1
|
Patel SK, Surve J, Parmar J, Ahmed K, Bui FM, Al-Zahrani FA. Recent Advances in Biosensors for Detection of COVID-19 and Other Viruses. IEEE Rev Biomed Eng 2023; 16:22-37. [PMID: 36197867 PMCID: PMC10009816 DOI: 10.1109/rbme.2022.3212038] [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: 03/21/2022] [Revised: 06/28/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
This century has introduced very deadly, dangerous, and infectious diseases to humankind such as the influenza virus, Ebola virus, Zika virus, and the most infectious SARS-CoV-2 commonly known as COVID-19 and have caused epidemics and pandemics across the globe. For some of these diseases, proper medications, and vaccinations are missing and the early detection of these viruses will be critical to saving the patients. And even the vaccines are available for COVID-19, the new variants of COVID-19 such as Delta, and Omicron are spreading at large. The available virus detection techniques take a long time, are costly, and complex and some of them generates false negative or false positive that might cost patients their lives. The biosensor technique is one of the best qualified to address this difficult challenge. In this systematic review, we have summarized recent advancements in biosensor-based detection of these pandemic viruses including COVID-19. Biosensors are emerging as efficient and economical analytical diagnostic instruments for early-stage illness detection. They are highly suitable for applications related to healthcare, wearable electronics, safety, environment, military, and agriculture. We strongly believe that these insights will aid in the study and development of a new generation of adaptable virus biosensors for fellow researchers.
Collapse
Affiliation(s)
- Shobhit K. Patel
- Department of Computer EngineeringMarwadi UniversityRajkot360003India
| | - Jaymit Surve
- Department of Electrical EngineeringMarwadi UniversityRajkot360003India
| | - Juveriya Parmar
- Department of Mechanical and Materials EngineeringUniversity of Nebraska - LincolnNebraska68588USA
- Department of Electronics and Communication EngineeringMarwadi UniversityRajkot360003India
| | - Kawsar Ahmed
- Department of Electrical and Computer EngineeringUniversity of SaskatchewanSaskatoonSKS79 5A9Canada
- Group of Bio-PhotomatiX, Department of Information and Communication TechnologyMawlana Bhashani Science and Technology UniversitySantoshTangail1902Bangladesh
| | - Francis M. Bui
- Department of Electrical and Computer EngineeringUniversity of SaskatchewanSaskatoonSKS79 5A9Canada
| | | |
Collapse
|
2
|
Hernandez MM, Banu R, Gonzalez-Reiche AS, Gray B, Shrestha P, Cao L, Chen F, Shi H, Hanna A, Ramírez JD, van de Guchte A, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Schutzbank TE, Simon V, van Bakel H, Sordillo EM, Paniz-Mondolfi AE. RT-PCR and Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry Diagnostic Target Performance Reflects Circulating Severe Acute Respiratory Syndrome Coronavirus 2 Variant Diversity in New York City. J Mol Diagn 2022; 24:738-749. [PMID: 35525388 PMCID: PMC9067105 DOI: 10.1016/j.jmoldx.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/07/2022] [Accepted: 04/06/2022] [Indexed: 12/20/2022] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern have emerged. New variants pose challenges for diagnostic platforms because sequence diversity can alter primer/probe-binding sites (PBSs), causing false-negative results. The Agena MassARRAY SARS-CoV-2 Panel (Agena Bioscience) uses RT-PCR and mass spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we use a data set of 256 SARS-CoV-2-positive specimens collected between April 11, 2021, and August 28, 2021, to evaluate target performance with paired sequencing data. During this time frame, two targets in the N gene (N2 and N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3'-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk, 20.02; 95% CI, 11.36 to 35.72; P < 0.0001). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3'-mismatch to the N2 probe PBS and increases target dropout risk (relative risk, 11.92; 95% CI, 8.17 to 14.06; P < 0.0001). These findings highlight the robust capability of Agena MassARRAY SARS-CoV-2 Panel target results to reveal circulating virus diversity, and they underscore the power of multitarget design to capture variants of concern.
Collapse
Affiliation(s)
- Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brandon Gray
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huanzhi Shi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ayman Hanna
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, a Mount Sinai venture, Stamford, Connecticut
| | - Melissa R Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael D Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| |
Collapse
|
3
|
Li M, Wan L, Law MK, Meng L, Jia Y, Mak PI, Martins RP. One-shot high-resolution melting curve analysis for KRAS point-mutation discrimination on a digital microfluidics platform. LAB ON A CHIP 2022; 22:537-549. [PMID: 34904611 DOI: 10.1039/d1lc00564b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-nucleotide polymorphism (SNP) plays a critical role in personalized medicine, forensics, pharmacogenetics, and disease diagnostics. Among different existing SNP genotyping techniques, melting curve analysis (MCA) becomes increasingly popular due to its high accuracy and straightforward procedures in extracting the melting temperature (Tm). Yet, its study on existing digital microfluidic (DMF) platforms has intrinsic limitations due to the temperature inhomogeneity within a thickened droplet during the on-chip rapid heating process. Although the utilization of an on-chip thermostat can regulate and monitor the dynamic melting process in real time, the limited Tm accuracy resulting from the insufficient system response time to accommodate the fast-melting evolution still poses a great challenge for precise MCA with high throughput. This work proposes a one-shot MCA on a DMF platform. The tailoring of a functional substrate with hierarchical micro/nano structure enables high-resolution patterning of pL-scale droplets. Specifically, the hydrothermal and photocatalysis treatment allows the functional substrate to exhibit a superwettability contrast of >170°, facilitating passive isolation of the pL-scale DNA sample into highly-resolved pL droplets above the 200 μm superhydrophilic patterns. This high-resolution MCA technique can successfully discriminate KRAS gene targets with single-nucleotide mutations in 3 seconds. The high accuracy and consistency in the acquired Tm when compared with off-chip results demonstrate its opportunities for near-patient diagnostics, precision medicines, genetic counseling, and prevention strategies on DMF platforms.
Collapse
Affiliation(s)
- Mingzhong Li
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macao, China.
| | - Liang Wan
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macao, China.
- Faculty of Science and Technology - Electrical and Computer Engineering, University of Macau, Macao, China
| | - Man-Kay Law
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macao, China.
- Faculty of Science and Technology - Electrical and Computer Engineering, University of Macau, Macao, China
| | - Li Meng
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macao, China.
- Faculty of Science and Technology - Electrical and Computer Engineering, University of Macau, Macao, China
| | - Yanwei Jia
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macao, China.
- Faculty of Science and Technology - Electrical and Computer Engineering, University of Macau, Macao, China
| | - Pui-In Mak
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macao, China.
- Faculty of Science and Technology - Electrical and Computer Engineering, University of Macau, Macao, China
| | - Rui P Martins
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macao, China.
- Faculty of Science and Technology - Electrical and Computer Engineering, University of Macau, Macao, China
- On leave from Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
4
|
Zhang H, Yan Z, Wang X, Gaňová M, Chang H, Laššáková S, Korabecna M, Neuzil P. Determination of Advantages and Limitations of qPCR Duplexing in a Single Fluorescent Channel. ACS OMEGA 2021; 6:22292-22300. [PMID: 34497918 PMCID: PMC8412922 DOI: 10.1021/acsomega.1c02971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Real-time (quantitative) polymerase chain reaction (qPCR) has been widely applied in molecular diagnostics due to its immense sensitivity and specificity. qPCR multiplexing, based either on fluorescent probes or intercalating dyes, greatly expanded PCR capability due to the concurrent amplification of several deoxyribonucleic acid sequences. However, probe-based multiplexing requires multiple fluorescent channels, while intercalating dye-based multiplexing needs primers to be designed for amplicons having different melting temperatures. Here, we report a single fluorescent channel-based qPCR duplexing method on a model containing the sequence of chromosomes 21 (Chr21) and 18 (Chr18). We combined nonspecific intercalating dye EvaGreen with a 6-carboxyfluorescein (FAM) probe specific to either Chr21 or Chr18. The copy number (cn) of the target linked to the FAM probe could be determined in the entire tested range from the denaturation curve, while the cn of the other one was determined from the difference between the denaturation and elongation curves. We recorded the amplitude of fluorescence at the end of denaturation and elongation steps, thus getting statistical data set to determine the limit of the proposed method in detail in terms of detectable concentration ratios of both targets. The proposed method eliminated the fluorescence overspilling that happened in probe-based qPCR multiplexing and determined the specificity of the PCR product via melting curve analysis. Additionally, we performed and verified our method using a commercial thermal cycler instead of a self-developed system, making it more generally applicable for researchers. This quantitative single-channel duplexing method is an economical substitute for a conventional rather expensive probe-based qPCR requiring different color probes and hardware capable of processing these fluorescent signals.
Collapse
Affiliation(s)
- Haoqing Zhang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Zhiqiang Yan
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Xinlu Wang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Martina Gaňová
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
| | - Honglong Chang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Soňa Laššáková
- Institute
of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital
in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Marie Korabecna
- Institute
of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital
in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Pavel Neuzil
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
- School
of Electrical Engineering and Computer Technology, Brno University of Technology, Technická 10, 612 00 Brno, Czech Republic
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Zhang H, Gaňová M, Yan Z, Chang H, Neužil P. PCR Multiplexing Based on a Single Fluorescent Channel Using Dynamic Melting Curve Analysis. ACS OMEGA 2020; 5:30267-30273. [PMID: 33251461 PMCID: PMC7689941 DOI: 10.1021/acsomega.0c04766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/29/2020] [Indexed: 06/12/2023]
Abstract
Since its invention in 1986, the polymerase chain reaction (PCR), has become a well-established method for the detection and amplification of deoxyribonucleic acid (DNA) with a specific sequence. Incorporating fluorescent probes, known as TaqMan probes, or DNA intercalating dyes, such as SYBR Green, into the PCR mixture allows real-time monitoring of the reaction progress and extraction of quantitative information. Previously reported real-time PCR product detection using intercalating dyes required melting curve analysis (MCA) to be performed following thermal cycling. Here, we propose a technique to perform dynamic MCA during each thermal cycle, based on a continuous fluorescence monitoring method, providing qualitative and quantitative sample information. We applied the proposed method in multiplexing detection of hepatitis B virus DNA and complementary DNA of human immunodeficiency virus as well as glyceraldehyde 3-phosphate dehydrogenase in different concentration ratios. We extracted the DNA melting curve and its derivative from each PCR cycle during the transition from the elongation to the denaturation temperature with a set heating rate of 0.8 K·s-1and then used the data to construct individual PCR amplification curves for each gene to determine the initial concentration of DNA in the sample. Our proposed method allows researchers to look inside the PCR in each thermal cycle, determining the PCR product specificity in real time instead of waiting until the end of the PCR. Additionally, the slow transition rate from elongation to denaturation provides a dynamic multiplexing assay, allowing the detection of at least three genes in real time.
Collapse
Affiliation(s)
- Haoqing Zhang
- Ministry
of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department
of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Martina Gaňová
- Ministry
of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department
of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
| | - ZhiQiang Yan
- Ministry
of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department
of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Honglong Chang
- Ministry
of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department
of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Pavel Neužil
- Ministry
of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department
of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
- Department
of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 3058/10, 616 00 Brno, Czech Republic
| |
Collapse
|
7
|
Li H, Zhang F, Tan M, Zeng Y, Yang Q, Tan J, Huang J, Huang Y, Kang Z. Research Note: A putative novel subtype of the avian hepatitis E virus of genotype 3, Jiangxi province, China. Poult Sci 2020; 99:6657-6663. [PMID: 33248582 PMCID: PMC7705056 DOI: 10.1016/j.psj.2020.09.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, the avian hepatitis E virus (HEV) has been widely spread in China, causing huge economic losses. Several studies have carried out detailed epidemiologic investigations of the avian HEV, but no data were from Jiangxi province. Since early April 2020, diseases similar to hepatic rupture hemorrhage syndrome caused by the avian HEV occurred in a Roman Brown layer farm in Jiangxi province, indicating this virus may also be epidemic there. To make this assumption clear, 20 liver samples were collected from the sick flock and then analyzed by detailed viral detection, which confirmed that the avian HEV should be responsible for the aforementioned disease (6 of 20). Then, the capsid gene of the virus was sequenced to show the molecular characteristics of the strain circulating in the aforementioned flock. Sequence comparison showed that it shared 80.7 to 94.7% identities with 12 published strains, while phylogenetic analysis confirmed that it belongs to a new subtype of genotype 3. Moreover, basing on a 242 bp fragment, the novel also shared high similarities to reference strains identified as genotypes before, revealing the genotype 3 maybe very popular in China and even can be divided into several subgroups. In conclusion, a novel avian HEV strain was identified in this study, which belongs to a new subtype of genotype 3. The analysis makes up for the molecular epidemiologic data of avian HEV and provides a basis for further understanding the spread of avian HEV in China.
Collapse
Affiliation(s)
- Haiqin Li
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Fanfan Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Meifang Tan
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Yanbing Zeng
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Qun Yang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Jia Tan
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Jiangnan Huang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Yu Huang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
| | - Zhaofeng Kang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China.
| |
Collapse
|
8
|
|
9
|
Naked eye detection of an amplified gene using metal particle-based DNA transport within functionalized porous interfaces. Talanta 2019; 195:97-102. [DOI: 10.1016/j.talanta.2018.11.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 11/17/2022]
|
10
|
Huang Q, Ye C, Chen T, Jiang J, Peng Y, Chen J, Fang R. EvaGreen-based real-time PCR assay for sensitive detection of enzootic nasal tumor virus 2. Mol Cell Probes 2019; 44:51-56. [PMID: 30771482 DOI: 10.1016/j.mcp.2019.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 01/26/2023]
Abstract
Enzootic nasal tumor virus 2 (ENTV-2), the aetiological agent of enzootic nasal adenocarcinoma in goats, is prevalent in China; resulting in substantial economic losses to the goat-breeding industry. Therefore, it is necessary to establish an efficient detection method for the diagnosis and prevention of ENTV-2 infection. More recently, EvaGreen is emerging as a novel alternative fluorescent dye for quantitative real-time PCR because of its low cost, specific amplification and high resolution. In this study, we developed a specific, sensitive, and cost-effective detection method-an EvaGreen-based real-time PCR assay for the detection of ENTV-2. This assay exhibited high specificity and sensitivity and was able to detect ENTV-2 at concentrations as low as 3.0 × 101 copies, which was more sensitive than the conventional PCR method (detection limit, 3.0 × 102 copies). In addition, the reproducibility test indicated that EvaGreen dye in our assay had a good reproducibility. In conclusion, we report that a highly sensitive, specific, and cost-effective EvaGreen-based real-time PCR assay is successful for the rapid detection of ENTV-2.
Collapse
Affiliation(s)
- Qingyuan Huang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Chao Ye
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Tingting Chen
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Jiali Jiang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Yuanyi Peng
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Jing Chen
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China.
| | - Rendong Fang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
11
|
Feng J, Svatoš V, Liu X, Chang H, Neužil P. High-performance microcalorimeters: Design, applications and future development. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
12
|
Park YM, Lim SY, Shin SJ, Kim CH, Jeong SW, Shin SY, Bae NH, Lee SJ, Na J, Jung GY, Lee TJ. A film-based integrated chip for gene amplification and electrochemical detection of pathogens causing foodborne illnesses. Anal Chim Acta 2018; 1027:57-66. [DOI: 10.1016/j.aca.2018.03.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/26/2018] [Indexed: 01/30/2023]
|
13
|
Su Q, Li Y, Zhang Y, Zhang Z, Meng F, Cui Z, Chang S, Zhao P. Characterization of the novel genotype avian hepatitis E viruses from outbreaks of hepatic rupture haemorrhage syndrome in different geographical regions of China. Transbound Emerg Dis 2018; 65:2017-2026. [PMID: 30086212 DOI: 10.1111/tbed.12987] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/21/2022]
Abstract
Since 2016, hepatic rupture haemorrhage syndrome (HRHS) has emerged in layer and broiler breeder hens in several provinces of China, and novel genotype avian hepatitis E viruses were detected from these chickens. To gain a better understanding of the genetic properties of the novel avian HEV strain, the capsid gene of four isolates from birds at four farms experiencing HRHS in different geographical regions were determined and compared with those of reported pathogenic and nonpathogenic avian HEV isolates as well as mammalian HEVs. Results showed that all those isolates share 80.1%-88.2% nucleotide sequence identity and 89.3%-91.9% amino acid sequence identity with other published avian HEV strains, while phylogenetic analysis further demonstrate that a novel genotype avian HEV was epidemic in China. Meanwhile, sequence analysis revealed that those novel isolates contain various amino acid mutations and even a hypervariable region in their major antigenic domains, which might be the critical factors for the pathogenicity elevation and even change their antigenicity. The data presented in this report will enhance the current understanding of the epidemiology and genetic diversity of the novel genotype avian HEV in China and provide additional insight into the critical factors that determine the pathogenicity of it.
Collapse
Affiliation(s)
- Qi Su
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, China
| | - Yang Li
- China Animal Health and Epidemiology Center, Qingdao, Shandong, China
| | - Yawen Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, China
| | - Zhihui Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, China
| | - Fanfeng Meng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, China
| | - Zhizhong Cui
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, China
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, China
| | - Peng Zhao
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, China
| |
Collapse
|
14
|
Su Q, Li Y, Meng F, Cui Z, Chang S, Zhao P. Hepatic rupture hemorrhage syndrome in chickens caused by a novel genotype avian hepatitis E virus. Vet Microbiol 2018; 222:91-97. [PMID: 30080679 DOI: 10.1016/j.vetmic.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/25/2018] [Accepted: 06/25/2018] [Indexed: 01/01/2023]
Abstract
Since 2016, severe outbreaks of hepatic rupture hemorrhage syndrome (HRHS) have emerged in chickens in several Chinese provinces and caused huge economic losses to the poultry industry, but the etiological characteristics and pathogenic potential of it has remained unclear. This study sequenced the partial helicase and capsid gene of the potentially novel avian hepatitis E virus (HEV) isolated from chickens with HRHS and tested the pathogenicity of it on SPF chicks, while the appearance of clinical signs, histopathological changes, viral distribution, viremia and viral shedding were monitored for 14 days post-infection (dpi). Analysis revealed that the HRHS related avian HEV belongs to a novel genotype, and infected chicks developed the typical symptoms of HRHS. Thus, this study successfully developed an experimental infection model for studying the pathogenicity and role of the novel avian HEV in HRHS. Meanwhile, the novel avian HEV mainly existed in the liver and spleen, inducing a rapid viremia and chronic viral shedding in infected chicks, and could cause 40% mortality before 14 dpi. In conclusion, this study found the novel genotype avian HEV and confirmed its role in HRHS.
Collapse
Affiliation(s)
- Qi Su
- College of Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China
| | - Yang Li
- China Animal Health and Epidemiology Center, 369 Nanjing Street, Qingdao, Shandong, 266000, China
| | - Fanfeng Meng
- College of Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China
| | - Zhizhong Cui
- College of Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China
| | - Shuang Chang
- College of Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China
| | - Peng Zhao
- College of Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China.
| |
Collapse
|
15
|
Mazumdar H, Kim TH, Lee JM, Ha JH, Ahrberg CD, Chung BG. Prediction analysis and quality assessment of microwell array images. Electrophoresis 2018; 39:948-956. [PMID: 29323408 DOI: 10.1002/elps.201700460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 11/11/2022]
Abstract
Microwell arrays are widely used for the analysis of fluorescent-labelled biomaterials. For rapid detection and automated analysis of microwell arrays, the computational image analysis is required. Support Vector Machines (SVM) can be used for this task. Here, we present a SVM-based approach for the analysis of microwell arrays consisting of three distinct steps: labeling, training for feature selection, and classification into three classes. The three classes are filled, partially filled, and unfilled microwells. Next, the partially filled wells are analyzed by SVM and their tendency towards filled or unfilled tested through applying a Gaussian filter. Through this, all microwells can be categorized as either filled or unfilled by our algorithm. Therefore, this SVM-based computational image analysis allows for an accurate and simple classification of microwell arrays.
Collapse
Affiliation(s)
- Hirak Mazumdar
- Department of Biomedical Engineering, Sogang University, Seoul, Republic of Korea
| | - Tae Hyeon Kim
- Department of Mechanical Engineering, Sogang University, Seoul, Republic of Korea
| | - Jong Min Lee
- Department of Mechanical Engineering, Sogang University, Seoul, Republic of Korea
| | - Jang Ho Ha
- Department of Mechanical Engineering, Sogang University, Seoul, Republic of Korea
| | - Christian D Ahrberg
- Department of Mechanical Engineering, Sogang University, Seoul, Republic of Korea
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Republic of Korea
| |
Collapse
|
16
|
Pryor RJ, Myrick JT, Palais RA, Sundberg SO, Paek JY, Wittwer CT, Knight IT. High-Speed Melting Analysis: The Effect of Melting Rate on Small Amplicon Microfluidic Genotyping. Clin Chem 2017; 63:1624-1632. [PMID: 28818830 DOI: 10.1373/clinchem.2017.276147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 07/06/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND High-resolution DNA melting analysis of small amplicons is a simple and inexpensive technique for genotyping. Microfluidics allows precise and rapid control of temperature during melting. METHODS Using a microfluidic platform for serial PCR and melting analysis, 4 targets containing single nucleotide variants were amplified and then melted at different rates over a 250-fold range from 0.13 to 32 °C/s. Genotypes (n = 1728) were determined manually by visual inspection after background removal, normalization, and conversion to negative derivative plots. Differences between genotypes were quantified by a genotype discrimination ratio on the basis of inter- and intragenotype differences using the absolute value of the maximum vertical difference between curves as a metric. RESULTS Different homozygous curves were genotyped by melting temperature and heterozygous curves were identified by shape. Technical artifacts preventing analysis (0.3%), incorrect (0.06%), and indeterminate (0.4%) results were minimal, occurring mostly at slow melting rates (0.13-0.5 °C/s). Genotype discrimination was maximal at around 8 °C/s (2-8 °C/s for homozygotes and 8-16 °C/s for heterozygotes), and no genotyping errors were made at rates >0.5 °C/s. PCR was completed in 10-12.2 min, followed by melting curve acquisition in 4 min down to <1 s. CONCLUSIONS Microfluidics enables genotyping by melting analysis at rates up to 32 °C/s, requiring <1 s to acquire an entire melting curve. High-speed melting reduces the time for melting analysis, decreases errors, and improves genotype discrimination of small amplicons. Combined with extreme PCR, high-speed melting promises nucleic acid amplification and genotyping in < 1 min.
Collapse
Affiliation(s)
- Robert J Pryor
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
| | | | - Robert A Palais
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT.,Department of Mathematics, Utah Valley University, Orem, UT
| | - Scott O Sundberg
- Canon Virginia, Inc., Newport News, VA.,Canon U.S. Life Sciences, Inc., Rockville, MD
| | | | - Carl T Wittwer
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT;
| | | |
Collapse
|
17
|
Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
Collapse
Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
| |
Collapse
|
18
|
Chen T, Jia Y, Dong C, Gao J, Mak PI, Martins RP. Sub-7-second genotyping of single-nucleotide polymorphism by high-resolution melting curve analysis on a thermal digital microfluidic device. LAB ON A CHIP 2016; 16:743-752. [PMID: 26781669 DOI: 10.1039/c5lc01533b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We developed a thermal digital microfluidic (T-DMF) device enabling ultrafast DNA melting curve analysis (MCA). Within 7 seconds, the T-DMF device succeeded in differentiating a melting point difference down to 1.6 °C with a variation of 0.3 °C in a tiny droplet sample (1.2 μL), which was 300 times faster and with 20 times less sample spending than the standard MCA (35 minutes, 25 μL) run in a commercial qPCR machine. Such a performance makes it possible for a rapid discrimination of single-nucleotide mutation relevant to prompt clinical decision-making. Also, aided by electronic intelligent control, the T-DMF device facilitates sample handling and pipelining in an automatic serial manner. An optimized oval-shaped thermal electrode is introduced to achieve high thermal uniformity. A device-sealing technique averts sample contamination and permits uninterrupted chemical/biological reactions. Simple fabrication using a single chromium layer fulfills both the thermal and typical transport electrode requirements. Capable of thermally modulating DNA samples with ultrafast MCA, this T-DMF device has the potential for a wide variety of life science analyses, especially for disease diagnosis and prognosis.
Collapse
Affiliation(s)
- Tianlan Chen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China.
| | | | | | | | | | | |
Collapse
|
19
|
Ahrberg CD, Manz A. Superheated droplets for protein thermal stability analyses of GFP, BSA and Taq-polymerase. RSC Adv 2016. [DOI: 10.1039/c6ra07079e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Here we describe a novel method for the study of protein thermal stability using superheated aqueous samples within virtual reaction chambers.
Collapse
|