manufacturing process chain of microfluidic cartridge from concept development and laboratory prototyping to scale-up production, where the scale-up production of commercial microfluidic cartridges is highlighted. Four suggestions from the aspect of cartridge design for manufacturing, professional involvement, material selection, and standardization are provided in order to help scientists from the laboratory to bring their innovations into pre-clinical, clinical, and mass production and improve the manufacturability of laboratory prototypes toward commercialization.
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Affiliation(s)
- Hengji Cong
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical & Materials Engineering, University College Dublin, Dublin 4, Ireland
| | - Nan Zhang
- Author to whom correspondence should be addressed:
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5
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Towards an in-situ non-lethal rapid test to accurately detect the presence of the nematode parasite, Anguillicoloides crassus, in European eel, Anguilla anguilla. Parasitology 2022; 149:605-611. [PMID: 35042576 PMCID: PMC10090626 DOI: 10.1017/s0031182021002146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Anguillicoloides crassus is an invasive nematode parasite of the critically endangered European eel, Anguilla anguilla, and possibly one of the primary drivers of eel population collapse, impacting many features of eel physiology and life history. Early detection of the parasite is vital to limit the spread of A. crassus, to assess its potential impact on spawning biomass. However accurate diagnosis of infection could only be achieved via necropsy. To support eel fisheries management we developed a rapid, non-lethal, minimally invasive and in situ DNA-based method to infer the presence of the parasite in the swim bladder. Screening of 131 wild eels was undertaken between 2017 and 2019 in Ireland and UK to validate the procedure. DNA extractions and PCR were conducted using both a Qiagen Stool kit and in situ using Whatman qualitative filter paper No1 and a miniPCR DNA Discovery-System™. Primers were specifically designed to target the cytochrome oxidase mtDNA gene region and in situ extraction and amplification takes approximately 3 h for up to 16 individuals. Our in-situ diagnostic procedure demonstrated positive predictive values at 96% and negative predictive values at 87% by comparison to necropsy data. Our method could be a valuable tool in the hands of fisheries managers to enable infection control and help protect this iconic but critically endangered species.
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6
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Gaňová M, Zhang H, Zhu H, Korabečná M, Neužil P. Multiplexed digital polymerase chain reaction as a powerful diagnostic tool. Biosens Bioelectron 2021; 181:113155. [PMID: 33740540 DOI: 10.1016/j.bios.2021.113155] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/13/2021] [Accepted: 03/06/2021] [Indexed: 01/30/2023]
Abstract
The digital polymerase chain reaction (dPCR) multiplexing method can simultaneously detect and quantify closely related deoxyribonucleic acid sequences in complex mixtures. The dPCR concept is continuously improved by the development of microfluidics and micro- and nanofabrication, and different complex techniques are introduced. In this review, we introduce dPCR techniques based on sample compartmentalization, droplet- and chip-based systems, and their combinations. We then discuss dPCR multiplexing methods in both laboratory research settings and advanced or routine clinical applications. We focus on their strengths and weaknesses with regard to the character of biological samples and to the required precision of such analysis, as well as showing recently published work based on those methods. Finally, we envisage possible future achievements in this field.
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Affiliation(s)
- Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Haoqing Zhang
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Hanliang Zhu
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Marie Korabečná
- 1st Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University and General University Hospital, 12800, Prague, Czech Republic
| | - Pavel Neužil
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China; The Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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7
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Zhang JY, Bender AT, Boyle DS, Drain PK, Posner JD. Current state of commercial point-of-care nucleic acid tests for infectious diseases. Analyst 2021; 146:2449-2462. [PMID: 33899053 PMCID: PMC8139840 DOI: 10.1039/d0an01988g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic has put the spotlight on the urgent need for integrated nucleic acid tests (NATs) for infectious diseases, especially those that can be used near patient ("point-of-care", POC), with rapid results and low cost, but without sacrificing sensitivity or specificity of gold standard PCR tests. In the US, the Clinical Laboratory Improvement Amendments Certificate of Waiver (CLIA-waiver) is mandated by the Food and Drug Administration (FDA) and designated to any laboratory testing with high simplicity and low risk for error, suitable for application in the POC. Since the first issuance of CLIA-waiver to Abbot's ID NOW Influenza A&B in 2015, many more NAT systems have been developed, received the CLIA-waiver in the US or World Health Organization (WHO)'s pre-qualification, and deployed to the front line of infectious disease detection. This review highlights the regulatory process for FDA and WHO in evaluating these NATs and the technology innovation of existing CLIA-waived systems. Understanding the technical advancement and challenges, unmet needs, and the trends of commercialization facilitated through the regulatory processes will help pave the foundation for future development and technology transfer from research to the market place.
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Affiliation(s)
- Jane Y Zhang
- Department of Mechanical Engineering, University of Washington, USA.
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8
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Blairon L, Thomas I, Lê PQ, Beukinga I, Tré-Hardy M. Diagnosis of respiratory syncytial virus and influenza A and B with cobas® Liat® from nasopharyngeal aspirations in pediatrics. Diagn Microbiol Infect Dis 2021; 100:115326. [PMID: 33581424 DOI: 10.1016/j.diagmicrobio.2021.115326] [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: 11/30/2020] [Revised: 01/05/2021] [Accepted: 01/24/2021] [Indexed: 10/22/2022]
Abstract
The cobas® Liat® Influenza A/B and respiratory syncytial virus assay was tested on nasopharyngeal aspirates. The resolution of invalid samples was performed using a preanalytical step. cobas® Liat® can be used on nasopharyngeal aspirates with a preanalytical processing step, with a slightly diminished performances in detecting respiratory syncytial virus but not for influenza.
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Affiliation(s)
- Laurent Blairon
- Laboratory Medicine, Iris Hospitals South, Brussels, Belgium.
| | | | - Phu-Quoc Lê
- Department of Pediatrics, Iris Hospitals South, Brussels, Belgium
| | - Ingrid Beukinga
- Laboratory Medicine, Iris Hospitals South, Brussels, Belgium
| | - Marie Tré-Hardy
- Laboratory Medicine, Iris Hospitals South, Brussels, Belgium; Faculty of Medicine, Université libre de bruxelles, Brussels, Belgium; Department of Pharmacy, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
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9
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Paper-Based Molecular Diagnostics. Bioanalysis 2021. [DOI: 10.1007/978-981-15-8723-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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10
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Everitt ML, Tillery A, David MG, Singh N, Borison A, White IM. A critical review of point-of-care diagnostic technologies to combat viral pandemics. Anal Chim Acta 2020; 1146:184-199. [PMID: 33461715 PMCID: PMC7548029 DOI: 10.1016/j.aca.2020.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
The COVID-19 global pandemic of 2019-2020 pointedly revealed the lack of diagnostic solutions that are able to keep pace with the rapid spread of the virus. Despite the promise of decades of lab-on-a-chip research, no commercial products were available to deliver rapid results or enable testing in the field at the onset of the pandemic. In this critical review, we assess the current state of progress on the development of point-of-care technologies for the diagnosis of viral diseases that cause pandemics. While many previous reviews have reported on progress in various lab-on-a-chip technologies, here we address the literature from the perspective of the testing needs of a rapidly expanding pandemic. First, we recommend a set of requirements to heed when designing point-of-care diagnostic technologies to address the testing needs of a pandemic. We then review the current state of assay technologies with a focus on isothermal amplification and lateral-flow immunoassays. Though there is much progress on assay development, we argue that the largest roadblock to deployment exists in sample preparation. We summarize current approaches to automate sample preparation and discuss both the progress and shortcomings of these developments. Finally, we provide our recommendations to the field of specific challenges to address in order to prepare for the next pandemic.
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Affiliation(s)
- Micaela L Everitt
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Alana Tillery
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Martha G David
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Nikita Singh
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Aviva Borison
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Ian M White
- Fischell Department of Bioengineering, University of Maryland, United States.
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11
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Zhu H, Zhang H, Xu Y, Laššáková S, Korabečná M, Neužil P. PCR past, present and future. Biotechniques 2020; 69:317-325. [PMID: 32815744 PMCID: PMC7439763 DOI: 10.2144/btn-2020-0057] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.
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Affiliation(s)
- Hanliang Zhu
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Haoqing Zhang
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Ying Xu
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Soňa Laššáková
- Institute of Biology & Medical Genetics, First
Faculty of Medicine, Charles University & General University Hospital in
Prague, Purkyně Institute, Albertov 4, Praha 2 128 00, Czech
Republic
| | - Marie Korabečná
- Institute of Biology & Medical Genetics, First
Faculty of Medicine, Charles University & General University Hospital in
Prague, Purkyně Institute, Albertov 4, Praha 2 128 00, Czech
Republic
| | - Pavel Neužil
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
- Brno University of Technology, Central European Institute
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Electrical
Engineering and Communications, Technická 3058/10, 616 00 Brno,
Czech Republic
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12
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Qin Z, Peng R, Baravik IK, Liu X. Fighting COVID-19: Integrated Micro- and Nanosystems for Viral Infection Diagnostics. MATTER 2020; 3:628-651. [PMID: 32838297 PMCID: PMC7346839 DOI: 10.1016/j.matt.2020.06.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) highlights the importance of rapid and sensitive diagnostics of viral infection that enables the efficient tracing of cases and the implementation of public health measures for disease containment. The immediate actions from both academia and industry have led to the development of many COVID-19 diagnostic systems that have secured fast-track regulatory approvals and have been serving our healthcare frontlines since the early stage of the pandemic. On diagnostic technologies, many of these clinically validated systems have significantly benefited from the recent advances in micro- and nanotechnologies in terms of platform design, analytical method, and system integration and miniaturization. The continued development of new diagnostic platforms integrating micro- and nanocomponents will address some of the shortcomings we have witnessed in the existing COVID-19 diagnostic systems. This Perspective reviews the previous and ongoing research efforts on developing integrated micro- and nanosystems for nucleic acid-based virus detection, and highlights promising technologies that could provide better solutions for the diagnosis of COVID-19 and other viral infectious diseases. With the summary and outlook of this rapidly evolving research field, we hope to inspire more research and development activities to better prepare our society for future public health crises.
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Affiliation(s)
- Zhen Qin
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Ran Peng
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Ilina Kolker Baravik
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Xinyu Liu
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
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13
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Zhu H, Zhang H, Ni S, Korabečná M, Yobas L, Neuzil P. The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond. Trends Analyt Chem 2020; 130:115984. [PMID: 32834243 PMCID: PMC7369599 DOI: 10.1016/j.trac.2020.115984] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Infectious diseases, such as the most recent case of coronavirus disease 2019, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfill this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis.
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Affiliation(s)
- Hanliang Zhu
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
| | - Haoqing Zhang
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
| | - Sheng Ni
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, S.A.R., PR China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, Prague 2, Czech Republic
| | - Levent Yobas
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, S.A.R., PR China,Corresponding author
| | - Pavel Neuzil
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China,CEITEC Brno University of Technology, Purkyňova 123, 612 00 Brno, Czech Republic,Faculty of Electrical Engineering and Communications, Brno University of Technology, Technická 3058/10, 616 00 Brno, Czech Republic,Corresponding author. Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
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14
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Verbakel JY, Matheeussen V, Loens K, Kuijstermans M, Goossens H, Ieven M, Butler CC. Performance and ease of use of a molecular point-of-care test for influenza A/B and RSV in patients presenting to primary care. Eur J Clin Microbiol Infect Dis 2020; 39:1453-1460. [PMID: 32172369 PMCID: PMC7343728 DOI: 10.1007/s10096-020-03860-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/04/2020] [Indexed: 12/11/2022]
Abstract
Annual influenza epidemics cause substantial morbidity and mortality, and the majority of patients with influenza-like illness present to primary care. Point-of-care influenza tests could support treatment decisions. It is critical to establish analytic performance of these platforms in real-life patient samples before uptake can be considered. We aimed to assess the analytical performance and ease of use of the cobas® Liat® PCR POCT in detecting influenza A/B and RSV in samples collected from patients with influenza-like illness in primary care. Sensitivity and specificity of the cobas® Liat® POCT are calculated in comparison with a commercial laboratory-based PCR test (Fast-Track Respiratory Pathogens 21 Plus kit (Fast-Track Diagnostics)). Samples with discordant results were analysed additionally by the RespiFinder 2Smart (PathoFinder) using an Extended Gold Standard (EGS). Acceptability was scored on a five-point Likert scale as well as a failure mode analysis of the cobas® Liat® POCT was performed. Nasal and oropharyngeal swabs were obtained from 140 children and nasopharyngeal swabs from 604 adults (744 patients). The cobas® Liat® POCT had a sensitivity and specificity of 100% (95% CI 99-100%) and 98.1% (95%CI 96.3-99%) for influenza A, 100% (95% CI 97.7-100%) and 99.7% (95%CI 98.7-99.9%) for influenza B and 100% (95% CI 87.1-100%) and 99.4% (95%CI 98.6-99.8%) for RSV, respectively. According to trained lab technicians, the cobas® Liat® POCT was considered easy-to-use, with a fast turn-around-time. Cobas® Liat® POCT is a promising decentralised test platform for influenza A/B and RSV in primary care as it provides fairly rapid results with excellent analytic performance. Point-of-care influenza tests could support treatment decisions in primary care. Cobas® Liat® POCT is a promising decentralised test platform for influenza A/B and RSV in primary care as it provides fairly rapid results with excellent analytic performance.
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Affiliation(s)
- Jan Y Verbakel
- NIHR Community Healthcare MIC, Nuffield Department of Primary Care Health Sciences, University of Oxford, Woodstock Road, Oxford, Oxfordshire, OX26GG, UK.
- Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 33, 3000, Leuven, Belgium.
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Woodstock Road, Oxford, Oxfordshire, OX26GG, UK.
| | - Veerle Matheeussen
- Laboratory of Clinical Microbiology, Antwerp University Hospital, Edegem, Belgium
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Katherine Loens
- Laboratory of Clinical Microbiology, Antwerp University Hospital, Edegem, Belgium
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Mandy Kuijstermans
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Clinical Microbiology, Antwerp University Hospital, Edegem, Belgium
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Antwerp University Hospital, Edegem, Belgium
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Christopher C Butler
- NIHR Community Healthcare MIC, Nuffield Department of Primary Care Health Sciences, University of Oxford, Woodstock Road, Oxford, Oxfordshire, OX26GG, UK
- Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 33, 3000, Leuven, Belgium
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15
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Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens. J Clin Microbiol 2020; 58:JCM.01793-19. [PMID: 32229601 PMCID: PMC7269373 DOI: 10.1128/jcm.01793-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/20/2020] [Indexed: 12/01/2022] Open
Abstract
QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay. QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay. Most of the discrepant results have been observed in the low-pathogen-load samples. In addition, the QIAstat-Dx RP assay detected 19 additional targets in 19 respiratory samples that were not detected by the ePlex RPP assay. Nine of these discordant targets were considered to represent true positives after discrepancy testing by a third method. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems, including the ePlex RPP assay, is the ability to generate cycle threshold (CT) values, which could help with the interpretation of results. Taking the data together, this study showed good performance of the QIAstat-Dx RP assay in comparison to the ePlex RPP assay for the detection of respiratory pathogens. The QIAstat-Dx RP assay offers a new, rapid, and accurate sample-to-answer multiplex panel for the detection of the most common viral and bacterial respiratory pathogens and therefore has the potential to direct appropriate therapy and infection control precautions.
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16
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Zidovec Lepej S, Poljak M. Portable molecular diagnostic instruments in microbiology: current status. Clin Microbiol Infect 2020; 26:411-420. [DOI: 10.1016/j.cmi.2019.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022]
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17
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Abstract
The timely and accurate diagnosis of respiratory virus infections has the potential to optimize downstream (posttesting) use of limited health care resources, including antibiotics, antivirals, ancillary testing, and inpatient and emergency department beds. Cost-effective algorithms for respiratory virus testing must take into consideration numerous factors, including which patients should be tested, what testing should be performed (for example, antigen testing versus reverse transcription-PCR testing or influenza A/B testing versus testing with a comprehensive respiratory virus panel), and the turnaround time necessary to achieve the desired posttesting outcomes. Despite the clinical impact of respiratory virus infections, the cost-effectiveness of respiratory virus testing is incompletely understood. In this article, we review the literature pertaining to the cost-effectiveness of respiratory virus testing in pediatric and adult patient populations, in emergency department, outpatient, and inpatient clinical settings. Furthermore, we consider the cost-effectiveness of a variety of testing methods, including rapid antigen tests, direct fluorescent antibody assays, and nucleic acid amplification tests.
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Maignan M, Viglino D, Hablot M, Termoz Masson N, Lebeugle A, Collomb Muret R, Mabiala Makele P, Guglielmetti V, Morand P, Lupo J, Forget V, Landelle C, Larrat S. Diagnostic accuracy of a rapid RT-PCR assay for point-of-care detection of influenza A/B virus at emergency department admission: A prospective evaluation during the 2017/2018 influenza season. PLoS One 2019; 14:e0216308. [PMID: 31063477 PMCID: PMC6504036 DOI: 10.1371/journal.pone.0216308] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/17/2019] [Indexed: 01/13/2023] Open
Abstract
STUDY OBJECTIVE To investigate the performance of a rapid RT-PCR assay to detect influenza A/B at emergency department admission. METHODS This single-center prospective study recruited adult patients attending the emergency department for influenza-like illness. Triage nurses performed nasopharyngeal swab samples and ran rapid RT-PCR assays using a dedicated device (cobas Liat, Roche Diagnostics, Meylan, France) located at triage. The same swab sample was also analyzed in the department of virology using conventional RT-PCR techniques. Patients were included 24 hours-a-day, 7 days-a-week. The primary outcome was the diagnostic accuracy of the rapid RT-PCR assay performed at triage. RESULTS A total of 187 patients were included over 11 days in January 2018. Median age was 70 years (interquartile range 44 to 84) and 95 (51%) were male. Nine (5%) assays had to be repeated due to failure of the first assay. The sensitivity of the rapid RT-PCR assay performed at triage was 0.98 (95% confidence interval (CI): 0.91-1.00) and the specificity was 0.99 (95% CI: 0.94-1.00). A total of 92 (49%) assays were performed at night-time or during the weekend. The median time from patient entry to rapid RT-PCR assay results was 46 [interquartile range 36-55] minutes. CONCLUSION Rapid RT-PCR assay performed by nurses at triage to detect influenza A/B is feasible and highly accurate.
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Affiliation(s)
- Maxime Maignan
- HP2 INSERM U1042, University Grenoble Alpes, Emergency department, Grenoble Alpes University Hospital, Grenoble, France
- * E-mail:
| | - Damien Viglino
- HP2 INSERM U1042, University Grenoble Alpes, Emergency department, Grenoble Alpes University Hospital, Grenoble, France
| | - Maud Hablot
- HP2 INSERM U1042, University Grenoble Alpes, Emergency department, Grenoble Alpes University Hospital, Grenoble, France
| | - Nicolas Termoz Masson
- HP2 INSERM U1042, University Grenoble Alpes, Emergency department, Grenoble Alpes University Hospital, Grenoble, France
| | - Anne Lebeugle
- HP2 INSERM U1042, University Grenoble Alpes, Emergency department, Grenoble Alpes University Hospital, Grenoble, France
| | - Roselyne Collomb Muret
- HP2 INSERM U1042, University Grenoble Alpes, Emergency department, Grenoble Alpes University Hospital, Grenoble, France
| | - Prudence Mabiala Makele
- HP2 INSERM U1042, University Grenoble Alpes, Emergency department, Grenoble Alpes University Hospital, Grenoble, France
| | - Valérie Guglielmetti
- HP2 INSERM U1042, University Grenoble Alpes, Emergency department, Grenoble Alpes University Hospital, Grenoble, France
| | - Patrice Morand
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Laboratoire de Virologie, Grenoble Alpes University Hospital, Grenoble, France
| | - Julien Lupo
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Laboratoire de Virologie, Grenoble Alpes University Hospital, Grenoble, France
| | - Virginie Forget
- TIMC-IMAG, CNRS, Grenoble INP, University Grenoble Alpes, Infection Control Unit, Grenoble Alpes University Hospital, Grenoble, France
| | - Caroline Landelle
- TIMC-IMAG, CNRS, Grenoble INP, University Grenoble Alpes, Infection Control Unit, Grenoble Alpes University Hospital, Grenoble, France
| | - Sylvie Larrat
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Laboratoire de Virologie, Grenoble Alpes University Hospital, Grenoble, France
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Rahamat‐Langendoen J, Groenewoud H, Kuijpers J, Melchers WJ, van der Wilt GJ. Impact of molecular point-of-care testing on clinical management and in-hospital costs of patients suspected of influenza or RSV infection: a modeling study. J Med Virol 2019; 91:1408-1414. [PMID: 30950066 PMCID: PMC7166495 DOI: 10.1002/jmv.25479] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/22/2019] [Accepted: 03/19/2019] [Indexed: 01/25/2023]
Abstract
Background At hospital admission, patients suspected of infection with influenza or respiratory syncytial virus (RSV) are placed in isolation, pending the outcome of diagnostics. In a significant number, isolated care proves unnecessary. We investigated the potential impact of molecular point‐of‐care (POC) diagnostics on patient management and in‐hospital costs. Method Prospective collection of data on resource utilization within the hospital from consecutive patients 18 years or older presenting at our university medical center with symptoms of respiratory tract infection from December 2016 to April 2017. A cost analysis was conducted using Markov modeling comparing the actual course of events (on the basis of routine diagnostic tests) with two hypothetical scenarios: when POC would impact time to diagnosis only (scenario 1) or on discharge from the hospital, too (scenario 2). Results A total of 283 patients were included, of whom 217 (76.7%) were admitted. Influenza and RSV were detected in 31% and 7% of the patients, respectively. Fifty‐four percent of patients tested negative, of which 79% were kept in isolated care waiting for test results, with a median duration of 24 hours. Median length of stay was 6.0 days. Mean total in‐hospital costs per patient were € 5243. Introducing POC would lower mean costs per patient to € 4904 (scenario 1) and € 4206 (scenario 2). At the hospital level, this would result in a total cost reduction of € 95 937 to € 293 471 in a single influenza season. Conclusions Introducing POC testing for patients presenting with symptoms of viral respiratory tract infection can reduce time‐to‐diagnosis, hospital stay and, thereby, in‐hospital costs.
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Affiliation(s)
| | - Hans Groenewoud
- Department of Health EvidenceRadboud University Medical CenterNijmegenThe Netherlands
| | - Judith Kuijpers
- Department of Medical MicrobiologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Willem J.G. Melchers
- Department of Medical MicrobiologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Gert Jan van der Wilt
- Department of Health EvidenceRadboud University Medical CenterNijmegenThe Netherlands
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20
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Kim JW, Lee CY, Nguyen TT, Kim IH, Kwon HJ, Kim JH. An optimized molecular method for detection of influenza A virus using improved generic primers and concentration of the viral genomic RNA and nucleoprotein complex. J Vet Diagn Invest 2019; 31:175-183. [PMID: 30795722 DOI: 10.1177/1040638719830760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
For reported primer sets used to detect influenza A viruses (IAVs), we verified the nucleotide identities with 9,103 complete sequences of matrix (M) genes. At best, only 93.2% and 85.3% of the sequences had a 100% match with reported forward and reverse primers, respectively. Therefore, we designed new degenerate forward and reverse primers with 100% identity to 94.4% and 96.2% of compared genes, respectively, and the primer set was used with SYBR-based reverse-transcription real-time PCR (SYBR-RT-rtPCR) for lower detection limits. The sensitivity of SYBR-RT-rtPCR with the new primers was 10-fold higher than that with a conventional method in ~2.37% of all M genes in the database used in our study. We successfully increased the sensitivity of SYBR-RT-rtPCR by concentrating the viral ribonucleoprotein (RNP) using immunomagnetic beads and Triton X-100. The improved generic primer set and RNP concentration method may be useful for sensitive detection of IAVs.
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Affiliation(s)
- Ji-Woon Kim
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Chung-Young Lee
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Thanh Trung Nguyen
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Il-Hwan Kim
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Hyuk-Joon Kwon
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
| | - Jae-Hong Kim
- Laboratory of Avian Diseases (J-W Kim, Lee, Nguyen, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Department of Farm Animal Medicine (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Farm Animal Clinical Training and Research Center, Institutes of Green Bio Science and Technology (Kwon), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Research Institute for Veterinary Science (Kwon, J-H Kim), College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.,Division of Antimicrobial Resistance, Center for Infectious Diseases, National Research Institute of Health, Cheongju, Republic of Korea (I-H Kim)
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21
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Li Z, Zhao J, Wu X, Zhu C, Liu Y, Wang A, Deng G, Zhu L. A rapid microfluidic platform with real-time fluorescence detection system for molecular diagnosis. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1561211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Zhigang Li
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Anhui Provincial Engineering Technology Research Center for Biomedical Optical Instrument, Anhui Provincial Engineering Laboratory for Medical Optical Diagnosis & Treatment Technology and Instrument, Hefei, PR China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, PR China
| | - Jun Zhao
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Anhui Provincial Engineering Technology Research Center for Biomedical Optical Instrument, Anhui Provincial Engineering Laboratory for Medical Optical Diagnosis & Treatment Technology and Instrument, Hefei, PR China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, PR China
| | - Xiaosong Wu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Anhui Provincial Engineering Technology Research Center for Biomedical Optical Instrument, Anhui Provincial Engineering Laboratory for Medical Optical Diagnosis & Treatment Technology and Instrument, Hefei, PR China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, PR China
| | - Cancan Zhu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Anhui Provincial Engineering Technology Research Center for Biomedical Optical Instrument, Anhui Provincial Engineering Laboratory for Medical Optical Diagnosis & Treatment Technology and Instrument, Hefei, PR China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, PR China
| | - Yong Liu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Anhui Provincial Engineering Technology Research Center for Biomedical Optical Instrument, Anhui Provincial Engineering Laboratory for Medical Optical Diagnosis & Treatment Technology and Instrument, Hefei, PR China
| | - An Wang
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Anhui Provincial Engineering Technology Research Center for Biomedical Optical Instrument, Anhui Provincial Engineering Laboratory for Medical Optical Diagnosis & Treatment Technology and Instrument, Hefei, PR China
| | - Guoqing Deng
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Anhui Provincial Engineering Technology Research Center for Biomedical Optical Instrument, Anhui Provincial Engineering Laboratory for Medical Optical Diagnosis & Treatment Technology and Instrument, Hefei, PR China
| | - Ling Zhu
- Institute of Applied Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Anhui Provincial Engineering Technology Research Center for Biomedical Optical Instrument, Anhui Provincial Engineering Laboratory for Medical Optical Diagnosis & Treatment Technology and Instrument, Hefei, PR China
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22
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Gosert R, Naegele K, Hirsch HH. Comparing the Cobas Liat Influenza A/B and respiratory syncytial virus assay with multiplex nucleic acid testing. J Med Virol 2018; 91:582-587. [PMID: 30345524 PMCID: PMC7166997 DOI: 10.1002/jmv.25344] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/13/2018] [Indexed: 01/21/2023]
Abstract
Influenza virus and respiratory syncytial virus (RSV) detection with short turn‐around‐time (TAT) is pivotal for rapid decisions regarding treatment and infection control. However, negative rapid testing results may come from poor assay sensitivity or from influenza‐like illnesses caused by other community‐acquired respiratory viruses (CARVs). We prospectively compared the performance of Cobas Liat Influenza A/B and RSV assay (LIAT) with our routine multiplexNAT‐1 (xTAG Respiratory Pathogen Panel; Luminex) and multiplexNAT‐2 (ePlex‐RPP; GenMark Diagnostics) using 194 consecutive nasopharyngeal swabs from patients with influenza‐like illness during winter 2017/2018. Discordant results were reanalyzed by specific in‐house quantitative nucleic acid amplification testing (NAT). LIAT was positive for influenza virus‐A, ‐B, and RSV in 18 (9.3%), 13 (6.7%), and 55 (28.4%) samples, and negative in 108 samples. Other CARVs were detected by multiplexNAT in 66 (34.0%) samples. Concordant results for influenza and RSV were seen in 190 (97.9%), discordant results in 4 (2.1%), which showed low‐level RSV (<40 000 copies/mL). Sensitivity and specificity of LIAT for influenza‐A, ‐B, and RSV were 100%, 100% and 100%, and 100%, 99.5% and 100%, respectively. The average TAT of LIAT was 20 minutes compared to 6 hours and 2 hours for the multiplexNAT‐1 and ‐2, respectively. Thus, LIAT demonstrated excellent sensitivity and specificity for influenza and RSV, which together with the simple sample processing and short TAT renders this assay suitable for near‐patient testing. Cobas Liat is highly sensitive and specific for Influenza and RSV in 86/194 children Other CARVs were detected by multiplex NAT in 66/196 children Simple processing and TAT of 20 min suitable for near‐patient testing LIAT assay shows excellent sensitivity and specificity for influenza and RSV Simple sample processing and short turn‐around‐time of 20 min render the assay suitable for near‐patient testing Barcode reading and direct transfer of results into the laboratory information system
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Affiliation(s)
- Rainer Gosert
- Division of Infection Diagnostics, Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland
| | - Klaudia Naegele
- Division of Infection Diagnostics, Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland
| | - Hans H Hirsch
- Division of Infection Diagnostics, Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland.,Transplantation and Clinical Virology, Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland.,Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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23
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Dziąbowska K, Czaczyk E, Nidzworski D. Detection Methods of Human and Animal Influenza Virus-Current Trends. BIOSENSORS-BASEL 2018; 8:bios8040094. [PMID: 30340339 PMCID: PMC6315519 DOI: 10.3390/bios8040094] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/03/2018] [Accepted: 10/12/2018] [Indexed: 12/11/2022]
Abstract
The basic affairs connected to the influenza virus were reviewed in the article, highlighting the newest trends in its diagnostic methods. Awareness of the threat of influenza arises from its ability to spread and cause a pandemic. The undiagnosed and untreated viral infection can have a fatal effect on humans. Thus, the early detection seems pivotal for an accurate treatment, when vaccines and other contemporary prevention methods are not faultless. Public health is being attacked with influenza containing new genes from a genetic assortment between animals and humankind. Unfortunately, the population does not have immunity for mutant genes and is attacked in every viral outbreak season. For these reasons, fast and accurate devices are in high demand. As currently used methods like Rapid Influenza Diagnostic Tests lack specificity, time and cost-savings, new methods are being developed. In the article, various novel detection methods, such as electrical and optical were compared. Different viral elements used as detection targets and analysis parameters, such as sensitivity and specificity, were presented and discussed.
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Affiliation(s)
- Karolina Dziąbowska
- Institute of Biotechnology and Molecular Medicine, 3 Trzy Lipy St., 80-172 Gdansk, Poland.
- SensDx SA, 14b Postepu St., 02-676 Warsaw, Poland.
| | - Elżbieta Czaczyk
- Institute of Biotechnology and Molecular Medicine, 3 Trzy Lipy St., 80-172 Gdansk, Poland.
- SensDx SA, 14b Postepu St., 02-676 Warsaw, Poland.
| | - Dawid Nidzworski
- Institute of Biotechnology and Molecular Medicine, 3 Trzy Lipy St., 80-172 Gdansk, Poland.
- SensDx SA, 14b Postepu St., 02-676 Warsaw, Poland.
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24
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Bender AT, Borysiak MD, Levenson AM, Lillis L, Boyle DS, Posner JD. Semiquantitative Nucleic Acid Test with Simultaneous Isotachophoretic Extraction and Amplification. Anal Chem 2018; 90:7221-7229. [PMID: 29761701 DOI: 10.1021/acs.analchem.8b00185] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid amplification tests (NAATs) provide high diagnostic accuracy for infectious diseases and quantitative results for monitoring viral infections. The majority of NAATs require complex equipment, cold chain dependent reagents, and skilled technicians to perform the tests. This largely confines NAATs to centralized laboratories and can significantly delay appropriate patient care. Low-cost, point-of-care (POC) NAATs are especially needed in low-resource settings to provide patients with diagnosis and treatment planning in a single visit to improve patient care. In this work, we present a rapid POC NAAT with integrated sample preparation and amplification using electrokinetics and paper substrates. We use simultaneous isotachophoresis (ITP) and recombinase polymerase amplification (RPA) to rapidly extract, amplify, and detect target nucleic acids from serum and whole blood in a paper-based format. We demonstrate simultaneous ITP and RPA can consistently detect 5 copies per reaction in buffer and 10 000 copies per milliliter of human serum with no intermediate user steps. We also show preliminary extraction and amplification of DNA from whole blood samples. Our test is rapid (results in less than 20 min) and made from low-cost materials, indicating its potential for detecting infectious diseases and monitoring viral infections at the POC in low resource settings.
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Affiliation(s)
- Andrew T Bender
- Mechanical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Mark D Borysiak
- Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Amanda M Levenson
- Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | | | | | - Jonathan D Posner
- Mechanical Engineering , University of Washington , Seattle , Washington 98195 , United States.,Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
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25
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Garg SK, Lu K, Duncan J, Peterson LR, Liesenfeld O. Equivalent Performance of the Cobas ® Cdiff Test for Use on the Cobas ® Liat ® System and the Cobas ® 4800 System. Eur J Microbiol Immunol (Bp) 2017; 7:310-318. [PMID: 29403660 PMCID: PMC5793701 DOI: 10.1556/1886.2017.00034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/11/2017] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile infection is a significant health burden, and innovative solutions are needed to shorten time to diagnosis and improve infection control. We evaluated the performance of the cobas® Cdiff test for use on the cobas® Liat® System (cobas® Liat® Cdiff), a single-sample, on-demand, and automated molecular solution with a 20-min turnaround time. The limit of detection was 45-90 colony-forming units (CFUs)/swab for toxigenic strains that covered the most prevalent toxinotypes, including the hyper-virulent epidemic 027/BI/NAP1 strain. Using 442 prospectively collected clinical stool specimens, we compared the performance of the cobas® Liat® Cdiff to direct culture and to the cobas® Cdiff test on the cobas® 4800 System (cobas® 4800 Cdiff) - a medium-throughput molecular platform. The sensitivity and specificity of the cobas® Liat® Cdiff compared to direct culture were 93.1% and 95.1%, respectively, and this performance did not statistically differ from the cobas® 4800 Cdiff (P < 0.05). Direct correlation of the cobas® Liat® and cobas® 4800 Cdiff tests yielded overall percent agreement of 98.6%. The test performance, automation, and turnaround time of the cobas® Liat® Cdiff enable its use for on-demand and out-of-hours testing as a complement to existing batch testing solutions like the cobas® 4800 Cdiff.
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Affiliation(s)
- Sachin K Garg
- Medical and Scientific Affairs, Roche Molecular Diagnostics, Pleasanton, CA, USA
| | - Kyle Lu
- Development, Roche Molecular Diagnostics, Pleasanton, CA, USA
| | - John Duncan
- Medical and Scientific Affairs, Roche Molecular Diagnostics, Pleasanton, CA, USA
| | | | - Oliver Liesenfeld
- Medical and Scientific Affairs, Roche Molecular Diagnostics, Pleasanton, CA, USA
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26
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Diagnostic accuracy of the real-time PCR cobas ® Liat ® Influenza A/B assay and the Alere i Influenza A&B NEAR isothermal nucleic acid amplification assay for the detection of influenza using adult nasopharyngeal specimens. J Clin Virol 2017; 94:86-90. [PMID: 28772170 DOI: 10.1016/j.jcv.2017.07.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Accurate detection of influenza requires diagnostic testing; however, methods such as RADTs and central laboratory-based tests are limited by low sensitivity and time constraints, respectively. OBJECTIVE To compare the performances of the cobas® Liat® Influenza A/B and Alere™ i Influenza A&B point-of-care (POC) assays for detecting influenza A and B viruses using fresh nasopharyngeal specimens with the GenMark Dx® Respiratory Viral Panel as the reference method, a FDA cleared IVD PCR test. STUDY DESIGN A total of 87 samples collected in viral transport medium from adults ≥18 years of age were re-tested on both POC assays (based on the reference PCR method, 29 were influenza A and 18 were influenza B virus positive). RESULTS The overall sensitivity and specificity of the cobas Influenza A/B for the detection of influenza A and B relative to reference PCR was 97.9% (95% confidence interval [CI] 88.9%, 99.6%) and 97.5% (95% CI: 87.1%, 99.6%), respectively, while the sensitivity of the Alere i Influenza A&B assay relative to the reference PCR method was 63.8% (95% CI: 49.5%, 76.0%) and the specificity was 97.5% (95% CI: 87.1%, 99.6%). The individual sensitivities and specificities of the cobas Influenza A/B assay for influenza A alone and influenza B alone were comparable to those of the reference PCR method (influenza A: sensitivity of 100% [95% CI: 88.3%, 100.0%] and specificity of 98.3% [95% CI: 90.9%, 99.7%]; influenza B: sensitivity of 94.4% [95% CI: 74.2%, 99.0%] and specificity of 100% [95% CI: 94.7%, 100.0%]). For the Alere i Influenza A&B assay, the individual specificities for influenza A and B were comparable to those of the reference PCR method (98.3% [95% CI: 90.9%, 99.7%] and 97.1% [95% CI: 90.0%, 99.2%], respectively), while the individual sensitivities were low relative to reference PCR (55.2% [95% CI: 37.5%, 71.6%] and 72.2% [95% CI: 49.1%, 87.5%], respectively). CONCLUSION The cobas Influenza A/B assay demonstrated performance equivalent to laboratory-based PCR, and could replace rapid antigen tests.
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