1
|
Peng B, Wang Y, Xie Y, Dong X, Liu W, Li D, Chen H. An overview of influenza A virus detection methods: from state-of-the-art of laboratories to point-of-care strategies. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4496-4515. [PMID: 38946516 DOI: 10.1039/d4ay00508b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Influenza A virus (IAV), a common respiratory infectious pathogen, poses a significant risk to personal health and public health safety due to rapid mutation and wide host range. To better prevent and treat IAV, comprehensive measures are needed for early and rapid screening and detection of IAV. Although traditional laboratory-based techniques are accurate, they are often time-consuming and not always feasible in emergency or resource-limited areas. In contrast, emerging point-of-care strategies provide faster results but may compromise sensitivity and specificity. Here, this review critically evaluates various detection methods for IAV from established laboratory-based procedures to innovative rapid diagnosis. By analyzing the recent research progress, we aim to address significant gaps in understanding the effectiveness, practicality, and applicability of these methods in different scenarios, which could provide information for healthcare strategies, guide public health response measures, and ultimately strengthen patient care in the face of the ongoing threat of IAV. Through a detailed comparison of diagnostic models, this review can provide a reliable reference for rapid, accurate and efficient detection of IAV, and to contribute to the diagnosis, treatment, prevention, and control of IAV.
Collapse
Affiliation(s)
- Bin Peng
- Guangzhou Huashang Vocational College, Guangzhou, 510000, China
| | - Yaqi Wang
- Guangzhou Institute for Food Inspection, Guangzhou, 510000, China
| | - Yueliang Xie
- Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, 510000, China
| | - Xiangyan Dong
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
| | - Wen Liu
- Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, 510000, China
| | - Dan Li
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China
| | - Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
| |
Collapse
|
2
|
Rheem I, Park J, Kim TH, Kim JW. Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens. Ann Lab Med 2012; 32:399-406. [PMID: 23130338 PMCID: PMC3486933 DOI: 10.3343/alm.2012.32.6.399] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/30/2012] [Accepted: 08/17/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In this study, we evaluated the analytical performance and clinical potential of a one-step multiplex real-time PCR assay for the simultaneous detection of 14 types of respiratory viruses using the AdvanSure RV real-time PCR Kit (LG Life Sciences, Korea). METHODS Three hundred and twenty clinical specimens were tested with the AdvanSure RV real-time PCR Kit and conventional multiplex reverse transcription (RT)-PCR assay. The assay results were analyzed and the one-step AdvanSure RV real-time PCR Kit was compared with the conventional multiplex RT-PCR assay with respect to the sensitivity and specificity of the detection of respiratory viruses. RESULTS The limit of detection (LOD) was 1.31 plaque-forming units (PFU)/mL for human rhinoviruses (hRVs), 4.93 PFU/mL for human coronavirus HCoV-229E/NL63, 2.67 PFU/mL for human coronavirus HCoV-OC43, 18.20 PFU/mL for parainfluenza virus 1 (PIV)-1, 24.57 PFU/mL for PIV-2, 1.73 PFU/mL for PIV-3, 1.79 PFU/mL for influenza virus group (Flu) A, 59.51 PFU/mL for FluB, 5.46 PFU/mL for human respiratory syncytial virus (hRSV)-A, 17.23 PFU/mL for hRSV-B, 9.99 PFU/mL for human adenovirus (ADVs). The cross-reactivity test for this assay against 23 types of non-respiratory viruses showed negative results for all viruses tested. The agreement between the one-step AdvanSure multiplex real-time PCR assay and the conventional multiplex RT-PCR assay was 98%. CONCLUSIONS The one-step AdvanSure RV multiplex real-time PCR assay is a simple assay with high potential for specific, rapid and sensitive laboratory diagnosis of respiratory viruses compared to conventional multiplex RT-PCR.
Collapse
Affiliation(s)
- Insoo Rheem
- Department of Laboratory Medicine, Dankook University College of Medicine, Cheonan, Korea
| | | | | | | |
Collapse
|
3
|
Pabbaraju K, Wong S, Drews SJ. Rethinking approaches to improve the utilization of nucleic acid amplification tests for detection and characterization of influenza A in diagnostic and reference laboratories. Future Microbiol 2011; 6:1443-60. [PMID: 22122441 DOI: 10.2217/fmb.11.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Influenza A virus (IFVA) is a significant cause of respiratory infections worldwide and was also responsible for a recent pandemic in 2009. Laboratory identification of IFVA can guide antiviral therapy, assist in cohorting of patients and prevent antibiotic use. Characterization of the virus can track the emergence of novel strains, identify resistance and determine how circulating strains match with vaccine components. The gold standard for detection and characterization of IFVA is nucleic acid amplification technology (e.g., reverse transcriptase PCR [RT-PCR]), which must contend with a constantly evolving viral genome. Although molecular technology has been available for over two decades, there is still an operational gap between assay design and utilization of these tests for the diagnosis and characterization of IFVA. This review will discuss issues surrounding the implementation and use of RT-PCR for the identification and characterization of IFVA, and speculate on why RT-PCR has not been used more widely in clinical laboratories or moved closer to the patient. Newer, less widely used technologies that may change our laboratory practices will be identified and the authors will close with an attempt to identify some future applications of RT-PCR-based technologies for the detection and characterization of IFVA.
Collapse
Affiliation(s)
- Kanti Pabbaraju
- Provincial Laboratory for Public Health, Microbiology, 3030 Hospital Drive NW, Calgary, Alberta T2N 4W4, Canada
| | | | | |
Collapse
|
4
|
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.
Collapse
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.
| | | | | |
Collapse
|
5
|
Chen H, Mammel M, Kulka M, Patel I, Jackson S, Goswami BB. Detection and identification of common food-borne viruses with a tiling microarray. Open Virol J 2011; 5:52-9. [PMID: 21660190 PMCID: PMC3109525 DOI: 10.2174/1874357901105010052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 02/24/2011] [Accepted: 03/08/2011] [Indexed: 01/03/2023] Open
Abstract
Microarray hybridization based identification of viral genotypes is increasingly assuming importance due to outbreaks of multiple pathogenic viruses affecting humans causing wide-spread morbidity and mortality. Surprisingly, microarray based identification of food-borne viruses, one of the largest groups of pathogenic viruses, causing more than 1.5 billion infections world-wide every year, has lagged behind. Cell-culture techniques are either unavailable or time consuming for routine application. Consequently, current detection methods for these pathogens largely depend on polymerase chain reaction (PCR) based techniques, generally requiring an investigator to preselect the target virus of interest. Here we describe the first attempt to use the microarray as an identification tool for these viruses. We have developed methodology to synthesize targets for virus identification without using PCR, making the process genuinely sequence independent. We show here that a tiling microarray can simultaneously detect and identify the genotype and strain of common food-borne viruses in a single experiment.
Collapse
Affiliation(s)
- Haifeng Chen
- Division of Molecular Biology, OARSA, Center for Food Safety and Applied Nutrition, U.S Food and Drug Administration, Laurel, MD 20708, USA
| | | | | | | | | | | |
Collapse
|
6
|
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.
Collapse
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:
| |
Collapse
|
7
|
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.
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- T M Straight
- Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX 78234, USA.
| | | | | | | | | | | | | | | |
Collapse
|