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Struijk R, van den Ouden A, Louwerse J, Čurová K, Burggrave R, McNally B, de Groot T, Mulder B, de Vos G. Ultrafast RNA extraction-free SARS-CoV-2 detection by direct RT-PCR using a rapid thermal cycling approach. Diagn Microbiol Infect Dis 2023; 107:115975. [PMID: 37343400 PMCID: PMC10154057 DOI: 10.1016/j.diagmicrobio.2023.115975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/24/2023] [Accepted: 04/29/2023] [Indexed: 06/23/2023]
Abstract
The COVID19 pandemic has underlined the need for quick and high-throughput SARS-CoV-2 detection assays. Here we report the development of a direct RT-PCR detection method that can reliably detect SARS-CoV-2 gRNA in nasopharyngeal swab samples in under 27 minutes without needing nucleic acid extraction. Fluorescence readouts were highly linear, robust, and sensitive with a LoD95% of determined at 1.46 copies/μL as determined by RT-PCR on a surrogate sample panel containing clinical samples with varying SARS-CoV-2 viral load. We benchmarked our direct RT-PCR method against a reference qPCR method in 368 nasopharyngeal swab samples, confirming a sensitivity score of 99.4% and a specificity score of 98.5% as compared to the reference method. In summary, we here describe a novel rapid direct RT-PCR method to detect SARS-CoV-2 gRNA in clinical specimens, which can be completed in significantly less time compared to conventional PCR methods making it ideal for large-scale screening applications.
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Affiliation(s)
- Robin Struijk
- Department of Research & Development, Molecular Biology Systems B.V., Goes, The Netherlands
| | - Anton van den Ouden
- Department of Research & Development, Molecular Biology Systems B.V., Goes, The Netherlands
| | - Jeroen Louwerse
- Department of Research & Development, Molecular Biology Systems B.V., Goes, The Netherlands
| | - Katarína Čurová
- Department of Medical and Clinical Microbiology, Faculty of Medicine, Pavol Jozef Šafárik University, Košice, Slovakia
| | - Ronald Burggrave
- Department of Research & Development, Molecular Biology Systems B.V., Goes, The Netherlands
| | - Brian McNally
- Department of Research & Development, Molecular Biology Systems B.V., Goes, The Netherlands
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Ziekenhuis, Nijmegen, The Netherlands
| | - Bert Mulder
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Ziekenhuis, Nijmegen, The Netherlands
| | - Gert de Vos
- Department of Research & Development, Molecular Biology Systems B.V., Goes, The Netherlands; Department of Physiology, Faculty of Medicine, Pavol Jozef Šafárik University, Košice, Slovakia.
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2
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Long S. In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the Raindance ddPCR platform. Methods 2022; 201:82-95. [PMID: 33839286 PMCID: PMC8501152 DOI: 10.1016/j.ymeth.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Sensitive PCR detection of viral nucleic acids plays a critical role in infectious disease research, diagnosis and monitoring. In the context of SARS-CoV-2 detection, recent reports indicate that digital PCR-based tests are significantly more sensitive than traditional qPCR tests. Numerous factors can influence digital PCR reaction sensitivity. In this review, using a model for human HIV infection and the Raindance ddPCR platform as an example, we describe technical aspects that contribute to sensitive viral signal detection in DNA and RNA from tissue samples, which often harbor viral reservoirs and serve as better predictors of disease outcome and indicators of treatment efficacy.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
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3
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Phommasone K, Xaiyaphet X, Garcia-Rivera JA, Hontz RD, Pathavongsa V, Keomoukda P, Vongsouvath M, Mayxay M, Vongsouvath M, Newton PN, Ashley EA, Dubot-Pérès A. A case-control study of the causes of acute respiratory infection among hospitalized patients in Northeastern Laos. Sci Rep 2022; 12:939. [PMID: 35042900 PMCID: PMC8766494 DOI: 10.1038/s41598-022-04816-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/31/2021] [Indexed: 11/18/2022] Open
Abstract
With the advent of highly sensitive real-time PCR, multiple pathogens have been identified from nasopharyngeal swabs of patients with acute respiratory infections (ARIs). However, the detection of microorganisms in the upper respiratory tract does not necessarily indicate disease causation. We conducted a matched case-control study, nested within a broader fever aetiology project, to facilitate determination of the aetiology of ARIs in hospitalised patients in Northeastern Laos. Consenting febrile patients of any age admitted to Xiengkhuang Provincial Hospital were included if they met the inclusion criteria for ARI presentation (at least one of the following: cough, rhinorrhoea, nasal congestion, sore throat, difficulty breathing, and/or abnormal chest auscultation). One healthy control for each patient, matched by sex, age, and village of residence, was recruited for the study. Nasopharyngeal swabs were collected from participants and tested for 33 pathogens by probe-based multiplex real-time RT-PCR (FastTrack Diagnostics Respiratory pathogen 33 kit). Attributable fraction of illness for a given microorganism was calculated by comparing results between patients and controls (= 100 * [OR - 1]/OR) (OR = odds ratio). Between 24th June 2019 and 24th June 2020, 205 consenting ARI patients and 205 matching controls were recruited. After excluding eight pairs due to age mismatch, 197 pairs were included in the analysis. Males were predominant with sex ratio 1.2:1 and children < 5 years old accounted for 59% of participants. At least one potential pathogen was detected in 173 (88%) patients and 175 (89%) controls. ARI in admitted patients were attributed to influenza B virus, influenza A virus, human metapneumovirus (HMPV), and respiratory syncytial virus (RSV) in 17.8%, 17.2%, 7.5%, and 6.5% of participants, respectively. SARS-CoV-2 was not detected in any cases or controls. Determining ARI aetiology in individual patients remains challenging. Among hospitalised patients with ARI symptoms presenting to a provincial hospital in Northeastern Laos, half were determined to be caused by one of several respiratory viruses, in particular influenza A virus, influenza B virus, HMPV, and RSV.
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Affiliation(s)
- Koukeo Phommasone
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR.
| | - Xaipasong Xaiyaphet
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Jose A Garcia-Rivera
- U.S. Naval Medical Research Unit TWO (NAMRU-2), Singapore and Phnom Penh, Cambodia
| | - Robert D Hontz
- U.S. Naval Medical Research Unit TWO (NAMRU-2), Singapore and Phnom Penh, Cambodia
| | | | - Patsalin Keomoukda
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Malavanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Institute of Research and Education Development (IRED), Ministry of Health, Vientiane, Lao PDR
- University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth A Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
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4
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Peghin M, Los-Arcos I, Hirsch HH, Codina G, Monforte V, Bravo C, Berastegui C, Jauregui A, Romero L, Cabral E, Ferrer R, Sacanell J, Román A, Len O, Gavaldà J. Community-acquired Respiratory Viruses Are a Risk Factor for Chronic Lung Allograft Dysfunction. Clin Infect Dis 2020; 69:1192-1197. [PMID: 30561555 PMCID: PMC7797743 DOI: 10.1093/cid/ciy1047] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/11/2018] [Indexed: 01/30/2023] Open
Abstract
Background The relationship between community-acquired respiratory viruses (CARVs) and chronic lung allograft dysfunction (CLAD) in lung transplant recipients is still controversial. Methods We performed a prospective cohort study (2009–2014) in all consecutive adult patients (≥18 years) undergoing lung transplantation in the Hospital Universitari Vall d’Hebron (Barcelona, Spain). We systematically collected nasopharyngeal swabs from asymptomatic patients during seasonal changes, from patients with upper respiratory tract infectious disease, lower respiratory tract infectious disease (LRTID), or acute rejection. Nasopharyngeal swabs were analyzed by multiplex polymerase chain reaction. Primary outcome was to evaluate the potential association of CARVs and development of CLAD. Time-dependent Cox regression models were performed to identify the independent risk factors for CLAD. Results Overall, 98 patients (67 bilateral lung transplant recipients; 63.3% male; mean age, 49.9 years) were included. Mean postoperative follow-up was 3.4 years (interquartile range [IQR], 2.5–4.0 years). Thirty-eight lung transplant recipients (38.8%) developed CLAD, in a median time of 20.4 months (IQR, 12–30.4 months). In time-controlled multivariate analysis, CARV-LRTID (hazard ratio [HR], 3.00 [95% confidence interval {CI}, 1.52–5.91]; P = .002), acute rejection (HR, 2.97 [95% CI, 1.51–5.83]; P = .002), and cytomegalovirus pneumonitis (HR, 3.76 [95% CI, 1.23–11.49]; P = .02) were independent risk factors associated with developing CLAD. Conclusions Lung transplant recipients with CARVs in the lower respiratory tract are at increased risk to develop CLAD.
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Affiliation(s)
- Maddalena Peghin
- Infectious Diseases Research Group, Vall d'Hebron Research Institute, Department of Infectious Diseases, Hospital Universitari Vall d'Hebron, Barcelona.,Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid.,Infectious Diseases Clinic, Department of Medicine, University of Udine and Santa Maria Misericordia Hospital, Italy
| | - Ibai Los-Arcos
- Infectious Diseases Research Group, Vall d'Hebron Research Institute, Department of Infectious Diseases, Hospital Universitari Vall d'Hebron, Barcelona.,Department of Medicine, Universitat Autònoma de Barcelona, Spain
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, Basel University Hospital, Switzerland
| | - Gemma Codina
- Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid.,Department of Microbiology, Hospital Universitari Vall d'Hebron, Barcelona
| | - Víctor Monforte
- Department of Pulmonology and Lung Transplant Unit, Hospital Universitari Vall d'Hebron, Barcelona
| | - Carles Bravo
- Department of Pulmonology and Lung Transplant Unit, Hospital Universitari Vall d'Hebron, Barcelona
| | - Cristina Berastegui
- Department of Pulmonology and Lung Transplant Unit, Hospital Universitari Vall d'Hebron, Barcelona
| | - Alberto Jauregui
- Department of Thoracic Surgery, Hospital Universitari Vall d'Hebron, Barcelona
| | - Laura Romero
- Department of Thoracic Surgery, Hospital Universitari Vall d'Hebron, Barcelona
| | - Evelyn Cabral
- Infectious Diseases Research Group, Vall d'Hebron Research Institute, Department of Infectious Diseases, Hospital Universitari Vall d'Hebron, Barcelona
| | - Ricard Ferrer
- Intensive Care Department, Hospital Universitari Vall d'Hebron, Barcelona.,Shock, Organ Dysfunction and Resuscitation Research Group, Vall d' Hebron Research Institute, Barcelona
| | - Judith Sacanell
- Intensive Care Department, Hospital Universitari Vall d'Hebron, Barcelona.,Shock, Organ Dysfunction and Resuscitation Research Group, Vall d' Hebron Research Institute, Barcelona
| | - Antonio Román
- Department of Pulmonology and Lung Transplant Unit, Hospital Universitari Vall d'Hebron, Barcelona.,Ciber Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Oscar Len
- Infectious Diseases Research Group, Vall d'Hebron Research Institute, Department of Infectious Diseases, Hospital Universitari Vall d'Hebron, Barcelona.,Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid
| | - Joan Gavaldà
- Infectious Diseases Research Group, Vall d'Hebron Research Institute, Department of Infectious Diseases, Hospital Universitari Vall d'Hebron, Barcelona.,Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid
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5
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Nguyen DK, Fleischman RJ, Friedlander S, Zangwill KM. Epidemiology of Admissions From the Emergency Department Among Febrile Infants Younger Than 90 Days in the United States, 2002 to 2012. Pediatr Emerg Care 2020; 36:e438-e446. [PMID: 28885390 DOI: 10.1097/pec.0000000000001262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND AND OBJECTIVES Febrile infants younger than 90 days are often subjected to invasive diagnostic evaluation and hospitalization to monitor for serious bacterial infection (SBI) despite recent changes in SBI risk and advances in diagnostics. Nationwide provider practices, over time, are unknown for this group. Our objective was to determine the likelihood of admission and associated complications of care for such infants, particularly those at lowest risk for SBI. METHODS This is a retrospective cohort study including multisite emergency department (ED) visits using administrative data from the Pediatric Emergency Care Applied Research Network Core Data Project. We examined uncomplicated febrile infants younger than 90 days seen in the ED from 2002 to 2012 who did not have an explicit infectious diagnosis, critical illness, or chronic condition. RESULTS We identified 38,224 infants, among whom, 11,600 (31%) were admitted. We observed a 3% increase in ED admission every year during the study period (P < 0.05). Age less than 30 days and black race were independent predictors of admission (P < 0.01). We identified 227 complications of care in the ED. Among those with a specified cause, 49% were attributed to antibiotic use or procedures related to the diagnosis and empiric treatment of suspected infection. CONCLUSIONS Despite the decreasing risk of SBI and diagnostic advances during the study period, the odds of hospital admission increased for febrile infants at low risk for sepsis. We also provide first data on therapeutic and diagnostic test-related adverse events in this setting. These data provide further justification for a consensus guideline on management of such infants.
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Affiliation(s)
| | | | - Scott Friedlander
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center
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6
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Nguyen DK, Friedlander S, Fleischman RJ, Zangwill KM. Length of Stay and Complications Associated With Febrile Infants <90 Days of Age Hospitalized in the United States, 2000-2012. Hosp Pediatr 2019; 8:746-752. [PMID: 30482790 DOI: 10.1542/hpeds.2018-0132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVES It is not known how changes in the epidemiology of serious bacterial infection (SBI) and greater availability of rapid viral diagnostic tests have impacted the hospital length of stay (LOS) and associated complications among young infants with suspected SBI. METHODS We used national administrative data from the Healthcare Cost and Utilization Project Kids' Inpatient Database and other state-specific data to identify febrile infants <90 days of age hospitalized in 2000, 2003, 2006, 2009, and 2012. We used multivariate analysis to determine LOS, risk factors for prolonged LOS, and complications of care among infants with isolated fever or viral respiratory disease, without concomitant serious infection. RESULTS We identified 44 875 infants. LOS for each clinical group did not change over time in a clinically significant way. Mean LOS was ≤2 days for approximately two-thirds of all infants and ≥4 days for 11% in each clinical group. Factors associated with longer LOS included age <31 days, critical clinical status, concomitant chronic disease, and the presence of complications (P < .05). We identified 289 (0.8%) infants with 351 complications of care, 18 (6%) of whom had >1. These infants had longer LOS (P < .001), and those with chronic disease and older age were at increased risk (P < .01). CONCLUSIONS Despite the changing epidemiology of SBI and increased availability of viral diagnostic testing, we did not detect a clinically significant change in LOS for febrile infants with suspected SBI. Complications associated with hospitalization of these infants was associated with increased LOS.
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Affiliation(s)
- Diana K Nguyen
- Division of Pediatric Infectious Diseases, Departments of Pediatrics and
| | - Scott Friedlander
- Los Angeles Biomedical Research Institute, Harbor-University of California, Los Angeles Medical Center, Torrance, California
| | - Ross J Fleischman
- Los Angeles Biomedical Research Institute, Harbor-University of California, Los Angeles Medical Center, Torrance, California.,Emergency Medicine, and
| | - Kenneth M Zangwill
- Division of Pediatric Infectious Diseases, Departments of Pediatrics and .,Los Angeles Biomedical Research Institute, Harbor-University of California, Los Angeles Medical Center, Torrance, California
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7
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Affiliation(s)
- Mark D Gonzalez
- Department of Pathology, Children's Healthcare of Atlanta, 1405 Clifton Road, Northeast, Atlanta, GA 30322, USA
| | - Erin McElvania
- Department of Pathology, NorthShore University Health System, 2650 Ridge Avenue, Evanston, IL 60201, USA.
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8
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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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9
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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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10
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Kim YG, Yun SG, Kim MY, Park K, Cho CH, Yoon SY, Nam MH, Lee CK, Cho YJ, Lim CS. Comparison between Saliva and Nasopharyngeal Swab Specimens for Detection of Respiratory Viruses by Multiplex Reverse Transcription-PCR. J Clin Microbiol 2017; 55:226-233. [PMID: 27807150 PMCID: PMC5228234 DOI: 10.1128/jcm.01704-16] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/28/2016] [Indexed: 12/24/2022] Open
Abstract
Nasopharyngeal swabs (NPSs) are being widely used as specimens for multiplex real-time reverse transcription (RT)-PCR for respiratory virus detection. However, it remains unclear whether NPS specimens are optimal for all viruses targeted by multiplex RT-PCR. In addition, the procedure to obtain NPS specimens causes coughing in most patients, which possibly increases the risk of nosocomial spread of viruses. In this study, paired NPS and saliva specimens were collected from 236 adult male patients with suspected acute respiratory illnesses. Specimens were tested for 16 respiratory viruses by multiplex real-time RT-PCR. Among the specimens collected from the 236 patients, at least 1 respiratory virus was detected in 183 NPS specimens (77.5%) and 180 saliva specimens (76.3%). The rates of detection of respiratory viruses were comparable for NPS and saliva specimens (P = 0.766). Nine virus species and 349 viruses were isolated, 256 from NPS specimens and 273 from saliva specimens (P = 0.1574). Adenovirus was detected more frequently in saliva samples (P < 0.0001), whereas influenza virus type A and human rhinovirus were detected more frequently in NPS specimens (P = 0.0001 and P = 0.0289, respectively). The possibility of false-positive adenovirus detection from saliva samples was excluded by direct sequencing. In conclusion, neither of the sampling methods was consistently more sensitive than the other. We suggest that these cost-effective methods for detecting respiratory viruses in mixed NPS-saliva specimens might be valuable for future studies.
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Affiliation(s)
- Young-Gon Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seung Gyu Yun
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Min Young Kim
- Armed Forces Medical Research Institute, Daejeon, Republic of Korea
| | - Kwisung Park
- Chungcheongnam-Do Health and Environment Research Institute, Hongseong, Republic of Korea
| | - Chi Hyun Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Young Yoon
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Myung Hyun Nam
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yun-Jung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea
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11
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Superiority of Digital Reverse Transcription-PCR (RT-PCR) over Real-Time RT-PCR for Quantitation of Highly Divergent Human Rhinoviruses. J Clin Microbiol 2016; 55:442-449. [PMID: 27881615 DOI: 10.1128/jcm.01970-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/16/2016] [Indexed: 01/31/2023] Open
Abstract
Human rhinoviruses (HRV) comprise 3 species representing more than 150 genotypes. As an important human respiratory pathogen, molecular detection is an indispensable tool for diagnosis and surveillance. However, the sequence diversity of HRV genotypes poses challenges for developing robust molecular methods that detect all genotypes with equal efficiencies. This study compares the accuracies of reverse transcription-quantitative PCR (RT-qPCR) and reverse transcription-digital PCR (RT-dPCR) for quantifying HRV RNA using genotype-specific primers and probes and a consensus primer/probe set targeting the 5' noncoding region of HRV. When using consensus primers and probes for the quantification of HRV, RT-dPCR outperformed RT-qPCR by consistently and accurately quantifying HRV RNAs across more genotype groups, despite the presence of up to 2 target-sequence mismatches within the primer or probe binding region. Because it does not rely on amplification efficiency, which can be affected by sequence mismatches in primer/probe binding regions, RT-dPCR may be the optimal molecular method for future HRV quantification studies and for quantitating other viruses with high sequence diversity.
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12
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Karlsson EA. Setting a trap for respiratory viruses. Virulence 2016; 7:740-1. [PMID: 27327437 DOI: 10.1080/21505594.2016.1204062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Erik A Karlsson
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA
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13
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Wang CH, Chang CP, Lee GB. Integrated microfluidic device using a single universal aptamer to detect multiple types of influenza viruses. Biosens Bioelectron 2016; 86:247-254. [PMID: 27376195 DOI: 10.1016/j.bios.2016.06.071] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
DNA aptamers that can bind specific molecular targets have great potential as probes for microbial diagnostic applications. However, aptamers may change their conformation under different operating conditions, thus affecting their affinity and specificity towards the target molecules. In this study, a new integrated microfluidic system was developed that exploited the predictable change in conformation of a single universal influenza aptamer exposed to differing ion concentrations in order to detect multiple types of the influenza virus. Furthermore, the fluorescent-labeled universal aptamer used in this system could distinguish and detect three different influenza viruses (influenza A H1N1, H3N2, and influenza B) at the same time in 20min and therefore has great potential for point-of-care applications requiring rapid diagnosis of influenza viruses.
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Affiliation(s)
- Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Peng Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan; Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, Taiwan; Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan.
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Essaidi-Laziosi M, Lyon M, Mamin A, Fernandes Rocha M, Kaiser L, Tapparel C. A new real-time RT-qPCR assay for the detection, subtyping and quantification of human respiratory syncytial viruses positive- and negative-sense RNAs. J Virol Methods 2016; 235:9-14. [PMID: 27180039 DOI: 10.1016/j.jviromet.2016.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/17/2022]
Abstract
Human respiratory syncytial virus (RSV) is a major health problem and the main cause of hospitalization due to bronchiolitis. RSV is divided into two antigenic subgroups, RSV-A and -B that co-circulate worldwide. Rapid and sensitive detection is desirable for proper patient handling while assessment of viral load may help to evaluate disease severity and progression. Finally RSV subtyping is needed to determine the prevalence and pathogenicity of each RSV subgroup, as well as their sensitivity to treatment. In this study, we took into account the most recent circulating RSV variants and designed two quantitative TaqMan one-step RT-PCR assays to detect and quantify both RSV subgroups separately. Standard dilutions of transcripts of positive and negative polarities were included in the assay validation to assess potential differences in sensitivity on negative-sense genomes and positive-sense RNAs. In addition, RSV detection in respiratory specimens of different types and sampled in different populations was compared to commercially available RSV diagnostic tools. Altogether, the RSV-A and -B assays revealed sensitive and quantitative over a wide range of viral loads, with a slight improved sensitivity of the RSV-B assay on positive sense transcripts, and allowed accurate RSV subtyping. We thus provide a useful tool for both RSV diagnostics and research.
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Affiliation(s)
- Manel Essaidi-Laziosi
- Faculty of Medicine of Geneva, Department of Microbiology and Molecular medicine, 1 rue Michel Servet, 1211 Geneva 4, Switzerland; Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Matthieu Lyon
- Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Aline Mamin
- Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Mélanie Fernandes Rocha
- Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Laurent Kaiser
- Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Caroline Tapparel
- Faculty of Medicine of Geneva, Department of Microbiology and Molecular medicine, 1 rue Michel Servet, 1211 Geneva 4, Switzerland; Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
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Abstract
OBJECTIVES To describe the strengths and limitations of the available influenza diagnostics, with a focus on rapid antigen detection assays and nucleic acid detection assays. METHODS A case-based presentation is used to illustrate the potential limitations of rapid antigen detection assays for influenza. RESULTS Influenza is a seasonal illness; estimates attribute influenza to approximately 200,000 hospitalizations and 41,000 deaths in the United States annually. Antigen detection assays for influenza are rapid and convenient, and thus are widely used in a variety of health care settings, even though the sensitivity of these assays may be suboptimal. The United States Food and Drug Administration has recently created new guidelines intended to improve the oversight and performance characteristics of influenza antigen detection assays. Molecular assays, although more costly and complex, are more sensitive and may be designed to simultaneously detect multiple respiratory pathogens within a single assay. CONCLUSIONS Diagnostic assays for influenza can vary greatly with regards to analytical performance characteristics, complexity, turnaround time and cost. This can have important patient care and infection prevention implications.
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Affiliation(s)
- Allison R McMullen
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO
| | - Neil W Anderson
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO
| | - Carey-Ann D Burnham
- From the Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO.
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16
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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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17
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García‐Arroyo L, Prim N, Martí N, Roig MC, Navarro F, Rabella N. Benefits and drawbacks of molecular techniques for diagnosis of viral respiratory infections. Experience with two multiplex PCR assays. J Med Virol 2016; 88:45-50. [PMID: 26100363 PMCID: PMC7166422 DOI: 10.1002/jmv.24298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 11/08/2022]
Abstract
Molecular techniques have represented a major step forward in the diagnosis of viral respiratory infections. They are considered highly sensitive and specific compared to conventional techniques. In this study two nucleic acid amplification tests (NAATs) were compared to conventional methods (immunofluorescence and viral culture). The aim of this work was to discuss the clinical interpretation of the results obtained by NAATs on the basis of the two-decade experience of our group and the literature. Eighty nasopharyngeal aspirates were collected from children under six years attended for acute respiratory illness at the pediatric emergency room of a third level Hospital. Both NAATs tested (Seeplex(®) and Clart(®)) showed an overall higher performance regarding sensitivity (76% and 90%, respectively). Compared to Seeplex(®), the Clart(®) system tripled the number of multiple detections (8 by Seeplex(®) vs. 25 by Clart(®)). In some specimens both NAATs detected different viruses. Given these discrepancies and the fact that detection of viral nucleic acids is not necessarily related to the current clinical syndrome, the interpretation of molecular results may not always be so straightforward. The pros and cons of NAATs should always be taken into account when giving a result.
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Affiliation(s)
| | - Núria Prim
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Neus Martí
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Maria Carme Roig
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Núria Rabella
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBarcelonaSpain
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Manuel O, López‐Medrano F, Kaiser L, Welte T, Carratalà J, Cordero E, Hirsch HH. Influenza and other respiratory virus infections in solid organ transplant recipients. Clin Microbiol Infect 2015; 20 Suppl 7:102-8. [PMID: 26451405 PMCID: PMC7129960 DOI: 10.1111/1469-0691.12595] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- O. Manuel
- Infectious Diseases Service and Transplantation CenterUniversity Hospital and University of LausanneLausanneSwitzerland
| | - F. López‐Medrano
- Unit of Infectious DiseasesHospital Universitario ‘12 de Octubre’Instituto de Investigación Hospital ‘12 de Octubre’ (i+12)School of MedicineUniversidad ComplutenseMadridSpain
| | - L. Kaiser
- Division of Infectious Diseases and Division of Laboratory MedicineUniversity of Geneva HospitalsGenevaSwitzerland
| | - T. Welte
- Department of Respiratory MedicineHannover Medical SchoolHannoverGermany
| | - J. Carratalà
- Department of Infectious DiseaseHospital Universitari de BellvitgeBarcelonaSpain
- Insitut d'Investigació Biomèdica de Bellvitge (IDIBELL)L'Hospitalet de LlobregatUniversity of BarcelonaBarcelonaSpain
| | - E. Cordero
- Hospital Universitario Virgen del RocíoInstituto de Biomedicina de SevillaSevilleSpain
| | - H. H. Hirsch
- Transplantation and Clinical VirologyDepartment of Biomedicine (Haus Petersplatz)University of BaselBaselSwitzerland
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Simões EAF, DeVincenzo JP, Boeckh M, Bont L, Crowe JE, Griffiths P, Hayden FG, Hodinka RL, Smyth RL, Spencer K, Thirstrup S, Walsh EE, Whitley RJ. Challenges and opportunities in developing respiratory syncytial virus therapeutics. J Infect Dis 2015; 211 Suppl 1:S1-S20. [PMID: 25713060 PMCID: PMC4345819 DOI: 10.1093/infdis/jiu828] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Two meetings, one sponsored by the Wellcome Trust in 2012 and the other by the Global Virology Foundation in 2013, assembled academic, public health and pharmaceutical industry experts to assess the challenges and opportunities for developing antivirals for the treatment of respiratory syncytial virus (RSV) infections. The practicalities of clinical trials and establishing reliable outcome measures in different target groups were discussed in the context of the regulatory pathways that could accelerate the translation of promising compounds into licensed agents. RSV drug development is hampered by the perceptions of a relatively small and fragmented market that may discourage major pharmaceutical company investment. Conversely, the public health need is far too large for RSV to be designated an orphan or neglected disease. Recent advances in understanding RSV epidemiology, improved point-of-care diagnostics, and identification of candidate antiviral drugs argue that the major obstacles to drug development can and will be overcome. Further progress will depend on studies of disease pathogenesis and knowledge provided from controlled clinical trials of these new therapeutic agents. The use of combinations of inhibitors that have different mechanisms of action may be necessary to increase antiviral potency and reduce the risk of resistance emergence.
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Affiliation(s)
- Eric A F Simões
- Department of Pediatrics, University of Colorado School of Medicine, and Colorado School of Public Health, Aurora
| | - John P DeVincenzo
- Department of Pediatrics, Division of Infectious Diseases, and Department of Microbiology, Immunology and Biochemistry, University of Tennessee School of Medicine Children's Foundation Research Institute at Le Bonheur Children's Hospital, Memphis
| | - Michael Boeckh
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle
| | - Louis Bont
- Department of Pediatrics and Laboratory of Translational Immunology, University Medical Center Utrecht, The Netherlands
| | - James E Crowe
- Department of Pediatrics and the Vanderbilt Vaccine Center, Vanderbilt University, Nashville, Tennessee
| | - Paul Griffiths
- Centre for Virology, University College London Medical School
| | - Frederick G Hayden
- Department of Medicine, University of Virginia School of Medicine, Charlottesville
| | - Richard L Hodinka
- Clinical Virology Laboratory, Children's Hospital of Philadelphia, Pennsylvania
| | - Rosalind L Smyth
- Department of Pediatrics, University College London Institute of Child Health
| | | | - Steffen Thirstrup
- NDA Advisory Services Ltd, Leatherhead, United Kingdom Department of Health Sciences, University of Copenhagen, Denmark
| | - Edward E Walsh
- Department of Medicine, Infectious Diseases Unit, Rochester General Hospital, New York
| | - Richard J Whitley
- Department of Pediatrics, Microbiology, Medicine and Neurosurgery, University of Alabama at Birmingham
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20
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Zhang H, Morrison S, Tang YW. Multiplex polymerase chain reaction tests for detection of pathogens associated with gastroenteritis. Clin Lab Med 2015; 35:461-86. [PMID: 26004652 DOI: 10.1016/j.cll.2015.02.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A wide range of enteric pathogens can cause infectious gastroenteritis. Conventional diagnostic algorithms are time-consuming and often lack sensitivity and specificity. Advances in molecular technology have provided new clinical diagnostic tools. Multiplex polymerase chain reaction (PCR)-based testing has been used in gastroenterology diagnostics in recent years. This article presents a review of recent laboratory-developed multiplex PCR tests and current commercial multiplex gastrointestinal pathogen tests. It focuses on two commercial syndromic multiplex tests: Luminex xTAG Gastrointestinal Pathogen Panel and BioFire FilmArray gastrointestinal test. Multiplex PCR tests have shown superior sensitivity to conventional methods for detection of most pathogens.
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Affiliation(s)
- Hongwei Zhang
- Luminex Corporation, 12212 Technology Boulevard, Austin, TX 78727, USA
| | - Scott Morrison
- Luminex Corporation, 12212 Technology Boulevard, Austin, TX 78727, USA
| | - Yi-Wei Tang
- Clinical Microbiology Service, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, Cornell University, 1275 York Avenue, S428, New York, NY 10065, USA.
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21
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Weidemaier K, Carrino J, Curry A, Connor JH, Liebmann-Vinson A. Advancing rapid point-of-care viral diagnostics to a clinical setting. Future Virol 2015. [DOI: 10.2217/fvl.14.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
ABSTRACT We discuss here critical factors in ensuring the success of a viral diagnostic at the point of care. Molecular and immunoassay approaches are reviewed with a focus on their ability to meet the infrastructure and workflow limitations in clinical settings in both the developed and developing world. In addition to being low cost, easy-to-use, accurate and adapted for the intended laboratory and healthcare environment, viral diagnostics must also provide information that appropriately directs clinical treatment decisions. We discuss the challenges and implications of linking diagnostics to clinical decision-making at the point of care using three examples: respiratory viruses in the developed world, differential fever diagnosis in the developing world and HPV detection in resource-limited settings.
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Affiliation(s)
- Kristin Weidemaier
- Diagnostic Sciences Department, BD Technologies, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - John Carrino
- BD Diagnostics, 10865 Road to the Cure, Suite 200, San Diego, CA 92121, USA
| | - Adam Curry
- Diagnostic Sciences Department, BD Technologies, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Andrea Liebmann-Vinson
- Diagnostic Sciences Department, BD Technologies, 21 Davis Drive, Research Triangle Park, NC 27709, USA
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