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Kazemi-Lomedasht F, Karami E. Biosensors: Types, features, and application in biomedicine. Asian Pac J Trop Biomed 2022. [DOI: 10.4103/2221-1691.354427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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2
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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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3
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Liu RH, Munro SB, Nguyen T, Siuda T, Suciu D, Bizak M, Slota M, Fuji HS, Danley D, McShea A. Integrated Microfluidic CustomArray Device for Bacterial Genotyping and Identification. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.jala.2006.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The ongoing threat of the potential use of biothreat agents (such as Bacillus anthracis) as a biochemical weapon emphasizes the need for a rapid, miniature, fully automated, and highly specific detection assay. An integrated and self-contained microfluidic device has been developed to rapidly detect B. anthracis and many other bacteria. The device consists of a semiconductor-based DNA microarray chip with 12,000 features and a microfluidic cartridge that automates the fluid handling steps required to carry out a genotyping assay for pathogen identification. This fully integrated and disposable device consists of low-cost microfluidic pumps, mixers, valves, fluid channels, reagent storage chambers, and DNA microarray silicon chip. Microarray hybridization and subsequent fluid handling and reactions were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. The genotyping results showed that the device was able to identify and distinguish B. anthracis from the other members of the closely related Bacillus cereus group, demonstrating the potential of integrated microfluidic and microarray technology for highly specific pathogen detection. The device provides a cost-effective solution to eliminate labor-intensive and time-consuming fluid handling steps and allows the detection and identification of biological warfare agents in a rapid and automated fashion.
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Vemula SV, Zhao J, Liu J, Wang X, Biswas S, Hewlett I. Current Approaches for Diagnosis of Influenza Virus Infections in Humans. Viruses 2016; 8:96. [PMID: 27077877 PMCID: PMC4848591 DOI: 10.3390/v8040096] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/15/2022] Open
Abstract
Despite significant advancement in vaccine and virus research, influenza continues to be a major public health concern. Each year in the United States of America, influenza viruses are responsible for seasonal epidemics resulting in over 200,000 hospitalizations and 30,000–50,000 deaths. Accurate and early diagnosis of influenza viral infections are critical for rapid initiation of antiviral therapy to reduce influenza related morbidity and mortality both during seasonal epidemics and pandemics. Several different approaches are currently available for diagnosis of influenza infections in humans. These include viral isolation in cell culture, immunofluorescence assays, nucleic acid amplification tests, immunochromatography-based rapid diagnostic tests, etc. Newer diagnostic approaches are being developed to overcome the limitations associated with some of the conventional detection methods. This review discusses diagnostic approaches currently available for detection of influenza viruses in humans.
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Affiliation(s)
- Sai Vikram Vemula
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Jiangqin Zhao
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Jikun Liu
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Xue Wang
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Santanu Biswas
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Indira Hewlett
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
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Sultankulova KT, Chervyakova OV, Kozhabergenov NS, Shorayeva KA, Strochkov VM, Orynbayev MB, Sandybayev NT, Sansyzbay AR, Vasin AV. Comparative evaluation of effectiveness of IAVchip DNA microarray in influenza A diagnosis. ScientificWorldJournal 2014; 2014:620580. [PMID: 25548788 PMCID: PMC4274914 DOI: 10.1155/2014/620580] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/22/2014] [Accepted: 09/28/2014] [Indexed: 01/30/2023] Open
Abstract
The paper describes comparative evaluation of IAVchip DNA microarray, reverse transcription PCR (RT-PCR), and real-time RT-PCR versus virus isolation in chicken embryos and shows their diagnostic effectiveness in detection and subtyping of influenza A virus. The tests were evaluated with use of 185 specimens from humans, animals, and birds. IAVchip DNA microarray demonstrates higher diagnostic effectiveness (99.45%) in early influenza A diagnosis as compared to the real-time PCR (98.38%) and RT-PCR (96.22%), thus showing its clear superiority. Diagnostic sensitivity of IAVchip DNA microarray (100%) exceeds the same of RT-PCR (95.95%) and real-time RT-PCR (97.96%) in the range of estimated confidence intervals. IAVchip DNA microarray and real-time RT-PCR displayed equal diagnostic specificity (98.85%), while diagnostic specificity of RT-PCR was 96.40%. IAVchip DNA microarray has an advantage over the other tests for influenza A diagnosis and virus identification as a more rapid method that allows performing simultaneous detection and subtyping of about tens of specimens within one experiment during 8-10 hours. The developed IAVchip DNA microarray is a general test tool that enables identifying simultaneously 16 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes of influenza A virus and also to screen the influenza A viruses from humans, animals, and birds by M and NP genes.
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Affiliation(s)
- K. T. Sultankulova
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - O. V. Chervyakova
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - N. S. Kozhabergenov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - K. A. Shorayeva
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - V. M. Strochkov
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - M. B. Orynbayev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - N. T. Sandybayev
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - A. R. Sansyzbay
- Research Institute for Biological Safety Problems (RIBSP), Science Committee of Ministry of Education and Science of Republic of Kazakhstan, Gvardeiskiy, Kordaiskiy Rayon, Zhambylskaya Oblast 080409, Kazakhstan
| | - A. V. Vasin
- Research Institute of Influenza, Ministry of Healthcare of the Russian Federation, Prof. Popov Street 15/17, Saint Petersburg 197376, Russia
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Chandler DP, Griesemer SB, Knickerbocker C, Golova JB, Lambarqui A, Perov AN, Zimmerman C, Wiles C, Rudy GB, St George K. Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. J Virol Methods 2014; 208:152-9. [PMID: 25066276 PMCID: PMC4175443 DOI: 10.1016/j.jviromet.2014.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 07/09/2014] [Accepted: 07/15/2014] [Indexed: 11/22/2022]
Abstract
The objectives of this study were to develop a user-friendly, gel element microarray test for influenza virus detection, subtyping, and neuraminidase inhibitor resistance detection, assess the performance characteristics of the assay, and perform a clinical evaluation on retrospective nasopharyngeal swab specimens. A streamlined microarray workflow enabled a single user to run up to 24 tests in an 8h shift. The most sensitive components of the test were the primers and probes targeting the A/H1 pdm09 HA gene with an analytical limit of detection (LoD) <100 gene copies (gc) per reaction. LoDs for all targets in nasopharyngeal swab samples were ≤1000 gc, with the exception of one target in the seasonal A/H1N1 subtype. Seasonal H275Y variants were detectable in a mixed population when present at >5% with wild type virus, while the 2009 pandemic H1N1 H275Y variant was detectable at ≤1% in a mixture with pandemic wild type virus. Influenza typing and subtyping results concurred with those obtained with real-time RT-PCR assays on more than 97% of the samples tested. The results demonstrate that a large panel of single-plex, real-time RT-PCR tests can be translated to an easy-to-use, sensitive, and specific microarray test for potential diagnostic use.
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Affiliation(s)
- Darrell P Chandler
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States.
| | - Sara B Griesemer
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, United States
| | | | - Julia B Golova
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Amine Lambarqui
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Alexander N Perov
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Cynthia Zimmerman
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Cory Wiles
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - George B Rudy
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, United States
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, United States
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7
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Abstract
Influenza viruses cause recurring epidemic outbreaks every year associated with high morbidity and mortality. Despite extensive research and surveillance efforts to control influenza outbreaks, the primary mitigation treatment for influenza is the development of yearly vaccine mixes targeted for the most prevalent virus strains. Consequently, the focus of many detection technologies has evolved toward accurate identification of subtype and understanding the evolution and molecular determinants of novel and pathogenic forms of influenza. The recent availability of potential antiviral treatments are only effective if rapid and accurate diagnostic tests for influenza epidemic management are available; thus, early detection of influenza infection is still important for prevention, containment, patient management, and infection control. This review discusses the current and emerging technologies for detection and strain identification of influenza virus and their specific gene targets, as well as their implications in patient management.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, U. S. Naval Research Laboratory, 4555 Overlook Avenue, S. W., Code 6900, Washington, DC, 20375, USA
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Grubaugh ND, McMenamy SS, Turell MJ, Lee JS. Multi-gene detection and identification of mosquito-borne RNA viruses using an oligonucleotide microarray. PLoS Negl Trop Dis 2013; 7:e2349. [PMID: 23967358 PMCID: PMC3744434 DOI: 10.1371/journal.pntd.0002349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 06/19/2013] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Arthropod-borne viruses are important emerging pathogens world-wide. Viruses transmitted by mosquitoes, such as dengue, yellow fever, and Japanese encephalitis viruses, infect hundreds of millions of people and animals each year. Global surveillance of these viruses in mosquito vectors using molecular based assays is critical for prevention and control of the associated diseases. Here, we report an oligonucleotide DNA microarray design, termed ArboChip5.1, for multi-gene detection and identification of mosquito-borne RNA viruses from the genera Flavivirus (family Flaviviridae), Alphavirus (Togaviridae), Orthobunyavirus (Bunyaviridae), and Phlebovirus (Bunyaviridae). METHODOLOGY/PRINCIPAL FINDINGS The assay utilizes targeted PCR amplification of three genes from each virus genus for electrochemical detection on a portable, field-tested microarray platform. Fifty-two viruses propagated in cell-culture were used to evaluate the specificity of the PCR primer sets and the ArboChip5.1 microarray capture probes. The microarray detected all of the tested viruses and differentiated between many closely related viruses such as members of the dengue, Japanese encephalitis, and Semliki Forest virus clades. Laboratory infected mosquitoes were used to simulate field samples and to determine the limits of detection. Additionally, we identified dengue virus type 3, Japanese encephalitis virus, Tembusu virus, Culex flavivirus, and a Quang Binh-like virus from mosquitoes collected in Thailand in 2011 and 2012. CONCLUSIONS/SIGNIFICANCE We demonstrated that the described assay can be utilized in a comprehensive field surveillance program by the broad-range amplification and specific identification of arboviruses from infected mosquitoes. Furthermore, the microarray platform can be deployed in the field and viral RNA extraction to data analysis can occur in as little as 12 h. The information derived from the ArboChip5.1 microarray can help to establish public health priorities, detect disease outbreaks, and evaluate control programs.
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Affiliation(s)
- Nathan D Grubaugh
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, United States of America.
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9
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Kostina EV, Riabinin VA, Maksakova GA, Siniakov AN. [The second generation universal oligonucleotide microarray for subtyping of influenza virus A]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 38:676-82. [PMID: 23547471 DOI: 10.1134/s1068162012060052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The microchip for influenza A subtyping was developed, functioning on a principle "one spot--one subtype". Each spot contains the set of oligonucleotide probes, specific for a particular subtype of hemagglutinin, neuraminidase or matrix gene. Reliability of the proposed chip version is the same as for earlier created in our group full-size microchip for separate hemagglutinin and neuraminidase subtyping. To visualize the image, analyzed DNA can be labeled by either fluorescent dye or biotin with the further fixation in system streptavidin-gold nanoparticles and image development by silver precipitation. In the second case common version of scanner can be used for the image analysis, that essentially simplifies procedure of influenza A subtyping.
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10
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Grubaugh ND, Petz LN, Melanson VR, McMenamy SS, Turell MJ, Long LS, Pisarcik SE, Kengluecha A, Jaichapor B, O'Guinn ML, Lee JS. Evaluation of a field-portable DNA microarray platform and nucleic acid amplification strategies for the detection of arboviruses, arthropods, and bloodmeals. Am J Trop Med Hyg 2012; 88:245-53. [PMID: 23249687 DOI: 10.4269/ajtmh.2012.12-0048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Highly multiplexed assays, such as microarrays, can benefit arbovirus surveillance by allowing researchers to screen for hundreds of targets at once. We evaluated amplification strategies and the practicality of a portable DNA microarray platform to analyze virus-infected mosquitoes. The prototype microarray design used here targeted the non-structural protein 5, ribosomal RNA, and cytochrome b genes for the detection of flaviviruses, mosquitoes, and bloodmeals, respectively. We identified 13 of 14 flaviviruses from virus inoculated mosquitoes and cultured cells. Additionally, we differentiated between four mosquito genera and eight whole blood samples. The microarray platform was field evaluated in Thailand and successfully identified flaviviruses (Culex flavivirus, dengue-3, and Japanese encephalitis viruses), differentiated between mosquito genera (Aedes, Armigeres, Culex, and Mansonia), and detected mammalian bloodmeals (human and dog). We showed that the microarray platform and amplification strategies described here can be used to discern specific information on a wide variety of viruses and their vectors.
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Affiliation(s)
- Nathan D Grubaugh
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
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Leski TA, Lin B, Malanoski AP, Stenger DA. Application of resequencing microarrays in microbial detection and characterization. Future Microbiol 2012; 7:625-37. [PMID: 22568717 DOI: 10.2217/fmb.12.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Microarrays are powerful, highly parallel assays that are transforming microbiological diagnostics and research. The adaptation of microarray-based resequencing technology for microbial detection and characterization resulted in the development of a number assays that have unique advantages over other existing technologies. This technological platform seems to be especially useful for sensitive and high-resolution multiplexed diagnostics for clinical syndromes with similar symptoms, screening environmental samples for biothreat agents, as well as genotyping and whole-genome analysis of single pathogens.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, SW, Washington, DC 20375, USA.
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12
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You Y, He L, Zhang M, Fu J, Gu Y, Zhang B, Tao X, Zhang J. Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome. PLoS One 2012; 7:e38528. [PMID: 22701658 PMCID: PMC3368837 DOI: 10.1371/journal.pone.0038528] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 05/07/2012] [Indexed: 02/06/2023] Open
Abstract
In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori (H. pylori) genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases.
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Affiliation(s)
- Yuanhai You
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lihua He
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Maojun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianying Fu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yixin Gu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Binghua Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoxia Tao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianzhong Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- * E-mail:
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Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets: Optimization and data analysis. Biosens Bioelectron 2012; 35:87-93. [DOI: 10.1016/j.bios.2012.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/23/2012] [Accepted: 02/10/2012] [Indexed: 11/21/2022]
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Barnard RT, Hall RA, Gould EA. Expecting the unexpected: nucleic acid-based diagnosis and discovery of emerging viruses. Expert Rev Mol Diagn 2011; 11:409-23. [PMID: 21545258 PMCID: PMC7103685 DOI: 10.1586/erm.11.24] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Extrapolation from recent disease history suggests that changes in the global environment, including virus, vector and human behavior, will continue to influence the spectrum of viruses to which humans are exposed. In this article, these environmental changes will be enumerated, and their potential impact on target-focused, nucleic acid-based diagnostic tests will be considered, followed by a presentation of some emerging technological responses.
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Affiliation(s)
- Ross Thomas Barnard
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia.
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15
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Universal oligonucleotide microarray for sub-typing of Influenza A virus. PLoS One 2011; 6:e17529. [PMID: 21559081 PMCID: PMC3084687 DOI: 10.1371/journal.pone.0017529] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 02/07/2011] [Indexed: 11/19/2022] Open
Abstract
A universal microchip was developed for genotyping Influenza A viruses. It contains two sets of oligonucleotide probes allowing viruses to be classified by the subtypes of hemagglutinin (H1-H13, H15, H16) and neuraminidase (N1-N9). Additional sets of probes are used to detect H1N1 swine influenza viruses. Selection of probes was done in two steps. Initially, amino acid sequences specific to each subtype were identified, and then the most specific and representative oligonucleotide probes were selected. Overall, between 19 and 24 probes were used to identify each subtype of hemagglutinin (HA) and neuraminidase (NA). Genotyping included preparation of fluorescently labeled PCR amplicons of influenza virus cDNA and their hybridization to microarrays of specific oligonucleotide probes. Out of 40 samples tested, 36 unambiguously identified HA and NA subtypes of Influenza A virus.
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16
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Riabinin VA, Kostina EV, Neverov AA, Maksakova GA, Siniakov AN. [Oligonucleotide microarray for subtyping of influenza virus A neuraminidase]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 36:688-99. [PMID: 21063456 DOI: 10.1134/s1068162010050122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Microarray for influenza A neuraminidase subtyping was presented. Selection of oligoprobes proceeded in two steps. First step included selection of peptides specific for each subtype of neuraminidase. At the second step oligoprobes were calculated using found peptides structures with the subsequent additional selection of the most specific and representative probes. From 19 to 24 probes were used for determination of each subtype of neuraminidase. Microchip testing for 19 samples with the most widespread types (N1 and N2) specifies in unequivocal definition 18 of them and only one isolate has not been identified.
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Hyun Seok, Park TH. Integration of biomolecules and nanomaterials: Towards highly selective and sensitive biosensors. Biotechnol J 2011; 6:1310-6. [DOI: 10.1002/biot.201100006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/10/2011] [Accepted: 02/10/2011] [Indexed: 01/15/2023]
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Gębala M, Hartwich G, Schuhmann W. Amplified detection of DNA hybridization using post-labelling with a biotin-modified intercalator. Faraday Discuss 2011; 149:11-22; discussion 63-77. [DOI: 10.1039/c005365a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm. BMC Genomics 2010; 11:586. [PMID: 20961419 PMCID: PMC3091733 DOI: 10.1186/1471-2164-11-586] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 10/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A resequencing microarray called PathogenID v2.0 has been developed and used to explore various strategies of sequence selection for its design. The part dedicated to influenza viruses was based on consensus sequences specific for one gene generated from global alignments of a large number of influenza virus sequences available in databanks. RESULTS For each HA (H1, H2, H3, H5, H7 and H9) and NA (N1, N2 and N7) molecular type chosen to be tested, 1 to 3 consensus sequences were computed and tiled on the microarray. A total of 12 influenza virus samples from different host origins (humans, pigs, horses and birds) and isolated over a period of about 50 years were used in this study. Influenza viruses were correctly identified, and in most cases with the accurate information of the time of their emergence. CONCLUSIONS PathogenID v2.0 microarray demonstrated its ability to type and subtype influenza viruses, often to the level of viral variants, with a minimum number of tiled sequences. This validated the strategy of using consensus sequences, which do not exist in nature, for our microarray design. The versatility, rapidity and high discriminatory power of the PathogenID v2.0 microarray could prove critical to detect and identify viral genome reassortment events resulting in a novel virus with epidemic or pandemic potential and therefore assist health authorities to make efficient decisions about patient treatment and outbreak management.
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Smith MW, Herfort L, Tyrol K, Suciu D, Campbell V, Crump BC, Peterson TD, Zuber P, Baptista AM, Simon HM. Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin. PLoS One 2010; 5:e13312. [PMID: 20967204 PMCID: PMC2954162 DOI: 10.1371/journal.pone.0013312] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 09/10/2010] [Indexed: 11/18/2022] Open
Abstract
Through their metabolic activities, microbial populations mediate the impact of high gradient regions on ecological function and productivity of the highly dynamic Columbia River coastal margin (CRCM). A 2226-probe oligonucleotide DNA microarray was developed to investigate expression patterns for microbial genes involved in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were directed toward validation of the platform and yielded high reproducibility in multiple tests. Bioinformatic and experimental validation also indicated that >85% of the microarray probes were specific for their corresponding target genes and for a few homologs within the same microbial family. The validated probe set was used to query gene expression responses by microbial assemblages to environmental variability. Sixty-four samples from the river, estuary, plume, and adjacent ocean were collected in different seasons and analyzed to correlate the measured variability in chemical, physical and biological water parameters to differences in global gene expression profiles. The method produced robust seasonal profiles corresponding to pre-freshet spring (April) and late summer (August). Overall relative gene expression was high in both seasons and was consistent with high microbial abundance measured by total RNA, heterotrophic bacterial production, and chlorophyll a. Both seasonal patterns involved large numbers of genes that were highly expressed relative to background, yet each produced very different gene expression profiles. April patterns revealed high differential gene expression in the coastal margin samples (estuary, plume and adjacent ocean) relative to freshwater, while little differential gene expression was observed along the river-to-ocean transition in August. Microbial gene expression profiles appeared to relate, in part, to seasonal differences in nutrient availability and potential resource competition. Furthermore, our results suggest that highly-active particle-attached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches.
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Affiliation(s)
- Maria W. Smith
- Division of Environmental & Biomolecular Systems, Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Lydie Herfort
- Division of Environmental & Biomolecular Systems, Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Kaitlin Tyrol
- Division of Environmental & Biomolecular Systems, Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Dominic Suciu
- CombiMatrix Corporation, Mukilteo, Washington, United States of America
| | - Victoria Campbell
- Division of Environmental & Biomolecular Systems, Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Byron C. Crump
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Tawnya D. Peterson
- Division of Environmental & Biomolecular Systems, Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Peter Zuber
- Division of Environmental & Biomolecular Systems, Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Antonio M. Baptista
- Division of Environmental & Biomolecular Systems, Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Holly M. Simon
- Division of Environmental & Biomolecular Systems, Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Beaverton, Oregon, United States of America
- * E-mail:
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Zhao J, Tang S, Storhoff J, Marla S, Bao YP, Wang X, Wong EY, Ragupathy V, Ye Z, Hewlett IK. Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay. BMC Biotechnol 2010; 10:74. [PMID: 20942949 PMCID: PMC2964543 DOI: 10.1186/1472-6750-10-74] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 10/13/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For more than a decade there has been increasing interest in the use of nanotechnology and microarray platforms for diagnostic applications. In this report, we describe a rapid and simple gold nanoparticle (NP)-based genomic microarray assay for specific identification of avian influenza virus H5N1 and its discrimination from other major influenza A virus strains (H1N1, H3N2). RESULTS Capture and intermediate oligonucleotides were designed based on the consensus sequences of the matrix (M) gene of H1N1, H3N2 and H5N1 viruses, and sequences specific for the hemaglutinin (HA) and neuraminidase (NA) genes of the H5N1 virus. Viral RNA was detected within 2.5 hours using capture-target-intermediate oligonucleotide hybridization and gold NP-mediated silver staining in the absence of RNA fragmentation, target amplification, and enzymatic reactions. The lower limit of detection (LOD) of the assay was less than 100 fM for purified PCR fragments and 103 TCID50 units for H5N1 viral RNA. CONCLUSIONS The NP-based microarray assay was able to detect and distinguish H5N1 sequences from those of major influenza A viruses (H1N1, H3N2). The new method described here may be useful for simultaneous detection and subtyping of major influenza A viruses.
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Affiliation(s)
- Jiangqin Zhao
- Lab of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA.
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22
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Enhancement of deoxyribonucleic acid microarray performance using post-hybridization signal amplification. Anal Chim Acta 2010; 679:85-90. [PMID: 20951861 DOI: 10.1016/j.aca.2010.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 09/02/2010] [Accepted: 09/07/2010] [Indexed: 11/22/2022]
Abstract
Microarray performance depends upon the ability to screen samples against a vast array of probes with the appropriate sensitivity and selectivity. While these factors are significantly influenced by probe design, they are also subject to the particular detection methodology and reagents employed. Herein we describe the incorporation of super avidin-biotin system (SABS) and secondary enzymatic enhancement (SEE) as post-hybridization signal amplification techniques to improve the sensitivity of oligonucleotide microarrays. To these ends, we tested these methods on electrochemically interrogated arrays using both purified influenza A PCR products and randomly amplified genomic Francisella tularensis DNA as targets. While SABS treatment did not improve sensitivity for CombiMatrix ElectraSense(®) arrays using purified influenza A cDNA, chip sensitivity was improved 10-fold for randomly amplified targets. SEE improved performance to a greater degree and was able to lower the detection limits 10-fold for influenza A and 100-fold for F. tularensis DNA. These results indicate the promising capability of post-hybridization amplification techniques for enhancing microarray performance.
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23
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Kaewpongsri S, Sukasem C, Srichunrusami C, Pasomsub E, Zwang J, Pairoj W, Chantratita W. An integrated bioinformatics approach to the characterization of influenza A/H5N1 viral sequences by microarray data: Implication for monitoring H5N1 emerging strains and designing appropriate influenza vaccines. Mol Cell Probes 2010; 24:387-95. [PMID: 20797431 DOI: 10.1016/j.mcp.2010.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Revised: 01/18/2010] [Accepted: 08/17/2010] [Indexed: 12/09/2022]
Abstract
In order to characterize A/H5N1 viral sequences, a bioinformatics approach accurately identified viral sequences from discovery of a sequence signature, which provided enough distinctive information for sequence identification. Eight highly pathogenic H5N1 viral isolations were collected from different areas of Thailand between 2003 and 2006, and were used for analysis of H5N1 genotypic testing with a semiconductor-based oligonucleotide microarray. All H5N1 samples and H1N1, H4N8 negative controls were correctly subtyped. Sensitivity of the eight oligonucleotide probes, with optimized cut-offs, ranged from 70% (95% CI 65-75) to 87% (95% CI 84-91), and the corresponding Kappa values ranged from 0.76 (95% CI 0.72-0.80) to 0.86 (95% CI 0.83-0.89). Semi-conductor-based oligonucleotide array and oligonucleotide probes corresponded well when detecting H5N1. After fully correcting the subtype from the result of microarray signal intensity, the microarray output method combined with bioinformatics tools, identified and monitored genetic variations of H5N1. Capability of distinguishing different strains of H5N1 from Thailand was the outstanding feature of this assay. Ninety percent of HA and NA (4/5) genes were sequenced correctly, in accordance with previous examinations performed by classical diagnostic methods. The low-medium-high bioinformatics resolutions were able to predict an epidemic strain of H5N1. This study also showed the advantage of using a large genotypic database to predict the epidemic strain of H5N1. However, the monitoring protocol of this new strain has been recommended for further study with a large-scale sample.
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Affiliation(s)
- Supaporn Kaewpongsri
- Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
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24
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Straight TM, Merrill G, Perez L, Livezey J, Robinson B, Lodes M, Suciu D, Anderson B. A novel electrochemical device to differentiate pandemic (H1N1) 2009 from seasonal influenza. Influenza Other Respir Viruses 2010; 4:73-9. [PMID: 20167047 PMCID: PMC5779286 DOI: 10.1111/j.1750-2659.2009.00123.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND One of the challenges of the recent pandemic (H1N1) 2009 influenza outbreak was to differentiate the virus from seasonal influenza when confronting clinical cases. The determination of the virus has implications on treatment choice, and obvious epidemiologic significance. OBJECTIVES We set out to apply a novel electrochemical device to samples derived from clinical cases of pandemic (H1N1) 2009 influenza to examine the ability of the device to differentiate these samples from cases of seasonal influenza. PATIENTS/METHODS An IRB approved protocol allowed for the use of original nasal wash samples from 24 confirmed human cases pandemic (H1N1) 2009 influenza. Clinical samples from cases of seasonal influenza (Influenza A/H1N1, A/H3N2, and B) were included as controls. Nucleic acids were extracted and samples examined by the ElectraSense Influenza A assay (CombiMatrix, Inc). Samples were also examined by RT-PCR or Luminex assays as a comparator. RESULTS AND CONCLUSIONS The ElectraSense Influenza A assay correctly identified 23 of 24 samples of laboratory-confirmed pandemic (H1N1) 2009 Influenza. The assay correctly identified all samples of influenza A/H1N1 and A/H3N2, and differentiated these from pandemic (H1N1) 2009 Influenza in all cases. The ElectraSense Influenza A assay proved to be a useful assay to quickly and accurately differentiate pandemic (H1N1) 2009 influenza from seasonal influenza.
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Affiliation(s)
- T M Straight
- Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX 78234, USA.
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25
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Leski TA, Malanoski AP, Stenger DA, Lin B. Target amplification for broad spectrum microbial diagnostics and detection. Future Microbiol 2010; 5:191-203. [DOI: 10.2217/fmb.09.126] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification. This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques. The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA and Nova Research Inc., 1900 Elkin Street, Suite 230, Alexandria, VA, USA
| | - Anthony P Malanoski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - David A Stenger
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
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26
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Li X, Qi X, Miao L, Wang Y, Liu F, Gu H, Lu S, Yang Y, Liu F. Detection and subtyping of influenza A virus based on a short oligonucleotide microarray. Diagn Microbiol Infect Dis 2009; 65:261-70. [PMID: 19733996 DOI: 10.1016/j.diagmicrobio.2009.07.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 07/02/2009] [Accepted: 07/03/2009] [Indexed: 01/07/2023]
Abstract
We report the design and characterization of a microarray with 46 short virus-specific oligonucleotides for detecting influenza A virus of 5 subtypes: H1N1, H1N2, H3N2, H5N1, and H9N2. A unique combination of 3 specific modifications was introduced into the microarray assay: (1) short probes of 19 to 27 nucleotides, (2) simple amplification of full-length hemagglutinin and neuraminidase cDNAs with universal primers, and (3) Klenow-mediated labeling and further amplification of the samples before hybridization. The assay correctly and specifically detected and subtyped 11 different influenza A isolates from human, avian, and swine species representing the 5 subtypes. When tested with 225 clinical samples, 20 were detected to be positive using our microarray-based assay, whereas only 10 were positive by the conventional culture method. The entire analysis was completed within 7 h. Thus, these modifications result in a specific, sensitive, and rapid microarray assay and may be used for constructing microarrays for the detection of all influenza subtypes and strains.
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Affiliation(s)
- Xihan Li
- Institute of Virology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
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27
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Ghindilis A, Smith M, Schwarzkopf K, Zhan C, Evans D, Baptista A, Simon H. Sensor Array: Impedimetric Label-Free Sensing of DNA Hybridization in Real Time for Rapid, PCR-Based Detection of Microorganisms. ELECTROANAL 2009. [DOI: 10.1002/elan.200904549] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Lin CH, Hung CH, Hsiao CY, Lin HC, Ko FH, Yang YS. Poly-silicon nanowire field-effect transistor for ultrasensitive and label-free detection of pathogenic avian influenza DNA. Biosens Bioelectron 2009; 24:3019-24. [PMID: 19362813 DOI: 10.1016/j.bios.2009.03.014] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Revised: 03/08/2009] [Accepted: 03/10/2009] [Indexed: 12/16/2022]
Abstract
Enhanced surveillance of influenza requires rapid, robust, and inexpensive analytical techniques capable of providing a detailed analysis of influenza virus strains. Functionalized poly-crystalline silicon nanowire field-effect transistor (poly-SiNW FET) was demonstrated to achieve specific and ultrasensitive (at fM level) detection of high pathogenic strain virus (H5 and H7) DNA of avian influenza (AI) which is an important infectious disease and has an immediate need for surveillance. The poly-SiNW FET was prepared by a simple and low-cost method that is compatible with current commercial semiconductor process without expensive E-beam lithography tools for large-scale production. Specific electric changes were observed for AI virus DNA sensing when nanowire surface of poly-SiNW FET was modified with complementary captured DNA probe and target DNA (H5) at fM to pM range could be distinguished. With its excellent electric properties and potential for mass commercial production, poly-SiNW FET can be developed to become a portable biosensor for field use and point-of-care diagnoses.
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Affiliation(s)
- Chih-Heng Lin
- Institute of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
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29
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Fesenko EE, Kireyev DE, Gryadunov DA, Mikhailovich VM, Grebennikova TV, L'vov DK, Zasedatelev AS. Oligonucleotide microchip for subtyping of influenza A virus. Influenza Other Respir Viruses 2009; 1:121-9. [PMID: 19453417 PMCID: PMC4941880 DOI: 10.1111/j.1750-2659.2007.00018.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Influenza A viruses are classified into subtypes depending on the antigenic properties of their two outer glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Sixteen subtypes of HA and nine of NA are known. Lately, the circulation of some subtypes (H7N7, H5N1) has been closely watched because of the epidemiological threat they present. OBJECTIVES This study assesses the potential of using gel-based microchip technology for fast and sensitive molecular subtyping of the influenza A virus. METHODS The method employs a microchip of 3D gel-based elements containing immobilized probes. Segments of the HA and NA genes are amplified using multiplex RT-PCR and then hybridized with the microchip. RESULTS The developed microchip was validated using a panel of 21 known reference strains of influenza virus. Selected strains represented different HA and NA subtypes derived from avian, swine and human hosts. The whole procedure takes 10 hours and enables one to identify 15 subtypes of HA and two subtypes of NA. Forty-one clinical samples isolated during the poultry fall in Novosibirsk (Russia, 2005) were successfully identified using the proposed technique. The sensitivity and specificity of the method were 76% and 100%, respectively, compared with the 'gold standard' techniques (virus isolation with following characterization by immunoassay). CONCLUSIONS We conclude that the method of subtyping using gel-based microchips is a promising approach for fast detection and identification of influenza A, which may greatly improve its monitoring.
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Affiliation(s)
- Eugeny E Fesenko
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Str. 32, Moscow, Russia.
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Gall A, Hoffmann B, Harder T, Grund C, Ehricht R, Beer M. Rapid haemagglutinin subtyping and pathotyping of avian influenza viruses by a DNA microarray. J Virol Methods 2009; 160:200-5. [PMID: 19447139 DOI: 10.1016/j.jviromet.2009.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 05/03/2009] [Accepted: 05/07/2009] [Indexed: 11/17/2022]
Abstract
Rapid and reliable methods are fundamental for the comprehensive characterization of emerging and evolving avian influenza viruses. Although microarrays provide new possibilities with their parallel approach, their use in diagnostic laboratories is still limited due to economical and practical factors. An easy-to-use, low-cost microarray-based assay for haemagglutinin subtyping and pathotyping of avian influenza viruses and specific detection of highly pathogenic H5N1/Asia clade 2.2 is described as a novel diagnostic tool. The ArrayTube platform is user-friendly, inexpensive and allows processing of many samples. The sensitivity of the assay developed was comparable to real-time RT-PCR, and the simultaneous detection of different subtypes was possible. Validation with 90 influenza A virus isolates representing all 16 haemagglutinin subtypes and 44 field samples (cloacal swabs from wild and domestic birds) demonstrated the feasibility of the system for sensitive and specific characterization of AIV. Facilitating haemagglutinin subtyping and pathotyping for the majority of influenza A-positive cloacal swabs within 24h, the new assay enables detailed AIV diagnosis even in less well-equipped laboratories.
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Affiliation(s)
- Astrid Gall
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
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Bolotin S, Lombos E, Yeung R, Eshaghi A, Blair J, Drews SJ. Verification of the Combimatrix influenza detection assay for the detection of influenza A subtype during the 2007-2008 influenza season in Toronto, Canada. Virol J 2009; 6:37. [PMID: 19321005 PMCID: PMC2664794 DOI: 10.1186/1743-422x-6-37] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 03/25/2009] [Indexed: 11/13/2022] Open
Abstract
The increase in adamantine resistance in influenza A (H3N2) and the emergence of oseltamivir resistance in influenza A (H1N1) has necessitated the use of rapid methodologies to detect influenza subtype. The purpose of this study was to evaluate the CombiMatrix influenza detection system compared to the FDA approved Luminex Respiratory virus panel (RVP) assay for influenza A subtyping. Verification of the CombiMatrix influenza detection system was carried out using the Luminex RVP assay as a reference method. A limit of detection (LOD) series was performed using the Luminex and CombiMatrix systems with both influenza A H3N2 and H1N1 viruses. Seventy-five clinical specimens were used in the study. Of these, 16 were influenza A (H3N2) positive and five were influenza A (H1N1) positive. Fifty-four specimens were influenza A negative or "no call" (inconclusive) or could not be subtyped. The LOD of the Luminex RVP assay was found to be 0.3 TCID50s/mL for influenza A (H3N2) and 16 TCID50s/mL for influenza A (H1N1). The LOD of the CombiMatrix influenza detection system was 200 TCID50s/mL for influenza A (H3N2) and 16 000 TCID50s/mL for influenza A (H1N1). The sensitivity of the CombiMatrix influenza detection system was 95.2% and the specificity was 100%. The CombiMatrix influenza detection system is an effective methodology for influenza A subtype analysis, specifically in laboratories with a constrained budget or limited molecular capabilities.
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Affiliation(s)
- Shelly Bolotin
- Ontario Agency for Health Protection and Promotion, 81 Resources Road, Toronto, Ontario, M9P 3T1, Canada.
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32
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Huang Y, Tang H, Duffy S, Hong Y, Norman S, Ghosh M, He J, Bose M, Henrickson KJ, Fan J, Kraft AJ, Weisburg WG, Mather EL. Multiplex assay for simultaneously typing and subtyping influenza viruses by use of an electronic microarray. J Clin Microbiol 2009; 47:390-6. [PMID: 19073867 PMCID: PMC2643674 DOI: 10.1128/jcm.01807-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 12/01/2008] [Indexed: 11/20/2022] Open
Abstract
We report on the use of an electronic microarray to simultaneously type influenza A and B viruses and to distinguish influenza A virus subtypes H1N1 and H3N2 from the potentially pandemic avian virus subtype H5N1. The assay targets seven genes: the H1, H3, H5, N1, and N2 genes of influenza A virus; the matrix protein M1 gene of influenza A virus; and the nonstructural protein (NS) gene of influenza B virus. By combining a two-step reverse transcription-multiplex PCR with typing and subtyping on the electronic microarray, the assay achieved an analytical sensitivity of 10(2) to 10(3) copies of transcripts per reaction for each of the genes. The assay correctly typed and subtyped 15 different influenza virus isolates, including two influenza B virus, five A/H1N1, six A/H3N2, and two A/H5N1 isolates. In addition, the assay correctly identified 8 out of 10 diluted, archived avian influenza virus specimens with complete typing and subtyping information and 2 specimens with partial subtyping information. In a study of 146 human clinical specimens that had previously been shown to be positive for influenza virus or another respiratory virus, the assay showed a clinical sensitivity of 96% and a clinical specificity of 100%. The assay is a rapid, accurate, user-friendly method for simultaneously typing and subtyping influenza viruses.
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MESH Headings
- Genotype
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/classification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza A Virus, H5N1 Subtype/classification
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/isolation & purification
- Influenza B virus/classification
- Influenza B virus/genetics
- Influenza B virus/isolation & purification
- Microarray Analysis/methods
- RNA, Viral/genetics
- Reverse Transcriptase Polymerase Chain Reaction/methods
- Sensitivity and Specificity
- Viral Proteins/genetics
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Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children. J Clin Microbiol 2009; 47:743-50. [PMID: 19158263 DOI: 10.1128/jcm.01297-08] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory virus infections are a major health concern and represent the primary cause of testing consultation and hospitalization for young children. We developed and compared two assays that allow the detection of up to 23 different respiratory viruses that frequently infect children. The first method consisted of single TaqMan quantitative real-time PCR assays in a 96-well-plate format. The second consisted of a multiplex PCR followed by primer extension and microarray hybridization in an integrated molecular diagnostic device, the Infiniti analyzer. Both of our assays can detect adenoviruses of groups A, B, C, and E; coronaviruses HKU1, 229E, NL63, and OC43; enteroviruses A, B, C, and D; rhinoviruses of genotypes A and B; influenza viruses A and B; human metapneumoviruses (HMPV) A and B, human respiratory syncytial viruses (HRSV) A and B; and parainfluenza viruses of types 1, 2, and 3. These tests were used to identify viruses in 221 nasopharyngeal aspirates obtained from children hospitalized for respiratory tract infections. Respiratory viruses were detected with at least one of the two methods in 81.4% of the 221 specimens: 10.0% were positive for HRSV A, 38.0% for HRSV B, 13.1% for influenzavirus A, 8.6% for any coronaviruses, 13.1% for rhinoviruses or enteroviruses, 7.2% for adenoviruses, 4.1% for HMPV, and 1.5% for parainfluenzaviruses. Multiple viral infections were found in 13.1% of the specimens. The two methods yielded concordant results for 94.1% of specimens. These tests allowed a thorough etiological assessment of respiratory viruses infecting children in hospital settings and would assist public health interventions.
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34
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Genotyping Arrays. MICROARRAYS 2009. [PMCID: PMC7123720 DOI: 10.1007/978-0-387-72719-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Although the most common use of DNA microarrays is gene expression profiling, microarrays are also used for many other applications, including genotyping, resequencing, SNP analysis, and DNA methylation assays. Here we describe genotyping arrays for Influenza A subtype identification and for upper respiratory pathogen diagnostics using standard hybridization techniques and we also describe resequencing, SNP, and methylation assays using an enzyme-based strategy [25, 26].
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35
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Földes-Papp Z. Viral Chip Technology in Genomic Medicine. GENOMIC AND PERSONALIZED MEDICINE 2009. [PMCID: PMC7149707 DOI: 10.1016/b978-0-12-369420-1.00048-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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36
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Design and validation of a microarray for detection, hemagglutinin subtyping, and pathotyping of avian influenza viruses. J Clin Microbiol 2008; 47:327-34. [PMID: 19052173 DOI: 10.1128/jcm.01330-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Continuing threats of devastating outbreaks in poultry and of human infections caused by highly pathogenic avian influenza virus (HPAIV) H5N1 emphasize the need for the further development of rapid and reliable methods of virus detection and characterization. Here we report on the design and comprehensive validation of a low-density microarray as a diagnostic tool for the detection and typing of avian influenza virus (AIV). The array consists of one probe for the conserved matrix gene and 97 probes targeting the HA(0) cleavage-site region. Following fragment amplification by a generic PCR approach, the array enables AIV detection, hemagglutinin (HA) subtyping, and pathotyping within a single assay. For validation, a panel of 92 influenza A viruses which included 43 reference strains representing all 16 HA subtypes was used. All reference strains were correctly typed with respect to their HA subtypes and pathotypes, including HPAIV H5N1/Asia, which caused outbreaks in Germany in 2006 and 2007. In addition, differentiation of strains of the Eurasian and North American lineages of the H5 and H7 subtypes was possible. The sensitivity of the microarray for the matrix gene is comparable to that of real-time reverse transcription-PCR (RT-PCR). It is, however, 10- to 100-fold lower than that of real-time RT-PCR with respect to HA subtyping and pathotyping. The specificity of the array was excellent, as no pathogens relevant for differential diagnosis yielded a positive reaction. Validation with field samples included 19 cloacal swab specimens from wild and domestic birds. Influenza A virus was verified in all samples, whereas the HA subtypes could be determined for 14 samples. The results demonstrate that the microarray assay described complements current methods and can accelerate the diagnosis and characterization of AIV.
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37
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Han X, Lin X, Liu B, Hou Y, Huang J, Wu S, Liu J, Mei L, Jia G, Zhu Q. Simultaneously subtyping of all influenza A viruses using DNA microarrays. J Virol Methods 2008; 152:117-21. [DOI: 10.1016/j.jviromet.2008.05.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2007] [Revised: 05/12/2008] [Accepted: 05/15/2008] [Indexed: 10/21/2022]
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38
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Kukol A, Li P, Estrela P, Ko-Ferrigno P, Migliorato P. Label-free electrical detection of DNA hybridization for the example of influenza virus gene sequences. Anal Biochem 2007; 374:143-53. [PMID: 18023405 DOI: 10.1016/j.ab.2007.10.035] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 10/17/2007] [Accepted: 10/22/2007] [Indexed: 10/22/2022]
Abstract
Microarrays based on DNA-DNA hybridization are potentially useful for detecting and subtyping viruses but require fluorescence labeling and imaging equipment. We investigated a label-free electrical detection system using electrochemical impedance spectroscopy that is able to detect hybridization of DNA target sequences derived from avian H5N1 influenza virus to gold surface-attached single-stranded DNA oligonucleotide probes. A 23-nt probe is able to detect a 120-nt base fragment of the influenza A hemagglutinin gene sequence. We describe a novel method of data analysis that is compatible with automatic measurement without operator input, contrary to curve fitting used in conventional electrochemical impedance spectroscopy (EIS) data analysis. A systematic investigation of the detection signal for various spacer molecules between the oligonucleotide probe and the gold surface revealed that the signal/background ratio improves as the length of the spacer increases, with a 12- to 18-atom spacer element being optimal. The optimal spacer molecule allows a detection limit between 30 and 100 fmol DNA with a macroscopic gold disc electrode of 1 mm radius. The dependence of the detection signal on the concentration of a 23-nt target follows a binding curve with an approximate 1:1 stoichiometry and a dissociation constant of KD=13+/-4 nM at 295 K.
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Affiliation(s)
- Andreas Kukol
- School of Life Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
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39
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Lodes MJ, Suciu D, Wilmoth JL, Ross M, Munro S, Dix K, Bernards K, Stöver AG, Quintana M, Iihoshi N, Lyon WJ, Danley DL, McShea A. Identification of upper respiratory tract pathogens using electrochemical detection on an oligonucleotide microarray. PLoS One 2007; 2:e924. [PMID: 17895966 PMCID: PMC1976596 DOI: 10.1371/journal.pone.0000924] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 08/31/2007] [Indexed: 11/19/2022] Open
Abstract
Bacterial and viral upper respiratory infections (URI) produce highly variable clinical symptoms that cannot be used to identify the etiologic agent. Proper treatment, however, depends on correct identification of the pathogen involved as antibiotics provide little or no benefit with viral infections. Here we describe a rapid and sensitive genotyping assay and microarray for URI identification using standard amplification and hybridization techniques, with electrochemical detection (ECD) on a semiconductor-based oligonucleotide microarray. The assay was developed to detect four bacterial pathogens (Bordetella pertussis, Streptococcus pyogenes, Chlamydia pneumoniae and Mycoplasma pneumoniae) and 9 viral pathogens (adenovirus 4, coronavirus OC43, 229E and HK, influenza A and B, parainfluinza types 1, 2, and 3 and respiratory syncytial virus. This new platform forms the basis for a fully automated diagnostics system that is very flexible and can be customized to suit different or additional pathogens. Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation. Because ECD uses an enzymatic reaction to create electrical signals that can be read directly from the array, there is no need for image analysis or for expensive and delicate optical scanning equipment. We show assay sensitivity and specificity that are excellent for a multiplexed format.
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MESH Headings
- Adenoviridae/genetics
- Adenoviridae/isolation & purification
- Bacterial Infections/diagnosis
- Bacterial Infections/microbiology
- Bordetella pertussis/genetics
- Bordetella pertussis/isolation & purification
- Chlamydophila pneumoniae/genetics
- Chlamydophila pneumoniae/isolation & purification
- Coronavirus 229E, Human/genetics
- Coronavirus 229E, Human/isolation & purification
- Coronavirus OC43, Human/genetics
- Coronavirus OC43, Human/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Electrochemistry/methods
- Humans
- Influenza A virus/genetics
- Influenza A virus/isolation & purification
- Influenza B virus/genetics
- Influenza B virus/isolation & purification
- Mycoplasma pneumoniae/genetics
- Mycoplasma pneumoniae/isolation & purification
- Oligonucleotide Array Sequence Analysis/methods
- Parainfluenza Virus 1, Human/genetics
- Parainfluenza Virus 1, Human/isolation & purification
- Parainfluenza Virus 2, Human/genetics
- Parainfluenza Virus 2, Human/isolation & purification
- Parainfluenza Virus 3, Human/genetics
- Parainfluenza Virus 3, Human/isolation & purification
- Polymerase Chain Reaction
- Reproducibility of Results
- Respiratory Syncytial Viruses/genetics
- Respiratory Syncytial Viruses/isolation & purification
- Respiratory System/microbiology
- Respiratory System/virology
- Sensitivity and Specificity
- Sequence Analysis, DNA
- Streptococcus pyogenes/genetics
- Streptococcus pyogenes/isolation & purification
- Virus Diseases/diagnosis
- Virus Diseases/virology
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40
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Quan PL, Palacios G, Jabado OJ, Conlan S, Hirschberg DL, Pozo F, Jack PJM, Cisterna D, Renwick N, Hui J, Drysdale A, Amos-Ritchie R, Baumeister E, Savy V, Lager KM, Richt JA, Boyle DB, García-Sastre A, Casas I, Perez-Breña P, Briese T, Lipkin WI. Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray. J Clin Microbiol 2007; 45:2359-64. [PMID: 17553978 PMCID: PMC1951265 DOI: 10.1128/jcm.00737-07] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acute respiratory infections are significant causes of morbidity, mortality, and economic burden worldwide. An accurate, early differential diagnosis may alter individual clinical management as well as facilitate the recognition of outbreaks that have implications for public health. Here we report on the establishment and validation of a comprehensive and sensitive microarray system for detection of respiratory viruses and subtyping of influenza viruses in clinical materials. Implementation of a set of influenza virus enrichment primers facilitated subtyping of influenza A viruses through the differential recognition of hemagglutinins 1 through 16 and neuraminidases 1 through 9. Twenty-one different respiratory virus species were accurately characterized, including a recently identified novel genetic clade of rhinovirus.
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Affiliation(s)
- Phenix-Lan Quan
- Jerome L. and Dawn Greene Infectious Disease Laboratory, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1801, New York, NY 10032, USA
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41
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Maynard JA, Myhre R, Roy B. Microarrays in infection and immunity. Curr Opin Chem Biol 2007; 11:306-15. [PMID: 17500025 PMCID: PMC7108391 DOI: 10.1016/j.cbpa.2007.01.727] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 01/08/2007] [Indexed: 01/21/2023]
Abstract
Over the past decade, microarrays have revolutionized the scientific world as dramatically as the internet has changed everyday life. From the initial applications of DNA microarrays to uncover gene expression patterns that are diagnostic and prognostic of cancer, understanding the interplay between immune responses and disease has been a prime application of this technology. More recent efforts have moved beyond genetic analysis to functional analysis of the molecules involved, including identification of immunodominant antigens and peptides as well as the role of post-translational glycosylation. Here, we focus on recent applications of microarray technology in understanding the detailed chemical biology of immune responses to disease in an effort to guide development of vaccines and other protective therapies.
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Affiliation(s)
- Jennifer A Maynard
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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42
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Liu RH, Lodes MJ, Nguyen T, Siuda T, Slota M, Fuji HS, McShea A. Validation of a fully integrated microfluidic array device for influenza A subtype identification and sequencing. Anal Chem 2007; 78:4184-93. [PMID: 16771549 DOI: 10.1021/ac060450v] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid detection and identification of influenza virus is becoming increasingly important in the face of concerns over an influenza pandemic. A fully integrated and self-contained microfluidic device has been developed to rapidly identify influenza A hemagglutinin and neuraminidase subtypes and sequence portions of both genes. The device consists of a DNA microarray with 12 000 features and a microfluidic cartridge that automates the fluidic handling steps required to carry out a genotyping assay for pathogen identification and sequencing. The fully integrated microfluidic device consists of microfluidic pumps, mixers, valves, fluid channels, reagent storage chambers, and DNA microarray silicon chip. Microarray hybridization and subsequent fluidic handling and reactions were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. A micromixing technique based on gas bubbling generated by electrochemical micropumps was developed. Low-cost check valves were implemented in the cartridge to prevent cross talk of the stored reagents. The genotyping results showed that the device identified influenza A hemagglutinin and neuraminidase subtypes and sequenced portions of both genes, demonstrating the potential of integrated microfluidic and microarray technology for multiple virus detection. The device provides a cost-effective solution to eliminate labor-intensive and time-consuming fluidic handling steps and allows the detection and identification of influenza virus in a rapid and automated fashion.
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Affiliation(s)
- Robin Hui Liu
- CombiMatrix Corp., 6500 Harbor Heights Parkway, Mukilteo, Washington 98275, USA.
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43
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Ghindilis AL, Smith MW, Schwarzkopf KR, Roth KM, Peyvan K, Munro SB, Lodes MJ, Stöver AG, Bernards K, Dill K, McShea A. CombiMatrix oligonucleotide arrays: Genotyping and gene expression assays employing electrochemical detection. Biosens Bioelectron 2007; 22:1853-60. [PMID: 16891109 DOI: 10.1016/j.bios.2006.06.024] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 06/14/2006] [Accepted: 06/20/2006] [Indexed: 11/15/2022]
Abstract
Electrochemical detection has been developed and assay performances studied for the CombiMatrix oligonucleotide microarray platform that contains 12,544 individually addressable microelectrodes (features) in a semiconductor matrix. The approach is based on the detection of redox active chemistries (such as horseradish peroxidase (HRP) and the associated substrate TMB) proximal to specific microarray electrodes. First, microarray probes are hybridized to biotin-labeled targets, second, the HRP-streptavidin conjugate binds to biotin, and enzymatic oxidation of the electron donor substrate then occurs. The detection current is generated due to electro-reduction of the HRP reaction product, and it is measured with the CombiMatrix ElectraSense Reader. Performance of the ElectraSense platform has been characterized using gene expression and genotyping assays to analyze: (i) signal to concentration dependence, (ii) assay resolution, (iii) coefficients of variation, (CV) and (iv) array-to-array reproducibility and data correlation. The ElectraSense platform was also compared to the standard fluorescent detection, and good consistency was observed between these two different detection techniques. A lower detection limit of 0.75 pM was obtained for ElectraSense as compared to the detection limit of 1.5 pM obtained for fluorescent detection. Thus, the ElectraSense platform has been used to develop nucleic acid assays for highly accurate genotyping of a variety of pathogens including bio-threat agents (such as Bacillus anthracis, Yersinia pestis, and other microorganisms including Escherichia coli, Bacillus subtilis, etc.) and common pathogens of the respiratory tract (e.g. influenza A virus).
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Affiliation(s)
- Andrey L Ghindilis
- CombiMatrix Corporation, 6500 Harbour Heights Pkwy, 301, Mukilteo, WA 98275, USA.
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44
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Bourinbaiar AS, Timofeev IV, Agwale SM. Recent advances in development of avian flu and influenza diagnostics. Expert Rev Mol Diagn 2006; 6:783-95. [PMID: 17140364 DOI: 10.1586/14737159.6.6.783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Stevens J, Blixt O, Paulson JC, Wilson IA. Glycan microarray technologies: tools to survey host specificity of influenza viruses. Nat Rev Microbiol 2006; 4:857-64. [PMID: 17013397 PMCID: PMC7097745 DOI: 10.1038/nrmicro1530] [Citation(s) in RCA: 260] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
New technologies are urgently required for rapid surveillance of the current H5N1 avian influenza A outbreaks to gauge the potential for adaptation of the virus to the human population, a crucial step in the emergence of pandemic influenza virus strains. Owing to the species-specific nature of the interaction between the virus and host glycans, attention has recently focused on novel glycan array technologies that can rapidly assess virus receptor specificity and the potential emergence of human-adapted H5N1 viruses.
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Affiliation(s)
- James Stevens
- Department of Molecular Biology,
- Glycan Array Synthesis Core-D, Consortium for Functional Glycomics,The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
| | - Ola Blixt
- Department of Molecular Biology,
- Glycan Array Synthesis Core-D, Consortium for Functional Glycomics,The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
| | - James C. Paulson
- Department of Molecular Biology,
- Glycan Array Synthesis Core-D, Consortium for Functional Glycomics,The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
| | - Ian A. Wilson
- Department of Molecular Biology,
- Glycan Array Synthesis Core-D, Consortium for Functional Glycomics,The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
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46
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Roth K, Peyvan K, Schwarzkopf K, Ghindilis A. Electrochemical Detection of Short DNA Oligomer Hybridization Using the CombiMatrix ElectraSense Microarray Reader. ELECTROANAL 2006. [DOI: 10.1002/elan.200603603] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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