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Jeong S, Park MJ, Song W, Kim HS. Advances in laboratory assays for detecting human metapneumovirus. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:608. [PMID: 32566634 PMCID: PMC7290561 DOI: 10.21037/atm.2019.12.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human metapneumovirus (HMPV) is one of the major causes of acute respiratory tract infection (ARI) and shows high morbidity and mortality, particularly in children and immunocompromised patients. Various methods for detecting HMPV have been developed and applied in clinical laboratories. When reviewing the literature, we found that polymerase chain reaction (PCR)-based assays have been most frequently and consistently used to detect HMPV. The most commonly used method was multiplex reverse transcriptase-PCR (RT-PCR; 57.4%), followed by real-time RT-PCR (38.3%). Multiplex RT-PCR became the more popular method in 2011-2019 (69.7%), in contrast to 2001-2009 (28.6%). The advent of multiplex PCR in detecting broader viral pathogens in one run and coinfected viruses influenced the change in user preference. Further, newly developed microarray technologies and ionization mass spectrometry were introduced in 2011-2019. Viral culture (including shell vial assays) and fluorescent immunoassays (with or without culture) were once the mainstays. However, the percentage of studies employing culture and fluorescent immunoassays decreased from 21.4% in 2001-2010 to 15.2% in 2011-2019. Meanwhile, the use of PCR-based methods of HMPV detection increased from 78.6% in 2001-2010 to 84.8% in 2011-2019. The increase in PCR-based methods might have occurred because PCR methods demonstrated better diagnostic performance, shorter hands-on and run times, less hazards to laboratory personnel, and more reliable results than traditional methods. When using these assays, it is important to acquire a comprehensive understanding of the principles, advantages, disadvantages, and precautions for data interpretation. In the future, the combination of nanotechnology and advanced genetic platforms such as next-generation sequencing will benefit patients with HMPV infection by facilitating efficient therapeutic intervention. Analytical and clinical validation are required before using new techniques in clinical laboratories.
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Affiliation(s)
- Seri Jeong
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Min-Jeong Park
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, South Korea
| | - Hyon-Suk Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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Features of the Course of Metapneumoviral Infection in Adults. Fam Med 2019. [DOI: 10.30841/2307-5112.5-6.2019.193437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Zhang G, DeVos J, Medina-Moreno S, Wagar N, Diallo K, Beard RS, Zheng DP, Mwachari C, Riwa C, Jullu B, Wangari NE, Kibona MS, Ng'Ang'A LW, Raizes E, Yang C. Utilization of dried blood spot specimens can expedite nationwide surveillance of HIV drug resistance in resource-limited settings. PLoS One 2018; 13:e0203296. [PMID: 30192818 PMCID: PMC6128523 DOI: 10.1371/journal.pone.0203296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 08/14/2018] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Surveillance of HIV drug resistance (HIVDR) is crucial to ensuring the continued success of antiretroviral therapy (ART) programs. With the concern of reduced genotyping sensitivity of HIV on dried blood spots (DBS), DBS for HIVDR surveillance have been limited to ART-naïve populations. To investigate if DBS under certain conditions may also be a feasible sample type for HIVDR testing in ART patients, we piloted nationwide surveys for HIVDR among ART patients using DBS in two African countries with rapid scale-up of ART. METHODS EDTA-venous blood was collected to prepare DBS from adult and pediatric ART patients receiving treatment during the previous 12-36 months. DBS were stored at ambient temperature for two weeks and then at -80°C until shipment at ambient temperature to the WHO-designated Specialized HIVDR Laboratory at CDC in Atlanta. Viral load (VL) was determined using NucliSENS EasyQ® HIV-1 v2.0 kits; HIVDR genotyping was performed using the ATCC HIV-1 Drug Resistance Genotyping kits. RESULTS DBS were collected from 1,368 and 1,202 ART patients; 244 and 255 these specimens had VL ≥1,000 copies/mL in Kenya and Tanzania, respectively. The overall genotyping rate of those DBS with VL ≥1,000 copies/mL was 93.0% (95% CI: 89.1%-95.6%) in Kenya and 91.8% (87.7%-94.6%) in Tanzania. The turnaround times for the HIVDR surveys from the time of collecting DBS to completing laboratory testing were 6.5 months and 9.3 months for the Kenya and Tanzania surveys, respectively. CONCLUSIONS The study demonstrates a favorable outcome of using DBS for nationwide surveillance of HIVDR in ART patients. Our results confirm that DBS collected and stored at ambient temperature for two weeks, and shipped with routine courier services are a reliable sample type for large-scale surveillance of acquired HIVDR.
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Affiliation(s)
- Guoqing Zhang
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, CDC, Atlanta, GA, United States of America
| | - Joshua DeVos
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, CDC, Atlanta, GA, United States of America
| | - Sandra Medina-Moreno
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Nicholas Wagar
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, CDC, Atlanta, GA, United States of America
| | - Karidia Diallo
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, CDC, Atlanta, GA, United States of America
| | - R. Suzanne Beard
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, CDC, Atlanta, GA, United States of America
| | - Du-Ping Zheng
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, CDC, Atlanta, GA, United States of America
| | | | - Carolyn Riwa
- The Ministry of Health Tanzania, Dar es Salaam, Tanzania
| | - Boniface Jullu
- The Ministry of Health Tanzania, Dar es Salaam, Tanzania
| | | | | | | | - Elliot Raizes
- Adult Care and Treatment Branch, Division of Global HIV & TB, Center for Global Health, CDC, Atlanta, GA, United States of America
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV & TB, Center for Global Health, CDC, Atlanta, GA, United States of America
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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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Mo QH, Wang HB, Tan H, Wu BM, Feng ZL, Wang Q, Lin JC, Yang Z. Comparative detection of rotavirus RNA by conventional RT-PCR, TaqMan RT-PCR and real-time nucleic acid sequence-based amplification. J Virol Methods 2015; 213:1-4. [DOI: 10.1016/j.jviromet.2014.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/06/2014] [Accepted: 11/18/2014] [Indexed: 12/01/2022]
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Respiratory virus identification by interval polymerase chain reaction testing in the southeastern United States. Am J Infect Control 2013; 41:769-72. [PMID: 23507154 DOI: 10.1016/j.ajic.2012.11.018] [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: 03/08/2012] [Revised: 11/21/2012] [Accepted: 11/26/2012] [Indexed: 11/20/2022]
Abstract
BACKGROUND This study was designed to determine if testing the first ~40 nasal washings (interval) each month for 1 year, could be used as an epidemiologic tool for seasonality and prevalence of respiratory viruses such as human metapneumovirus in an adult and pediatric population in the southeastern United States. MATERIALS AND METHODS Results of interval polymerase chain reaction (PCR) testing of 469 specimens for 8 viruses were compared with our current procedures using PCR, culture, or respiratory synctial virus antigen for all 7435 specimens (routine). RESULTS One hundred thirty-six viruses out of 469 specimens (29.0%) and 1,495 viruses out of 7,435 specimens (20.1%) were identified by interval and routine testing, respectively. Seasonal detection varied among viruses and to some degree between interval and routine testing. A higher percent of positives and dual infections were detected by interval testing of pediatric specimens, likely due to the use of PCR for viruses commonly seen in this population. Human metapneumovirus was detected in both pediatric and adult specimens between January and August. CONCLUSIONS Interval testing can be used to provide a snapshot of prevalence and seasonality of respiratory viruses, although as currently designed they may not be sensitive enough to identify the beginning of a specific virus season. Exclusive use of interval PCR testing identified several dual infections, including human metapneumovirus, throughout most of the year in Florida. A rapid turnaround time to results translates into improved infection control and improved patient care.
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Shulman LM, Hindiyeh M, Muhsen K, Cohen D, Mendelson E, Sofer D. Evaluation of four different systems for extraction of RNA from stool suspensions using MS-2 coliphage as an exogenous control for RT-PCR inhibition. PLoS One 2012; 7:e39455. [PMID: 22815706 PMCID: PMC3397973 DOI: 10.1371/journal.pone.0039455] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 05/21/2012] [Indexed: 12/30/2022] Open
Abstract
Knowing when, and to what extent co-extracted inhibitors interfere with molecular RNA diagnostic assays is of utmost importance. The QIAamp Viral RNA Mini Kit (A); MagNA Pure LC2.0 Automatic extractor (B); KingFisher (C); and NucliSENS EasyMag (D) RNA extraction systems were evaluated for extraction efficiency and co-purification of inhibitors from stool suspensions. Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) of MS-2 coliphage spiked into each system's lysis buffer served as an external control for both. Cycle thresholds (Cts) of the MS2 were determined for RNA extracted from stool suspensions containing unknown (n = 93) or varying amounts of inhibitors (n = 92). Stool suspensions from the latter group were also used to determine whether MS-2 and enterovirus rRT-PCR inhibitions were correlated. Specifically 23 RNA extracts from stool suspensions were spiked with enterovirus RNA after extraction and 13 of these stool suspension were spiked with intact enterovirus before extraction. MS2 rRT-PCR inhibition varied for RNAs extracted by the different systems. Inhibition was noted in 12 (13.0%), 26 (28.3%), 7 (7.6%), and 7 (7.6%) of the first 93 RNA extracts, and 58 (63.0%), 55 (59.8%), 37 (40.2%) and 30 (32.6%) of the second 92 extracts for A, B, C, and D, respectively. Furthermore, enterovirus rRT-PCR inhibition correlated with MS2 rRT-PCR inhibition for added enterovirus RNA or virus particles. In conclusion, rRT-PCR for MS-2 RNA is a good predictor of inhibition of enterovirus RNA extracted from stool suspensions. EasyMag performed the best, however all four extraction methods were suitable provided that external controls identified problematic samples.
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Affiliation(s)
- Lester M Shulman
- Central Virology Laboratory, Public Health Services, Israel Ministry of Health, Sheba Medical Center, Tel Hashomer, Israel.
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Abstract
Recent technical advances have begun to realize the potential of molecular beacons to test for diverse infections in clinical diagnostic laboratories. These include the ability to test for, and quantify, multiple pathogens in the same clinical sample, and to detect antibiotic resistant strains within hours. The design principles of molecular beacons have also spawned a variety of allied technologies.
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Affiliation(s)
- Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey225 Warren Street, Newark, NJ 07103USA
| | - Fred Russell Kramer
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey225 Warren Street, Newark, NJ 07103USA
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, University of Medicine and Dentistry of New Jersey225 Warren Street, Newark, NJ 07103USA
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Abstract
It has been 10 years since human metapneumovirus (HMPV) was identified as a causative agent of respiratory illness in humans. Since then, numerous studies have contributed to a substantial body of knowledge on many aspects of HMPV. This review summarizes our current knowledge on HMPV, HMPV disease pathogenesis, and disease intervention strategies and identifies a number of areas with key questions to be addressed in the future.
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Ali SA, Gern JE, Hartert TV, Edwards KM, Griffin MR, Miller EK, Gebretsadik T, Pappas T, Lee WM, Williams JV. Real-world comparison of two molecular methods for detection of respiratory viruses. Virol J 2011; 8:332. [PMID: 21714915 PMCID: PMC3154182 DOI: 10.1186/1743-422x-8-332] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/29/2011] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Molecular polymerase chain reaction (PCR) based assays are increasingly used to diagnose viral respiratory infections and conduct epidemiology studies. Molecular assays have generally been evaluated by comparing them to conventional direct fluorescent antibody (DFA) or viral culture techniques, with few published direct comparisons between molecular methods or between institutions. We sought to perform a real-world comparison of two molecular respiratory viral diagnostic methods between two experienced respiratory virus research laboratories. METHODS We tested nasal and throat swab specimens obtained from 225 infants with respiratory illness for 11 common respiratory viruses using both a multiplex assay (Respiratory MultiCode-PLx Assay [RMA]) and individual real-time RT-PCR (RT-rtPCR). RESULTS Both assays detected viruses in more than 70% of specimens, but there was discordance. The RMA assay detected significantly more human metapneumovirus (HMPV) and respiratory syncytial virus (RSV), while RT-rtPCR detected significantly more influenza A. We speculated that primer differences accounted for these discrepancies and redesigned the primers and probes for influenza A in the RMA assay, and for HMPV and RSV in the RT-rtPCR assay. The tests were then repeated and again compared. The new primers led to improved detection of HMPV and RSV by RT-rtPCR assay, but the RMA assay remained similar in terms of influenza detection. CONCLUSIONS Given the absence of a gold standard, clinical and research laboratories should regularly correlate the results of molecular assays with other PCR based assays, other laboratories, and with standard virologic methods to ensure consistency and accuracy.
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Affiliation(s)
- S Asad Ali
- Department of Pediatrics, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI, 53705, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI, 53705, USA
| | - Tina V Hartert
- Department of Medicine, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - Marie R Griffin
- Department of Medicine, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
- Department of Preventive Medicine, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - E Kathryn Miller
- Department of Pediatrics, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - Tebeb Gebretsadik
- Department of Medicine, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - Tressa Pappas
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI, 53705, USA
| | - Wai- ming Lee
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI, 53705, USA
| | - John V Williams
- Department of Pediatrics, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
- Department of Microbiology and Immunology, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN, 37232, USA
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Molecular Detection of Respiratory Viruses. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kehl SC, Kumar S. Utilization of nucleic acid amplification assays for the detection of respiratory viruses. Clin Lab Med 2010; 29:661-71. [PMID: 19892227 PMCID: PMC7131773 DOI: 10.1016/j.cll.2009.07.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Sue C Kehl
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226-0509, USA.
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Beneri C, Ginocchio CC, Manji R, Sood S. Comparison of clinical features of pediatric respiratory syncytial virus and human metapneumovirus infections. Infect Control Hosp Epidemiol 2010; 30:1240-1. [PMID: 19888849 DOI: 10.1086/648665] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Evaluation of the combination of the NucliSENS easyMAG® and the EasyQ® applications for the detection of Mycoplasma pneumoniae and Chlamydia pneumoniae in respiratory tract specimens. Eur J Clin Microbiol Infect Dis 2009; 29:187-90. [DOI: 10.1007/s10096-009-0839-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 11/01/2009] [Indexed: 10/20/2022]
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Pignanelli S, Shurdhi A, Delucca F, Donati M. Simultaneous use of direct and indirect diagnostic techniques in atypical respiratory infections from Chlamydophila pneumoniae and Mycoplasma pneumoniae. J Clin Lab Anal 2009; 23:206-9. [PMID: 19623657 DOI: 10.1002/jcla.20332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In 2008, 50 samples (BAL), coming from hospital patients, with acute respiratory symptoms have been investigated using two real-time PCR methods: one assay for the single detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae DNA and one commercially available real-time duplex PCR assay for the detection of C. pneumoniae and M. pneumoniae DNA. Both techniques used here showed compliant results, with 100% concordance for detection of C. pneumoniae and 98% for detection of M. pneumoniae. The positive results obtained agreed with the clinical suspicion of such infections in some cases and with the presence of IgM specific for C. pneumoniae and M. pneumoniae in all cases of acute infection.
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Affiliation(s)
- S Pignanelli
- DESOS--Section of Microbiology, Policlinico S. Orsola, University of Bologna, 40138, Bologna, Italy.
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