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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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Blair RH, Dawson ED, Taylor AW, Johnson JE, Slinskey AH, O'Neil K, Smolak AW, Toth E, Liikanen K, Stoughton RS, Smith CB, Talbot S, Rowlen KL. Clinical validation of the FluChip-8G Influenza A+B Assay for influenza type and subtype identification. J Clin Virol 2019; 118:20-27. [PMID: 31382226 PMCID: PMC6717662 DOI: 10.1016/j.jcv.2019.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND The FluChip-8G Influenza A+B Assay is a multiplexed influenza RT-PCR and microarray-based assay with same day turnaround time, developed to subtype seasonal A viruses (H1N1pdm2009 and H3N2), distinguish B viruses as Yamagata or Victoria lineage, and is the only FDA cleared assay capable of positive identification of a wide variety of A subtypes as "non-seasonal" A viruses from human nasal specimens. OBJECTIVE To evaluate clinical performance of the FluChip-8G Influenza A+B Assay for detection of seasonal influenza viruses in nasal and nasopharyngeal swab specimens, and to evaluate performance for detection of non-seasonal influenza viruses using contrived samples. STUDY DESIGN For seasonal viruses, a multisite study of the FluChip-8G Influenza A+B Assay using prospectively and retrospectively collected nasal and nasopharyngeal swabs was performed using the FDA-cleared CDC Human Flu Dx Panel as the comparator assay. For non-seasonal viruses, testing was performed at a single site using contrived samples from 100 unique non-seasonal strains representing 41 subtypes. RESULTS Sensitivity (95% CI) and specificity (95% CI) for each target group, respectively, from results of 1689 clinical specimens were: seasonal H1N1pdm2009: 96.4% (87.9-99.0), 99.3% (98.8-99.6), seasonal H3N2: 91.8% (87.7-94.7), 99.7% (99.2-99.9), Influenza B Victoria: 100% (94.0-100.0), 99.9% (99.6-100.0), and Influenza B Yamagata: 95.6% (89.2-98.3), 99.9% (99.6-100.0). The sensitivity and specificity from contrived influenza A non-seasonal viruses was determined to be 99.0% (94.6-99.8) and 100% (96.7-100.0). CONCLUSION The FluChip-8G Influenza A+B Assay has robust sensitivity and specificity for detecting and identifying all target virus groups, including non-seasonal influenza A, with same day results.
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Affiliation(s)
- Rebecca H Blair
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Erica D Dawson
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA.
| | - Amber W Taylor
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - James E Johnson
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Amelia H Slinskey
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Kelly O'Neil
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Andrew W Smolak
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Evan Toth
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | - Kyle Liikanen
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
| | | | - Catherine B Smith
- Influenza Division, the Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30333, USA
| | - Sarah Talbot
- Influenza Division, the Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30333, USA
| | - Kathy L Rowlen
- InDevR, Inc. 2100 Central Avenue, Suite 106, Boulder, CO, 80301, USA
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Meena JP, Brijwal M, Seth R, Gupta AK, Jethani J, Kapil A, Jat KR, Choudhary A, Kabra SK, Dwivedi SN, Dar L. Prevalence and clinical outcome of respiratory viral infections among children with cancer and febrile neutropenia. Pediatr Hematol Oncol 2019; 36:330-343. [PMID: 31512959 DOI: 10.1080/08880018.2019.1631920] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: The role of respiratory viruses (RV) in children with cancer having febrile neutropenic episodes has not been well studied. The objectives of our study were to investigate the prevalence and clinical outcomes of Respiratory viral infection (RVI). Methods: Children with cancer and febrile neutropenia (FN) having acute respiratory infections (ARI) were considered as cases and febrile neutropenic cancer patients without ARI were considered as controls. A throat swab sample was obtained for the detection of 21-respiratory pathogens. Results: A total of 81 episodes of FN in cases and 37 episodes of FN in controls were included. Prevalence of RVI (at least 1 RV) was seen in 76.5% of cases and 48.6% of controls (p = 0.005). The mixed-respiratory viruses (co-infections of ≥2 viruses) were seen only in cases (26%) (p = 0.00). Rhinovirus (36.8%) and respiratory syncytial virus (13.6%) were the most frequently detected viruses. Median duration of fever before presentation was more in cases with RVI compared to without RVI [2 (1-5) days vs 1 (1-5) day (p = 0.012)]. The median total duration of febrile period was 4 (IQR, 3-6) days in cases with RVI and 3 (IQR, 1-4) days in cases without RVI (p = 0.005). The median duration of antibiotic days were longer in cases with RVI as compared to patients without RVI [9 (IQR, 7-17) days vs 7 (IQR, 6-10) days (p = 0.046)] respectively. Conclusion: There was high prevalence of RVI in children with cancer and FN; more in association with ARI. The RVI were associated with prolonged febrile period and days of antibiotics therapy.
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Affiliation(s)
- Jagdish Prasad Meena
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - Megha Brijwal
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
| | - Rachna Seth
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - Aditya Kumar Gupta
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - Jyoti Jethani
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
| | - Kana Ram Jat
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - Aashish Choudhary
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
| | - S K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences , New Delhi , India
| | - S N Dwivedi
- Department of Biostatistics, All India Institute of Medical Sciences , New Delhi , India
| | - Lalit Dar
- Department of Microbiology, All India Institute of Medical Sciences , New Delhi , India
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Locher K, Roscoe D, Jassem A, Wong T, Hoang LMN, Charles M, Bryce E, Grant J, Stefanovic A. FilmArray respiratory panel assay: An effective method for detecting viral and atypical bacterial pathogens in bronchoscopy specimens. Diagn Microbiol Infect Dis 2019; 95:114880. [PMID: 31607515 PMCID: PMC7132745 DOI: 10.1016/j.diagmicrobio.2019.114880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/05/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022]
Abstract
The BioFire FilmArray Respiratory Panel (FA RP) is a rapid multiplexed molecular assay approved for detection of viral and atypical bacterial pathogens in nasopharyngeal specimens. This study aimed to evaluate the performance of the BioFire FilmArray Respiratory Panel v1.7 on bronchoscopy specimens. We tested 133 bronchial specimens (87 archived and 46 prospectively collected) with the FA RP and compared the results to the Luminex NxTAG Respiratory Pathogen Panel (NxTAG RPP). After discordant analysis, 123 specimens gave concordant results using the FA RP and the NxTAG RPP for an overall agreement of 93.9% (kappa = 0.88 [95% CI 0.80–0.96]), a positive percent agreement of 93.7% (95% CI 83.7–97.7) and a negative percent agreement of 94.1% (95% CI 84.9–98.1). In conclusion, the BioFire FilmArray RP performed reliably to detect a broad range of respiratory pathogens in bronchoscopy specimens.
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Affiliation(s)
- Kerstin Locher
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada.
| | - Diane Roscoe
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Agatha Jassem
- British Columbia Center for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Titus Wong
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Linda M N Hoang
- British Columbia Center for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Marthe Charles
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Elizabeth Bryce
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Jennifer Grant
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Vancouver Coastal Health, British Columbia, Canada; University of British Columbia, Faculty of Medicine, Vancouver, British Columbia, Canada
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Koopman G, Mortier D, Michels S, Hofman S, Fagrouch Z, Remarque EJ, Verschoor EJ, Mooij P, Bogers WM. Influenza virus infection as well as immunization with DNA encoding haemagglutinin protein induces potent antibody-dependent phagocytosis (ADP) and monocyte infection-enhancing responses in macaques. J Gen Virol 2019; 100:738-751. [DOI: 10.1099/jgv.0.001251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Gerrit Koopman
- 1Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Daniella Mortier
- 1Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Samira Michels
- 1Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Sam Hofman
- 2Department of Parasitology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Zahra Fagrouch
- 1Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Edmond J. Remarque
- 1Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Ernst J. Verschoor
- 1Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Petra Mooij
- 1Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
| | - Willy M.J.M. Bogers
- 1Department of Virology, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands
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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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Kaku N, Hashiguchi K, Iwanaga Y, Akamatsu N, Matsuda J, Kosai K, Uno N, Morinaga Y, Kitazaki T, Hasegawa H, Miyazaki T, Fukuda M, Izumikawa K, Mukae H, Yanagihara K. Evaluation of FilmArray respiratory panel multiplex polymerase chain reaction assay for detection of pathogens in adult outpatients with acute respiratory tract infection. J Infect Chemother 2018; 24:734-738. [PMID: 29895452 PMCID: PMC7128419 DOI: 10.1016/j.jiac.2018.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 05/01/2018] [Accepted: 05/16/2018] [Indexed: 12/27/2022]
Abstract
Although viruses are the major pathogen that causes upper respiratory tract infection (URTI) and acute bronchitis, antibiotics have been prescribed. This was a prospective observational study in influenza epidemics that enrolled adult outpatients who visited a hospital with respiratory tract infection symptoms. In this study, we evaluated the usefulness of FilmArray respiratory panel (RP). Fifty patients were enrolled. FilmArray RP detected the pathogens in 28 patients. The common pathogens were influenza virus (n = 14), respiratory syncytial virus (n = 6), and human rhinovirus (n = 6). Of the 14 patients with influenza virus, 6 were negative for the antigen test. The physicians diagnosed and treated the patients without the result of FilmArray in this study. Of the patients with positive FilmArray RP, 9 were treated with antibiotics; however, bacteria were detected in only 3 patients. By implementing FilmArray RP, URTI and acute bronchitis would be precisely diagnosed, and inappropriate use of antibiotics can be reduced.
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Affiliation(s)
- Norihito Kaku
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
| | - Kohji Hashiguchi
- Department of Respiratory Medicine, Japanese Red Cross Nagasaki Genbaku Hospital, Nagasaki, Japan
| | - Yuki Iwanaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Norihiko Akamatsu
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Junichi Matsuda
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naoki Uno
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Kitazaki
- Department of Respiratory Medicine, Japanese Red Cross Nagasaki Genbaku Hospital, Nagasaki, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Taiga Miyazaki
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masaaki Fukuda
- Department of Respiratory Medicine, Japanese Red Cross Nagasaki Genbaku Hospital, Nagasaki, Japan
| | - Koichi Izumikawa
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Momčilović S, Cantacessi C, Arsić-Arsenijević V, Otranto D, Tasić-Otašević S. Rapid diagnosis of parasitic diseases: current scenario and future needs. Clin Microbiol Infect 2018; 25:290-309. [PMID: 29730224 DOI: 10.1016/j.cmi.2018.04.028] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/22/2018] [Accepted: 04/24/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND Parasitic diseases are one of the world's most devastating and prevalent infections, causing millions of morbidities and mortalities annually. In the past, many of these infections have been linked predominantly to tropical or subtropical areas. Nowadays, however, climatic and vector ecology changes, a significant increase in international travel, armed conflicts, and migration of humans and animals have influenced the transmission of some parasitic diseases from 'book pages' to reality in developed countries. It has also been noted that many patients who have never travelled to endemic areas suffer from blood-borne infections caused by protozoa. In the light of existing knowledge, this new trend can be explained by the fact that in the process of migration a large number of asymptomatic carriers become a part of the blood bank donor and transplant donor populations. Accurate and rapid diagnosis represents the crucial weapon in the fight against parasitic infections. AIMS To review old and new approaches for rapid diagnosis of parasitic infections. SOURCES Data for this review were obtained through searches of PubMed using combinations of the following terms: parasitological diagnostics, microscopy, lateral flow assays, immunochromatographic assays, multiplex-PCR, and transplantation. CONTENT In this review, we provide a brief account of the advantages and limitations of rapid methods for diagnosis of parasitic diseases and focus our attention on current and future research in this area. The approximate costs associated with the use of different techniques and their applicability in endemic and non-endemic areas are also discussed. IMPLICATIONS Microscopy remains the cornerstone of parasitological diagnostics, especially in the field and low-resource settings, and provides epidemiological assessment of parasite burden. However, increased use and availability of point-of-care tests and molecular assays in modern era allow more rapid and accurate diagnoses and increased sensitivity in the identification of parasitic infections.
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Affiliation(s)
- S Momčilović
- Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia.
| | - C Cantacessi
- Department of Veterinary Medicine, University of Cambridge, UK
| | - V Arsić-Arsenijević
- Department for Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Serbia
| | - D Otranto
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Italy
| | - S Tasić-Otašević
- Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia; Center of Microbiology and Parasitology, Public Health Institute Niš, Serbia
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Otašević S, Momčilović S, Stojanović NM, Skvarč M, Rajković K, Arsić-Arsenijević V. Non-culture based assays for the detection of fungal pathogens. J Mycol Med 2018; 28:236-248. [PMID: 29605542 PMCID: PMC7110445 DOI: 10.1016/j.mycmed.2018.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 01/05/2023]
Abstract
Traditional, culture based methods for the diagnosis of fungal infections are still considered as gold standard, but they are time consuming and low sensitive. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. In this brief review, we highlighted the advantages and disadvantages of conventional diagnostic methods and possibility of non-culture based assays in diagnosis of superficial fungal infections and presented the overview on currently available immunochromatographic assays as well as availability of biomarkers detection by immunodiagnostic procedures in prompt and accurate diagnosis of invasive fungal infections. In addition, we presented diagnostic efficiency of currently available molecular panels and researches in this area.
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Affiliation(s)
- S Otašević
- Center of Microbiology and Parasitology, Public Health Institute Niš, Serbia, boulevard Zorana Djindjica 50, 18000 Niš, Serbia; Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia.
| | - S Momčilović
- Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - N M Stojanović
- Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - M Skvarč
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Zaloska 4, Ljubljana, Slovenia
| | - K Rajković
- High Chemical and Technological School for Professional Studies, Kosančićeva 36, 37000 Kruševac, Serbia
| | - V Arsić-Arsenijević
- Department for Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Serbia, Dr Subotića 1, 11000 Belgrade, Serbia
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Huang HS, Tsai CL, Chang J, Hsu TC, Lin S, Lee CC. Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis. Clin Microbiol Infect 2017; 24:1055-1063. [PMID: 29208560 PMCID: PMC7128951 DOI: 10.1016/j.cmi.2017.11.018] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/16/2017] [Accepted: 11/22/2017] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)-BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays-on the detection of viral respiratory infections. METHODS A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay. RESULTS Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848-0.949), 0.949 (95% confidence interval, 0.882-0.979) and 0.954 (95% confidence interval, 0.871-0.985), respectively. The three mPCRs were comparable in terms of detection of FluA. CONCLUSIONS Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.
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Affiliation(s)
- H-S Huang
- Department of Medicine, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan
| | - C-L Tsai
- Department of Medicine, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - J Chang
- Department of Gastroenterology, Nutrition, and Hepatology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - T-C Hsu
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - S Lin
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Industrial Engineering and Operations Research Department at the University of California, Berkeley, California, USA
| | - C-C Lee
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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Abstract
Acute upper and lower respiratory infections are a major public health problem and a leading cause of morbidity and mortality worldwide. At greatest risk are young children, the elderly, the chronically ill, and those with suppressed or compromised immune systems. Viruses are the predominant cause of respiratory tract illnesses and include RNA viruses such as respiratory syncytial virus, influenza virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus. Laboratory testing is required for a reliable diagnosis of viral respiratory infections, as a clinical diagnosis can be difficult since signs and symptoms are often overlapping and not specific for any one virus. Recent advances in technology have resulted in the development of newer diagnostic assays that offer great promise for rapid and accurate detection of respiratory viral infections. This chapter emphasizes the fundamental characteristics and clinical importance of the various RNA viruses that cause upper and lower respiratory tract diseases in the immunocompromised host. It highlights the laboratory methods that can be used to make a rapid and definitive diagnosis for the greatest impact on the care and management of ill patients, and the prevention and control of hospital-acquired infections and community outbreaks.
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12
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Miranda VDJ, Porto WF, Fernandes GDR, Pogue R, Nolasco DO, Araujo ACG, Cota LV, Freitas CGD, Dias SC, Franco OL. Comparative transcriptomic analysis indicates genes associated with local and systemic resistance to Colletotrichum graminicola in maize. Sci Rep 2017; 7:2483. [PMID: 28559543 PMCID: PMC5449407 DOI: 10.1038/s41598-017-02298-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 04/10/2017] [Indexed: 01/21/2023] Open
Abstract
The hemibiotrophic fungus Colletotrichum graminicola may cause severe damage to maize, affecting normal development of the plant and decreasing grain yield. In this context, understanding plant defense pathways at the inoculation site and systemically in uninoculated tissues can help in the development of genetic engineering of resistance against this pathogen. Previous work has discussed the molecular basis of maize - C. graminicola interaction. However, many genes involved in defense have not yet been exploited for lack of annotation in public databases. Here, changes in global gene expression were studied in root, male and female inflorescences of maize under local and systemic fungal infection treatments, respectively. RNA-Seq with qPCR was used to indicate genes involved in plant defense. We found that systemic acquired resistance induction in female inflorescences mainly involves accumulation of salicylic acid (SA)-inducible defense genes (ZmNAC, ZmHSF, ZmWRKY, ZmbZIP and PR1) and potential genes involved in chromatin modification. Furthermore, transcripts involved in jasmonic acid (JA) and ethylene (ET) signaling pathways were also accumulated and may participate in plant immunity. Moreover, several genes were functionally re-annotated based on domain signature, indicating novel candidates to be tested in strategies involving gene knockout and overexpression in plants.
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Affiliation(s)
- Vívian de Jesus Miranda
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília-DF, Brazil
| | - William Farias Porto
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília-DF, Brazil
- Porto Reports, Brasília, DF, Brazil
| | | | - Robert Pogue
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Diego Oliveira Nolasco
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília-DF, Brazil
- Research Laboratory of Electronics - Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | | | - Camila Guimarães de Freitas
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília-DF, Brazil
- Instituto Federal de Brasília, DF, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Octavio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília-DF, Brazil.
- S-Inova Biotech, Pos-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.
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13
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Yun SG, Kim MY, Choi JM, Lee CK, Lim CS, Cho Y, Suh IB. Comparison of three multiplex PCR assays for detection of respiratory viruses: Anyplex II RV16, AdvanSure RV, and Real-Q RV. J Clin Lab Anal 2017; 32. [PMID: 28397965 PMCID: PMC5836940 DOI: 10.1002/jcla.22230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/10/2017] [Indexed: 12/25/2022] Open
Abstract
Background Due to its great sensitivity, the nucleic acid amplification test (NAAT) is widely used for detection of respiratory viruses (RV). However, few reports have described a direct comparison between multiplex RT‐PCR assays for RV. The objective of this study was to perform a direct comparison of three multiplex RT‐PCR assays for the detection of respiratory viruses. Methods A total of 201 respiratory samples (161 nasopharyngeal swab samples and 40 sputum samples) were tested with three commercial RV assays: Seegene Anyplex II RV16 (AP), LG AdvanSure RV (AD), and Biosewoom Real‐Q RV (RQ). The additional tests for the discrepant results were conducted by repeat RV assay or monoplex PCR coupled direct sequencing. Data analysis using percent agreement, kappa, and prevalence‐adjusted and bias‐adjusted kappa (PABAK) values was performed for comparisons among the three RV assays. Results Of the 201 samples, AP, AD, and RQ detected 105 (52.2%), 99 (49.3%), and 95 (47.3%) positive cases respectively. The overall agreement, kappa, and PABAK values for the three assays ranged between 97%‐98%, 0.76‐0.86, and 0.93‐0.96 respectively. The performance of the three assays was very similar, with 94%‐100% agreement for all comparisons, each virus types. The additional testing of samples showed discrepant results demonstrating that AD assay had the highest rate of concordance with original results. Conclusions We suggest that all multiplex assay would be suitable for the detection of for respiratory viruses in clinical setting.
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Affiliation(s)
- Seung Gyu Yun
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Min Young Kim
- Armed Forces Medical Research Institute, Daejeon, Korea
| | - Jong Moon Choi
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - In Bum Suh
- Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
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14
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Ladhani L, Pardon G, Meeuws H, van Wesenbeeck L, Schmidt K, Stuyver L, van der Wijngaart W. Sampling and detection of airborne influenza virus towards point-of-care applications. PLoS One 2017; 12:e0174314. [PMID: 28350811 PMCID: PMC5369763 DOI: 10.1371/journal.pone.0174314] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 03/07/2017] [Indexed: 12/17/2022] Open
Abstract
Airborne transmission of the influenza virus contributes significantly to the spread of this infectious pathogen, particularly over large distances when carried by aerosol droplets with long survival times. Efficient sampling of virus-loaded aerosol in combination with a low limit of detection of the collected virus could enable rapid and early detection of airborne influenza virus at the point-of-care setting. Here, we demonstrate a successful sampling and detection of airborne influenza virus using a system specifically developed for such applications. Our system consists of a custom-made electrostatic precipitation (ESP)-based bioaerosol sampler that is coupled with downstream quantitative polymerase chain reaction (qPCR) analysis. Aerosolized viruses are sampled directly into a miniaturized collector with liquid volume of 150 μL, which constitutes a simple and direct interface with subsequent biological assays. This approach reduces sample dilution by at least one order of magnitude when compared to other liquid-based aerosol bio-samplers. Performance of our ESP-based sampler was evaluated using influenza virus-loaded sub-micron aerosols generated from both cultured and clinical samples. Despite the miniaturized collection volume, we demonstrate a collection efficiency of at least 10% and sensitive detection of a minimum of 3721 RNA copies. Furthermore, we show that an improved extraction protocol can allow viral recovery of down to 303 RNA copies and a maximum sampler collection efficiency of 47%. A device with such a performance would reduce sampling times dramatically, from a few hours with current sampling methods down to a couple of minutes with our ESP-based bioaerosol sampler.
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Affiliation(s)
- Laila Ladhani
- KTH Royal Institute of Technology, Department of Micro and Nanosystems, Stockholm, Sweden
| | - Gaspard Pardon
- KTH Royal Institute of Technology, Department of Micro and Nanosystems, Stockholm, Sweden
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15
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Rogan DT, Kochar MS, Yang S, Quinn JV. Impact of Rapid Molecular Respiratory Virus Testing on Real-Time Decision Making in a Pediatric Emergency Department. J Mol Diagn 2017; 19:460-467. [PMID: 28341587 DOI: 10.1016/j.jmoldx.2017.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/25/2017] [Indexed: 11/24/2022] Open
Abstract
Acute respiratory illnesses (ARIs) are usually viral [influenza, respiratory syncytial virus (RSV)] and account for 25% of emergency department (ED) peak-season visits. Laboratory PCR testing is accurate albeit slow, whereas rapid antigen testing is inaccurate. We determined the impact of bedside PCR (molecular point-of-care test; mPOCT) on pediatric ARI management. This was a prospective cohort study of consecutive pediatric patients with ED-ordered respiratory PCR test, enrolled over 9 weeks during peak flu season. On ordering, ED physicians were interviewed to ascertain real-time plans if given immediate influenza/RSV PCR results for the current patient. Two groups were compared: actual management and management adjusted for mPOCT results. We compared ED length of stay (LOS), tests ordered, and antibiotic/antiviral ordering. One-hundred thirty-six respiratory PCR panels were ordered, 71 by admitting team, 61 for ED management. Of 61 ED-initiated tests, physicians indicated in 39 cases (64%) they would change patient management were bedside viral results available. Physicians would have decreased ED LOS by 33 minutes, ordered fewer tests (18%; P < 0.001) with average patient charge savings of $669, fewer antibiotics among discharged patients (17%; P = 0.043), and increased appropriate antiviral use (13%; P = 0.023). Rapid bedside ARI mPOCT PCR has the potential to decrease ED LOS, reduce diagnostic tests and patient charges, and increase appropriate use of antibiotics and antiviral agents.
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Affiliation(s)
- Daniel T Rogan
- Department of Health Research and Policy, Stanford University, Stanford, California
| | - Mohit S Kochar
- Department of Emergency Medicine, Stanford University, Stanford, California
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, California.
| | - James V Quinn
- Department of Emergency Medicine, Stanford University, Stanford, California.
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16
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Millman AJ, Reed C, Kirley PD, Aragon D, Meek J, Farley MM, Ryan P, Collins J, Lynfield R, Baumbach J, Zansky S, Bennett NM, Fowler B, Thomas A, Lindegren ML, Atkinson A, Finelli L, Chaves SS. Improving Accuracy of Influenza-Associated Hospitalization Rate Estimates. Emerg Infect Dis 2016; 21:1595-601. [PMID: 26292017 PMCID: PMC4550134 DOI: 10.3201/eid2109.141665] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Adjusting for diagnostic test sensitivity enables more accurate and timely comparisons over time. Diagnostic test sensitivity affects rate estimates for laboratory-confirmed influenza–associated hospitalizations. We used data from FluSurv-NET, a national population-based surveillance system for laboratory-confirmed influenza hospitalizations, to capture diagnostic test type by patient age and influenza season. We calculated observed rates by age group and adjusted rates by test sensitivity. Test sensitivity was lowest in adults >65 years of age. For all ages, reverse transcription PCR was the most sensitive test, and use increased from <10% during 2003–2008 to ≈70% during 2009–2013. Observed hospitalization rates per 100,000 persons varied by season: 7.3–50.5 for children <18 years of age, 3.0–30.3 for adults 18–64 years, and 13.6–181.8 for adults >65 years. After 2009, hospitalization rates adjusted by test sensitivity were ≈15% higher for children <18 years, ≈20% higher for adults 18–64 years, and ≈55% for adults >65 years of age. Test sensitivity adjustments improve the accuracy of hospitalization rate estimates.
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17
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Wadle S, Lehnert M, Rubenwolf S, Zengerle R, von Stetten F. Real-time PCR probe optimization using design of experiments approach. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 7:1-8. [PMID: 27077046 PMCID: PMC4827641 DOI: 10.1016/j.bdq.2015.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/16/2015] [Accepted: 12/16/2015] [Indexed: 12/28/2022]
Abstract
Primer and probe sequence designs are among the most critical input factors in real-time polymerase chain reaction (PCR) assay optimization. In this study, we present the use of statistical design of experiments (DOE) approach as a general guideline for probe optimization and more specifically focus on design optimization of label-free hydrolysis probes that are designated as mediator probes (MPs), which are used in reverse transcription MP PCR (RT-MP PCR). The effect of three input factors on assay performance was investigated: distance between primer and mediator probe cleavage site; dimer stability of MP and target sequence (influenza B virus); and dimer stability of the mediator and universal reporter (UR). The results indicated that the latter dimer stability had the greatest influence on assay performance, with RT-MP PCR efficiency increased by up to 10% with changes to this input factor. With an optimal design configuration, a detection limit of 3-14 target copies/10 μl reaction could be achieved. This improved detection limit was confirmed for another UR design and for a second target sequence, human metapneumovirus, with 7-11 copies/10 μl reaction detected in an optimum case. The DOE approach for improving oligonucleotide designs for real-time PCR not only produces excellent results but may also reduce the number of experiments that need to be performed, thus reducing costs and experimental times.
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Affiliation(s)
- S. Wadle
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard Institut für Mikro-und Informationstechnik, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - M. Lehnert
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - S. Rubenwolf
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - R. Zengerle
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard Institut für Mikro-und Informationstechnik, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- BIOSS—Centre for Biological Signalling Studies, University of Freiburg, 79110 Freiburg, Germany
| | - F. von Stetten
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard Institut für Mikro-und Informationstechnik, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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18
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Beal SG, Assarzadegan N, Rand KH. Sample-to-result molecular infectious disease assays: clinical implications, limitations and potential. Expert Rev Mol Diagn 2016; 16:323-41. [PMID: 26689497 PMCID: PMC7103687 DOI: 10.1586/14737159.2016.1134325] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/17/2015] [Indexed: 01/01/2023]
Abstract
Molecular infectious disease diagnostic tests have undergone major advances in the past decade and will continue to rapidly evolve. Assays have become extraordinarily simple to perform, eliminating the need for pre-analytic sample preparation and post-amplification analysis. This allows these tests to be performed in settings without sophisticated expertise in molecular biology, including locations with limited resources. Additionally, the sensitivity and specificity of these assays is superb and many offer extremely fast turn-around times. These tests have major impacts on patient care, but also have some limitations.
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Affiliation(s)
- Stacy G. Beal
- Department of Pathology, Immunology and Laboratory Medicine,
University of Florida College of Medicine, Gainesville, FL,
USA
| | - Naziheh Assarzadegan
- Department of Pathology, Immunology and Laboratory Medicine,
University of Florida College of Medicine, Gainesville, FL,
USA
| | - Kenneth H. Rand
- Department of Pathology, Immunology and Laboratory Medicine,
University of Florida College of Medicine, Gainesville, FL,
USA
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19
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Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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Leonard DG. Respiratory Infections. MOLECULAR PATHOLOGY IN CLINICAL PRACTICE 2016. [PMCID: PMC7123443 DOI: 10.1007/978-3-319-19674-9_52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The majority of respiratory tract infections (RTIs) are community acquired and are the single most common cause of physician office visits and among the most common causes of hospitalizations. The morbidity and mortality associated with RTIs are significant and the financial and social burden high due to lost time at work and school. The scope of clinical symptoms can significantly overlap among the respiratory pathogens, and the severity of disease can vary depending on patient age, underlying disease, and immune status, thereby leading to inaccurate presumptions about disease etiology. The rapid and accurate diagnosis of the causative agent of RTIs improves patient care, reduces morbidity and mortality, promotes effective hospital bed utilization and antibiotic stewardship, and reduces length of stay. This chapter focuses on the clinical utility, advantages, and disadvantages of viral and bacterial tests cleared by the Food and Drug Administration (FDA), and new promising technologies for the detection of bacterial agents of pneumonia currently in development or in US FDA clinical trials are briefly reviewed.
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Affiliation(s)
- Debra G.B. Leonard
- Pathology and Laboratory Medicine, University of Vermont College of Medicine and University of Vermont Medical Center, Burlington, Vermont USA
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21
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Performance of a Novel Point-of-Care Molecular Assay for Detection of Influenza A and B Viruses and Respiratory Syncytial Virus (Enigma MiniLab) in Children with Acute Respiratory Infection. J Clin Microbiol 2015; 54:212-5. [PMID: 26560540 DOI: 10.1128/jcm.02887-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 10/30/2015] [Indexed: 02/08/2023] Open
Abstract
The performance of the Enigma MiniLab assay for influenza A and B viruses and respiratory syncytial virus (RSV) was compared to a centralized laboratory respiratory virus panel. The positive and negative percent agreement for influenza A virus, influenza B virus, and RSV were 79.2% (95% confidence interval [95% CI], 57.8 to 92.9%) and 99.4% (95% CI, 98.4 to 99.9), 100% (95% CI, 47.8 to 100%) and 100% (95% CI, 99.3 to 100%), 98.5% (95% CI, 94.6 to 99.8%) and 94.5% (95% CI, 91.9 to 96.4%), respectively.
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22
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Correlation between Virus Replication and Antibody Responses in Macaques following Infection with Pandemic Influenza A Virus. J Virol 2015; 90:1023-33. [PMID: 26537681 DOI: 10.1128/jvi.02757-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED Influenza virus infection of nonhuman primates is a well-established animal model for studying pathogenesis and for evaluating prophylactic and therapeutic intervention strategies. However, usually a standard dose is used for the infection, and there is no information on the relation between challenge dose and virus replication or the induction of immune responses. Such information is also very scarce for humans and largely confined to evaluation of attenuated virus strains. Here, we have compared the effect of a commonly used dose (4 × 10(6) 50% tissue culture infective doses) versus a 100-fold-higher dose, administered by intrabronchial installation, to two groups of 6 cynomolgus macaques. Animals infected with the high virus dose showed more fever and had higher peak levels of gamma interferon in the blood. However, virus replication in the trachea was not significantly different between the groups, although in 2 out of 6 animals from the high-dose group it was present at higher levels and for a longer duration. The virus-specific antibody response was not significantly different between the groups. However, antibody enzyme-linked immunosorbent assay, virus neutralization, and hemagglutination inhibition antibody titers correlated with cumulative virus production in the trachea. In conclusion, using influenza virus infection in cynomolgus macaques as a model, we demonstrated a relationship between the level of virus production upon infection and induction of functional antibody responses against the virus. IMPORTANCE There is only very limited information on the effect of virus inoculation dose on the level of virus production and the induction of adaptive immune responses in humans or nonhuman primates. We found only a marginal and variable effect of virus dose on virus production in the trachea but a significant effect on body temperature. The induction of functional antibody responses, including virus neutralization titer, hemagglutination inhibition titer, and antibody-dependent cell-mediated cytotoxicity, correlated with the level of virus replication measured in the trachea. The study reveals a relationship between virus production and functional antibody formation, which could be relevant in defining appropriate criteria for new influenza virus vaccine candidates.
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23
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Van Wesenbeeck L, D'Haese D, Tolboom J, Meeuws H, Dwyer DE, Holmes M, Ison MG, Katz K, McGeer A, Sadoff J, Weverling GJ, Stuyver L. A Downward Trend of the Ratio of Influenza RNA Copy Number to Infectious Viral Titer in Hospitalized Influenza A-Infected Patients. Open Forum Infect Dis 2015; 2:ofv166. [PMID: 26677457 PMCID: PMC4680923 DOI: 10.1093/ofid/ofv166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/07/2015] [Indexed: 01/02/2023] Open
Abstract
Background. Efficacy endpoints in influenza clinical trials may include clinical symptoms and virological measurements, although virology cannot serve as the primary endpoint. We investigated the relationship between influenza A RNA copy number and quantity of infectious viruses in hospitalized influenza patients. Methods. One hundred fifty influenza-infected, hospitalized patients were included in this prospective cohort study spanning the 2012-2013 influenza season. Daily nasopharyngeal samples were collected during hospitalization, and influenza A RNA copy number and infectious viral titer were monitored. Results. The decay rate for 50% tissue culture infectious dose (TCID50) was 0.51 ± 0.14 log10 TCID50/mL per day, whereas the RNA copy number decreased at a rate of 0.41 ± 0.04 log10 copies/mL per day (n = 433). The log ratio of the RNA copy number to the infectious viral titer within patient changes significantly with -0.25 ± 0.09 units per day (P = .0069). For a 12-day observation period, the decay corresponds to a decline of this ratio of 3 log influenza RNA copies. Conclusions. Influenza RNA copy number in nasal swabs is co-linear with culture, although the rate of decay of cell culture-based viral titers was faster than that observed with molecular methods. The study documented a clear decreasing log ratio of the RNA copy number to the infectious viral titer of the patients over time.
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Affiliation(s)
| | | | | | | | | | | | - Michael G Ison
- Northwestern University Feinberg School of Medicine , Chicago, Illinois
| | | | - Allison McGeer
- Department of Microbiology , Mount Sinai Hospital , Toronto , Canada
| | - Jerald Sadoff
- Janssen Infectious Diseases , Leiden , The Netherlands
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24
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Impagliazzo A, Milder F, Kuipers H, Wagner MV, Zhu X, Hoffman RMB, van Meersbergen R, Huizingh J, Wanningen P, Verspuij J, de Man M, Ding Z, Apetri A, Kükrer B, Sneekes-Vriese E, Tomkiewicz D, Laursen NS, Lee PS, Zakrzewska A, Dekking L, Tolboom J, Tettero L, van Meerten S, Yu W, Koudstaal W, Goudsmit J, Ward AB, Meijberg W, Wilson IA, Radošević K. A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen. Science 2015; 349:1301-6. [PMID: 26303961 DOI: 10.1126/science.aac7263] [Citation(s) in RCA: 436] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/29/2015] [Indexed: 12/14/2022]
Abstract
The identification of human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem revitalized hopes of developing a universal influenza vaccine. Using a rational design and library approach, we engineered stable HA stem antigens ("mini-HAs") based on an H1 subtype sequence. Our most advanced candidate exhibits structural and bnAb binding properties comparable to those of full-length HA, completely protects mice in lethal heterologous and heterosubtypic challenge models, and reduces fever after sublethal challenge in cynomolgus monkeys. Antibodies elicited by this mini-HA in mice and nonhuman primates bound a wide range of HAs, competed with human bnAbs for HA stem binding, neutralized H5N1 viruses, and mediated antibody-dependent effector activity. These results represent a proof of concept for the design of HA stem mimics that elicit bnAbs against influenza A group 1 viruses.
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Affiliation(s)
- Antonietta Impagliazzo
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands.
| | - Fin Milder
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Harmjan Kuipers
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Michelle V Wagner
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ryan M B Hoffman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ruud van Meersbergen
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Jeroen Huizingh
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Patrick Wanningen
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Johan Verspuij
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Martijn de Man
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Zhaoqing Ding
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Adrian Apetri
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Başak Kükrer
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Eveline Sneekes-Vriese
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Danuta Tomkiewicz
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Nick S Laursen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter S Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anna Zakrzewska
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Liesbeth Dekking
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Jeroen Tolboom
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Lisanne Tettero
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Sander van Meerten
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Wouter Koudstaal
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Jaap Goudsmit
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Wim Meijberg
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Katarina Radošević
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
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Emerging technologies for the clinical microbiology laboratory. Clin Microbiol Rev 2015; 27:783-822. [PMID: 25278575 DOI: 10.1128/cmr.00003-14] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.
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Economic analysis of rapid and sensitive polymerase chain reaction testing in the emergency department for influenza infections in children. Pediatr Infect Dis J 2015; 34:577-82. [PMID: 25973935 DOI: 10.1097/inf.0000000000000703] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Rapid multiplex polymerase chain reaction (PCR) assays simultaneously detect several respiratory viral pathogens with high sensitivity. Maximizing detection of influenza at the point of care has the potential to reduce unnecessary antibiotic use, laboratory tests and hospitalizations. However, the cost-effectiveness of rapid multiplex PCR assays for influenza has not been compared with other diagnostic methods in children. METHODS For children presenting to the emergency department with influenza-like illness, we compared costs and outcomes using 4 different testing strategies for detection of influenza: (1) a rapid multiplex PCR platform (FilmArray); (2) traditional PCR; (3) direct-fluorescent antibody and (4) rapid antigen tests. Costs were assessed from the hospital perspective, and effectiveness was defined as quality-adjusted life years (QALYs). Input parameters were obtained from previous studies, and the model was run separately for children aged 3-36 months and 3-18 years. RESULTS Rapid multiplex PCR testing was the most effective testing strategy for children in both age groups. The incremental cost-effectiveness when compared with rapid antigen tests was $115,556 per QALY for children aged 3-36 months and from $228,000 per QALY for children aged 3-18 years. The cost-effectiveness of rapid multiplex PCR was sensitive to estimates for influenza prevalence, the proportion of patients treated with antivirals and the cost per test. CONCLUSIONS Our model identifies scenarios in which identification of influenza in the emergency department using rapid multiplex PCR testing is a cost-effective strategy for infants and children 3 months through 18 years. Including detection of other respiratory viruses in the analysis would further improve cost-effectiveness.
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Goldenberg SD, Edgeworth JD. The Enigma ML FluAB-RSV assay: a fully automated molecular test for the rapid detection of influenza A, B and respiratory syncytial viruses in respiratory specimens. Expert Rev Mol Diagn 2015; 15:23-32. [PMID: 25399865 DOI: 10.1586/14737159.2015.983477] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Enigma(®) ML FluAB-RSV assay (Enigma Diagnostics, Porton Down, Salisbury, UK) is a CE-IVD marked multiplex molecular panel for the detection of influenza A, B and respiratory syncytial viruses in nasopharyngeal swabs. The assay runs on the fully automated Enigma ML platform without further specimen manipulation and provides a sample-to-answer result within 95 min. The reported sensitivity and specificity for influenza A are 100% (95% CI: 98.2-100) and 98.3% (95% CI: 95.5-99.4), respectively, for influenza B are 100% (95% CI: 98.2-100) and 98.7% (95% CI: 96-99.6), respectively, and for respiratory syncytial virus are 100% (95% CI: 98.2-100) and 99.4% (95% CI: 97.2-99.9), respectively.
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Affiliation(s)
- Simon D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's and St Thomas' NHS Foundation Trust, London SE1 7EH, UK
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Van Wesenbeeck L, Meeuws H, D'Haese D, Ispas G, Houspie L, Van Ranst M, Stuyver LJ. Sampling variability between two mid-turbinate swabs of the same patient has implications for influenza viral load monitoring. Virol J 2014; 11:233. [PMID: 25539740 PMCID: PMC4304201 DOI: 10.1186/s12985-014-0233-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 12/19/2014] [Indexed: 11/23/2022] Open
Abstract
Background With the clinical development of several antiviral intervention strategies for influenza, it becomes crucial to explore viral load shedding in the nasal cavity as a biomarker for treatment success, but also to explore sampling strategies for sensible and reliable virus collection. Findings In this study, 244 patients suffering from Influenza like Illness and/or acute respiratory tract infection were enrolled. Sampling was done using mid-turbinate flocked swabs and two swabs per patient were collected (one swab per nostril). The influenza A viral loads of two mid-turbinate flocked swabs (one for each nostril) per patient were compared and we have also assessed whether normalization for human cellular DNA in the swabs could be useful. The Influenza mid-turbinate nasal swab testing resulted in considerable sampling variability that could not be normalized against co-isolated human cellular DNA. Conclusions Influenza viral load monitoring in nasal swabs could be very valuable as virological endpoints in clinical trials to monitor treatment efficacy, in analogy to HIV, HBV & HCV viral load monitoring. However, the differences between left and right nostrils, as observed in this study, highlight the importance of proper sampling and the need for standardized sampling procedures.
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Affiliation(s)
| | - Hanne Meeuws
- Janssen Infectious Diseases - Diagnostics BVBA, Turnhoutseweg 30, B2340, Beerse, Belgium.
| | - David D'Haese
- Janssen Infectious Diseases - Diagnostics BVBA, Turnhoutseweg 30, B2340, Beerse, Belgium.
| | - Gabriela Ispas
- Janssen Infectious Diseases - Diagnostics BVBA, Turnhoutseweg 30, B2340, Beerse, Belgium.
| | - Lieselot Houspie
- Laboratory of Clinical Virology, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B3000, Leuven, Belgium.
| | - Marc Van Ranst
- Laboratory of Clinical Virology, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B3000, Leuven, Belgium.
| | - Lieven J Stuyver
- Janssen Infectious Diseases - Diagnostics BVBA, Turnhoutseweg 30, B2340, Beerse, Belgium.
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Standardization of Nucleic Acid Tests for Clinical Measurements of Bacteria and Viruses. J Clin Microbiol 2014; 53:2008-14. [PMID: 25392365 DOI: 10.1128/jcm.02136-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nucleic acid-based tests for infectious diseases currently used in the clinical laboratory and in point-of-care devices are diverse. Measurement challenges associated with standardization of quantitative viral load testing are discussed in relation to human cytomegalovirus, BK virus, and Epstein-Barr virus, while the importance of defining the performance of qualitative methods is illustrated with Mycobacterium tuberculosis and influenza virus. The development of certified reference materials whose values are traceable to higher-order standards and reference measurement procedures, using, for instance, digital PCR, will further contribute to the understanding of analytical performance characteristics and promote clinical data comparability.
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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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Butt SA, Maceira VP, McCallen ME, Stellrecht KA. Comparison of three commercial RT-PCR systems for the detection of respiratory viruses. J Clin Virol 2014; 61:406-10. [PMID: 25183359 PMCID: PMC7172935 DOI: 10.1016/j.jcv.2014.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/07/2014] [Accepted: 08/10/2014] [Indexed: 12/23/2022]
Abstract
BACKGROUND Due to the insensitivity of rapid tests for respiratory viruses, nucleic acid amplification tests are quickly becoming the standard of care. OBJECTIVES AND STUDY DESIGN The performance of the FilmArray Respiratory Panel (RP) and Verigene RV+ (RV+) were compared in a retrospective analysis of 89 clinical specimens previously determined to be positive for the following viruses by our test of record, Prodesse (Pro): influenza A (29, FluA), influenza B (13, FluB), respiratory syncytial virus (12, RSV), human metapneumovirus (10, hMPV), parainfluenza (14, PIV), and adenovirus (10, AdV). Samples positive for influenza A, B or RSV were tested by both methods, while the remainder were tested by RP only. True positives were defined as positive by two or more assays. RESULTS Limit of detection (LOD) analyses demonstrated Pro had the lowest LOD for all FluA strains tested, PIV1, PIV2 and AdV; RV+ had the lowest LOD for FluB; and RP had the lowest LOD for RSV, PIV3 and hMPV. Of the 55 samples tested by RV+, all 54 true positive samples were positive by RV+. Of the 89 samples tested by RP, 85 of the 88 true positive samples were positive by RP. From these results, the overall sensitivities for influenza A, B and RSV were 100% and 98% for RV+ and RP, respectively. The overall sensitivity of RP for all viruses was 97%. CONCLUSIONS In summary, these systems demonstrated excellent performance. Furthermore, each system has benefits which will ensure they will all have a niche in a clinical laboratory.
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Affiliation(s)
- S A Butt
- Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, NY, United States
| | - V P Maceira
- Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, NY, United States
| | - M E McCallen
- Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, NY, United States
| | - K A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, NY, United States; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, United States.
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Lai YH, Lee CC, King CC, Chuang MC, Ho JAA. Exploitation of stem-loop DNA as a dual-input gene sensing platform: extension to subtyping of influenza A viruses. Chem Sci 2014. [DOI: 10.1039/c4sc01289e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Cho HJ, Jang JW, Ko SY, Choi SH, Lim CS, An SSA. Evaluation and verification of the nanosphere Verigene RV+ assay for detection of influenza A/B and H1/H3 subtyping. J Med Virol 2014; 87:18-24. [DOI: 10.1002/jmv.23970] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Han Jin Cho
- Department of Emergency Medicine; Korea University; Seoul Republic of Korea
| | - Jin Woo Jang
- Department of Laboratory Medicine; College of Medicine; Korea University; Seoul Republic of Korea
| | - Sun Young Ko
- Department of Laboratory Medicine; College of Medicine; Korea University; Seoul Republic of Korea
| | - Sung Hyuk Choi
- Department of Emergency Medicine; Korea University; Seoul Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine; College of Medicine; Korea University; Seoul Republic of Korea
| | - Seong Soo A. An
- College of Bionanotechnology & Gachon Medical Research Institute; Gachon University & Gil Medical Center; Seongnam-si Gyeonggi Do Republic of Korea
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Abstract
Influenza continues to be a significant health care issue. Although vaccination is the major line of defense, antiviral drugs play an important role in prophylaxis and disease management. Approved drugs for influenza are currently limited to those that target the viral matrix protein or neuraminidase enzyme. Resistance-associated sequence changes in the genes encoding these proteins have been extensively studied. Available methods for genotypic and phenotypic antiviral susceptibility testing have expanded and are being further developed and improved. The sporadic emergence of drug-resistant variants and the global spread of resistant strains have demonstrated the ongoing need for vigilant testing and surveillance.
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Affiliation(s)
- Jennifer Laplante
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, PO Box 22002, Albany, NY 12201-2002, USA
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, PO Box 22002, Albany, NY 12201-2002, USA.
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The changing culture of the microbiology laboratory. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2014; 24:125-8. [PMID: 24421822 DOI: 10.1155/2013/101630] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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