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Utami D, Meale SJ, Young AJ. Bacterial Leaf Spot Susceptibility Screening of Chili Pepper Cultivars Using qPCR Determination of Xanthomonas euvesicatoria pv. euvesicatoria Titers. Phytopathology 2024; 114:681-689. [PMID: 38079287 DOI: 10.1094/phyto-12-22-0479-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Bacterial leaf spot is a serious disease of chili pepper (Capsicum spp.) caused by Xanthomonas euvesicatoria pv. euvesicatoria. Conventional resistance screening is time and resource intensive. It was considered that a quick and simple determination of cultivar susceptibility could be achieved through estimating bacterial titers of inoculated plants. A SYBR quantitative polymerase chain reaction (qPCR)-based assay was compared with conventional PCR, then used to detect and enumerate pathogen titers in serial dilutions and DNA extracted from infected plant leaves. The qPCR detection limit was approximately 1 CFU µl-1, 10 times more sensitive than conventional PCR. A linear correlation (R2 = 0.994) was obtained from the standard curve comparing plate-truthed serial dilutions of the pathogen with the qPCR cycle threshold. Six strains were used to inoculate cultivars Hugo and Warlock. One strain, X. euvesicatoria pv. euvesicatoria BRIP62403, was consistently the most virulent based on visual symptoms and pathogen titers in planta inferred by qPCR performed on DNA extracted from infected leaves 2 and 6 weeks postinoculation. Visual observations 6 weeks after inoculation were highly correlated (R2 = 0.8254) to pathogen titers. The qPCR method was used to categorize 20 chili pepper cultivars 2 weeks after inoculation. A high positive correlation (R2 = 0.6826) was observed between visual scoring and pathogen titers from 20 chili pepper cultivars, facilitating categorization of susceptible, intermediate, and resistant cultivars. The qPCR approach developed here facilitates susceptibility screening of chili pepper cultivars at an early stage of selection and could be readily adapted to a range of other pathosystems.
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Affiliation(s)
- Desi Utami
- School of Agriculture and Food Sustainability, Faculty of Science, The University of Queensland, Queensland, 4343, Australia
- Department of Agricultural Microbiology, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Sarah J Meale
- School of Agriculture and Food Sustainability, Faculty of Science, The University of Queensland, Queensland, 4343, Australia
| | - Anthony J Young
- School of Agriculture and Food Sustainability, Faculty of Science, The University of Queensland, Queensland, 4343, Australia
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2
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Jin T, Kim JK, Byun HS, Choi HS, Cha B, Kwak HR, Kim M. Occurrence and Multiplex PCR Detection of Citrus Yellow Vein Clearing Virus in Korea. Plant Pathol J 2024; 40:125-138. [PMID: 38606443 PMCID: PMC11016552 DOI: 10.5423/ppj.oa.09.2023.0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/20/2024] [Accepted: 02/07/2024] [Indexed: 04/13/2024]
Abstract
Citrus yellow vein clearing virus (CYVCV) is a member of the Alphaflexiviridae family that causes yellow vein clearing symptoms on citrus leaves. A total of 118 leaf samples from nine regions of six provinces in Korea were collected from various citrus species in 2020 and 2021. Viral diagnosis using next-generation sequencing and reverse transcription polymerase chain reaction (RT-PCR) identified four viruses: citrus tristeza virus, citrus leaf blotch virus, citrus vein enation virus, and CYVCV. A CYVCV incidence of 9.3% was observed in six host plants, including calamansi, kumquat, Persian lime, and Eureka lemon. Among the citrus infected by CYVCV, only three samples showed a single infection; the other showed a mixed infection with other viruses. Eureka lemon and Persian lime exhibited yellow vein clearing, leaf distortion, and water-soak symptom underside of the leaves, while the other hosts showed only yellowing symptoms on the leaves. The complete genome sequences were obtained from five CYVCV isolates. Comparison of the isolates reported from the different geographical regions and hosts revealed the high sequence identity (95.2% to 98.8%). Phylogenetic analysis indicated that all the five isolates from Korea were clustered into same clade but were not distinctly apart from isolates from China, Pakistan, India, and Türkiye. To develop an efficient diagnosis system for the four viruses, a simultaneous detection method was constructed using multiplex RT-PCR. Sensitivity evaluation, simplex RT-PCR, and stability testing were conducted to verify the multiplex RT-PCR system developed in this study. This information will be useful for developing effective disease management strategies for citrus growers in Korea.
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Affiliation(s)
- Taemin Jin
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Ji-Kwang Kim
- Chungcheongnam-do Agricultural Research and Extension Services, Buyeo 33168, Korea
| | - Hee-Seong Byun
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365, Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365, Korea
| | - Byeongjin Cha
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365, Korea
| | - Mikyeong Kim
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Korea
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He X, Wang S, Ma C, Xu GR, Ma J, Xie H, Zhu W, Liu H, Wang L, Wang Y. Utilizing Electrochemical Biosensors as an Innovative Platform for the Rapid and On-Site Detection of Animal Viruses. Animals (Basel) 2023; 13:3141. [PMID: 37835747 PMCID: PMC10571726 DOI: 10.3390/ani13193141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/19/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Animal viruses are a significant threat to animal health and are easily spread across the globe with the rise of globalization. The limitations in diagnosing and treating animal virus infections have made the transmission of diseases and animal deaths unpredictable. Therefore, early diagnosis of animal virus infections is crucial to prevent the spread of diseases and reduce economic losses. To address the need for rapid diagnosis, electrochemical sensors have emerged as promising tools. Electrochemical methods present numerous benefits, including heightened sensitivity and selectivity, affordability, ease of use, portability, and rapid analysis, making them suitable for real-time virus detection. This paper focuses on the construction of electrochemical biosensors, as well as promising biosensor models, and expounds its advantages in virus detection, which is a promising research direction.
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Affiliation(s)
- Xun He
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Shan Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Caoyuan Ma
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Guang-Ri Xu
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Jinyou Ma
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Hongbing Xie
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Wei Zhu
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Hongyang Liu
- Shuangliao Animal Disease Control Center, Siping 136400, China;
| | - Lei Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450046, China
| | - Yimin Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450046, China
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Beran P, Stehlikova D, Cohen SP, Rost M, Beranova K, Curn V. Utilization of a New Hundred-Genomes Pipeline to Design a Rapid Duplex LAMP Detection Assay for Xanthomonas euvesicatoria and X. vesicatoria in Tomato. Plant Dis 2023:PDIS05221098RE. [PMID: 36428255 DOI: 10.1094/pdis-05-22-1098-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Xanthomonas euvesicatoria and X. vesicatoria are two economically important causal agents of bacterial spot (BS) of tomato and pepper. Management of BS in the field requires rapid and accurate detection. Therefore, this work aimed to develop a pipeline to design a simple, fast, and reliable assay for the detection of X. euvesicatoria and X. vesicatoria by loop-mediated isothermal amplification. In total, 109 publicly available whole genomic sequences of 24 different species of bacterial pathogens were used to design primers that would amplify the DNA of the two target species. Laboratory testing of the assay was performed on pure bacterial cultures and artificially infected plants, and amplification was conducted with both a sophisticated laboratory instrument and a simple mobile platform. The testing of the assay confirmed its specificity with a sensitivity reaching 1 pg µl-1 for both pathogens with an assay duration of 40 min on a mobile detection platform. Our diagnostics development pipeline enables the easy and fast design of a reliable detection assay in the genomics age. By validating the pipeline with X. euvesicatoria and X. vesicatoria pathogens, we have simultaneously developed an assay with high specificity, sensitivity, and speed, which will allow it to be deployed, contributing to successful management of BS.
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Affiliation(s)
- Pavel Beran
- University of South Bohemia in Ceske Budejovice, Faculty of Agriculture and Technology, Biotechnological Centre, 37005 České Budějovice, Czech Republic
| | - Dagmar Stehlikova
- University of South Bohemia in Ceske Budejovice, Faculty of Agriculture and Technology, Biotechnological Centre, 37005 České Budějovice, Czech Republic
| | - Stephen P Cohen
- United States Department of Agriculture-Agricultural Research Service, Sustainable Perennial Crops Laboratory, Beltsville, MD 20705, U.S.A
| | - Michael Rost
- University of South Bohemia in Ceske Budejovice, Faculty of Agriculture and Technology, Biotechnological Centre, 37005 České Budějovice, Czech Republic
| | - Kristina Beranova
- University of South Bohemia in Ceske Budejovice, Faculty of Agriculture and Technology, Biotechnological Centre, 37005 České Budějovice, Czech Republic
| | - Vladislav Curn
- University of South Bohemia in Ceske Budejovice, Faculty of Agriculture and Technology, Biotechnological Centre, 37005 České Budějovice, Czech Republic
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Kaur H, Gelain J, Marin MV, Peres NA, Schnabel G. Development of a Molecular Tool for Identification of a New Neopestalotiopsis sp. Associated with Disease Outbreaks on Strawberry. Plant Dis 2023:PDIS09222117RE. [PMID: 36383989 DOI: 10.1094/pdis-09-22-2117-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A new Neopestalotiopsis sp. was recently reported causing outbreaks of leaf spot and fruit rot on strawberry in Florida, Georgia, and South Carolina. In contrast to other Pestalotiopsis pathogens, the new species appears more aggressive and destructive on strawberry. Current chemical options for management are disease suppressive at best, and affected growers have been experiencing major yield losses. In this study, we developed a molecular method based on polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) for identification of the new Neopestalotiopsis sp. from strawberry. Isolates of the new Neopestalotiopsis sp. collected in Florida; isolates of N. rosae, N. honoluluana, N. ellipsopora, N. saprophytica, N. samarangensis, and P. rhododendri; and isolates from South Carolina suspected to be the new Neopestalotiopsis sp. were included in this study. This method is based on PCR amplification of a β-tubulin gene fragment using a previously published set of primers (Bt2a and Bt2b), followed by use of the restriction enzyme BsaWI. The enzyme cuts the PCR product from the new Neopestalotiopsis sp. twice, yielding fragments of 290 base pairs (bp) and 130 and 20 bp in size, whereas fragments from other species are only cut once, yielding fragments of 420 and 20 bp. This method will aid research labs and diagnostic clinics in the accurate and fast identification of the aggressive Neopestalotiopsis sp. variant from strawberry.
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Affiliation(s)
- Harleen Kaur
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC
| | - Jhulia Gelain
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC
| | - Marcus Vinicius Marin
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL
| | - Natalia A Peres
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL
| | - Guido Schnabel
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC
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Uhlik M, Pointing D, Iyer S, Ausec L, Štajdohar M, Cvitkovič R, Žganec M, Culm K, Santos VC, Pytowski B, Malafa M, Liu H, Krieg AM, Lee J, Rosengarten R, Benjamin L. Xerna™ TME Panel is a machine learning-based transcriptomic biomarker designed to predict therapeutic response in multiple cancers. Front Oncol 2023; 13:1158345. [PMID: 37251949 PMCID: PMC10213262 DOI: 10.3389/fonc.2023.1158345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Most predictive biomarkers approved for clinical use measure single analytes such as genetic alteration or protein overexpression. We developed and validated a novel biomarker with the aim of achieving broad clinical utility. The Xerna™ TME Panel is a pan-tumor, RNA expression-based classifier, designed to predict response to multiple tumor microenvironment (TME)-targeted therapies, including immunotherapies and anti-angiogenic agents. Methods The Panel algorithm is an artificial neural network (ANN) trained with an input signature of 124 genes that was optimized across various solid tumors. From the 298-patient training data, the model learned to discriminate four TME subtypes: Angiogenic (A), Immune Active (IA), Immune Desert (ID), and Immune Suppressed (IS). The final classifier was evaluated in four independent clinical cohorts to test whether TME subtype could predict response to anti-angiogenic agents and immunotherapies across gastric, ovarian, and melanoma datasets. Results The TME subtypes represent stromal phenotypes defined by angiogenesis and immune biological axes. The model yields clear boundaries between biomarker-positive and -negative and showed 1.6-to-7-fold enrichment of clinical benefit for multiple therapeutic hypotheses. The Panel performed better across all criteria compared to a null model for gastric and ovarian anti-angiogenic datasets. It also outperformed PD-L1 combined positive score (>1) in accuracy, specificity, and positive predictive value (PPV), and microsatellite-instability high (MSI-H) in sensitivity and negative predictive value (NPV) for the gastric immunotherapy cohort. Discussion The TME Panel's strong performance on diverse datasets suggests it may be amenable for use as a clinical diagnostic for varied cancer types and therapeutic modalities.
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Affiliation(s)
- Mark Uhlik
- OncXerna Therapeutics, Inc., Waltham, MA, United States
| | | | - Seema Iyer
- OncXerna Therapeutics, Inc., Waltham, MA, United States
| | - Luka Ausec
- Genialis, Inc., Boston, MA, United States
| | | | | | | | - Kerry Culm
- OncXerna Therapeutics, Inc., Waltham, MA, United States
| | | | | | - Mokenge Malafa
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Hong Liu
- Checkmate Pharmaceuticals, Inc., Cambridge, MA, United States
| | - Arthur M. Krieg
- Checkmate Pharmaceuticals, Inc., Cambridge, MA, United States
| | - Jeeyun Lee
- Department of Hematology and Oncology, Samsung Medical Center, Seoul, Republic of Korea
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Brown VR, Miller RS, Bowden CF, Smyser TJ, Ledesma NA, Hartwig A, Gordy P, Anderson AM, Porter SM, Alexander K, Gouker Z, Gidlewski T, Bowen RA, Bosco-Lauth AM. Disease Progression and Serological Assay Performance in Heritage Breed Pigs following Brucella suis Experimental Challenge as a Model for Naturally Infected Feral Swine. Pathogens 2023; 12:pathogens12050638. [PMID: 37242308 DOI: 10.3390/pathogens12050638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Invasive feral swine (Sus scrofa) are one of the most important wildlife species for disease surveillance in the United States, serving as a reservoir for various diseases of concern for the health of humans and domestic animals. Brucella suis, the causative agent of swine brucellosis, is one such pathogen carried and transmitted by feral swine. Serology assays are the preferred field diagnostic for B. suis infection, as whole blood can be readily collected and antibodies are highly stable. However, serological assays frequently have lower sensitivity and specificity, and few studies have validated serological assays for B. suis in feral swine. We conducted an experimental infection of Ossabaw Island Hogs (a breed re-domesticated from feral animals) as a disease-free proxy for feral swine to (1) improve understanding of bacterial dissemination and antibody response following B. suis infection and (2) evaluate potential changes in the performance of serological diagnostic assays over the course of infection. Animals were inoculated with B. suis and serially euthanized across a 16-week period, with samples collected at the time of euthanasia. The 8% card agglutination test performed best, whereas the fluorescence polarization assay demonstrated no capacity to differentiate true positive from true negative animals. From a disease surveillance perspective, using the 8% card agglutination test in parallel with either the buffered acidified plate antigen test or the Brucella abortus/suis complement fixation test provided the best performance with the highest probability of a positive assay result. Application of these combinations of diagnostic assays for B. suis surveillance among feral swine would improve understanding of spillover risks at the national level.
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Affiliation(s)
- Vienna R Brown
- National Feral Swine Damage Management Program, USDA APHIS Wildlife Services, Fort Collins, CO 80521, USA
| | - Ryan S Miller
- Centers for Epidemiology and Animal Health, USDA APHIS Veterinary Services, Fort Collins, CO 80521, USA
| | - Courtney F Bowden
- National Wildlife Research Center, USDA APHIS Wildlife Services, Fort Collins, CO 80521, USA
| | - Timothy J Smyser
- National Wildlife Research Center, USDA APHIS Wildlife Services, Fort Collins, CO 80521, USA
| | - Nicholas A Ledesma
- National Veterinary Services Laboratories, USDA APHIS Veterinary Services, Ames, IA 50010, USA
| | - Airn Hartwig
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Paul Gordy
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Aaron M Anderson
- National Wildlife Research Center, USDA APHIS Wildlife Services, Fort Collins, CO 80521, USA
| | - Stephanie M Porter
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Kate Alexander
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Zane Gouker
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Thomas Gidlewski
- National Wildlife Disease Program, USDA APHIS Wildlife Services, Fort Collins, CO 80521, USA
| | - Richard A Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Angela M Bosco-Lauth
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80521, USA
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Brown J, Poonsuk K, Cheng TY, Rademacher C, Kalkwarf E, Tian L, McKeen LA, Wang C, Gimenez-Lirola L, Baum D, Karriker LA. Comparison of Two Diagnostic Assays for the Detection of Serum Neutralizing Antibody to Porcine Epidemic Diarrhea Virus. Animals (Basel) 2023; 13:ani13040757. [PMID: 36830544 PMCID: PMC9951927 DOI: 10.3390/ani13040757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/22/2023] Open
Abstract
Lactogenic immunity is important for the protection of piglets against many pathogens including porcine epidemic diarrhea virus. Circulating neutralizing antibodies levels in sow sera may help determine if a detectable immune response could confer protection to piglets. Neutralizing antibodies can be detected through various diagnostic assays. This study evaluated the diagnostic characteristics of two neutralizing antibody assays for porcine epidemic diarrhea virus neutralizing antibodies in serum of challenged gilts. Four treatment groups, control, non-vaccinated, vaccinated prior to challenge, and vaccinated following challenge, were comprised of 20 gilts. Serum sample were collected from each gilt prior to and following challenge with porcine epidemic diarrhea virus. Samples were evaluated for the presence of neutralizing antibodies via a fluorescent focus neutralization assay and a high-throughput neutralization assay. Diagnostic sensitivity and specificity for the fluorescent focus neutralization and high-throughput neutralization assays for this study were optimized at a cutoff of a dilution of 80 and 80% fluorescent reduction respectively and demonstrated moderate agreement based off the kappa statistic. The focus fluorescent neutralization and high-throughput neutralization assays can be used to monitor the status of neutralizing antibodies within animals or a population of animals. The high-throughput assay has advantages over the focus fluorescent assay in that it has a higher specificity at the indicated cut-off and the nature of the results allows for more discrimination between individual results.
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Affiliation(s)
- Justin Brown
- Swine Medicine Education Center, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
- Correspondence: ; Tel.: +1-515-245-4508
| | - Korakrit Poonsuk
- Nebraska Veterinary Diagnostic Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Ting-Yu Cheng
- Veterinary Preventive Medicine, College of Veterinary Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Chris Rademacher
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Erin Kalkwarf
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Liying Tian
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Lauren A. McKeen
- Department of Statistics, Iowa State University, 1121 Snedecor Hall, Ames, IA 50011, USA
| | - Chong Wang
- Department of Statistics, Iowa State University, 1121 Snedecor Hall, Ames, IA 50011, USA
| | - Luis Gimenez-Lirola
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - David Baum
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Locke A. Karriker
- Swine Medicine Education Center, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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Sakharkar A, Yang J. Designing a Novel Monitoring Approach for the Effects of Space Travel on Astronauts' Health. Life (Basel) 2023; 13:life13020576. [PMID: 36836933 PMCID: PMC9964234 DOI: 10.3390/life13020576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Space exploration and extraterrestrial civilization have fascinated humankind since the earliest days of human history. It was only in the last century that humankind finally began taking significant steps towards these goals by sending astronauts into space, landing on the moon, and building the International Space Station. However, space voyage is very challenging and dangerous, and astronauts are under constant space radiation and microgravity. It has been shown that astronauts are at a high risk of developing a broad range of diseases/disorders. Thus, it is critical to develop a rapid and effective assay to monitor astronauts' health in space. In this study, gene expression and correlation patterns were analyzed for 10 astronauts (8 male and 2 female) using the publicly available microarray dataset E-GEOD-74708. We identified 218 differentially expressed genes between In-flight and Pre-flight and noticed that space travel decreased genome regulation and gene correlations across the entire genome, as well as individual signaling pathways. Furthermore, we systematically developed a shortlist of 32 genes that could be used to monitor astronauts' health during space travel. Further studies, including microgravity experiments, are warranted to optimize and validate the proposed assay.
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Affiliation(s)
- Anurag Sakharkar
- College of Arts and Science, University of Saskatchewan, 9 Campus Drive, Saskatoon, SK S7N 5A5, Canada
| | - Jian Yang
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
- Correspondence:
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Čelešnik H, Potočnik U. Blood-Based mRNA Tests as Emerging Diagnostic Tools for Personalised Medicine in Breast Cancer. Cancers (Basel) 2023; 15. [PMID: 36831426 DOI: 10.3390/cancers15041087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Molecular diagnostic tests help clinicians understand the underlying biological mechanisms of their patients' breast cancer (BC) and facilitate clinical management. Several tissue-based mRNA tests are used routinely in clinical practice, particularly for assessing the BC recurrence risk, which can guide treatment decisions. However, blood-based mRNA assays have only recently started to emerge. This review explores the commercially available blood mRNA diagnostic assays for BC. These tests enable differentiation of BC from non-BC subjects (Syantra DX, BCtect), detection of small tumours <10 mm (early BC detection) (Syantra DX), detection of different cancers (including BC) from a single blood sample (multi-cancer blood test Aristotle), detection of BC in premenopausal and postmenopausal women and those with high breast density (Syantra DX), and improvement of diagnostic outcomes of DNA testing (variant interpretation) (+RNAinsight). The review also evaluates ongoing transcriptomic research on exciting possibilities for future assays, including blood transcriptome analyses aimed at differentiating lymph node positive and negative BC, distinguishing BC and benign breast disease, detecting ductal carcinoma in situ, and improving early detection further (expression changes can be detected in blood up to eight years before diagnosing BC using conventional approaches, while future metastatic and non-metastatic BC can be distinguished two years before BC diagnosis).
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Bodiybadu K, Danielewski J, Plummer E, Bradshaw CS, Machalek DA, Garland SM, Vodstrcil LA, Murray GL. Comparison of Seegene AnyPlexTM II STI-7e with standard-of-care diagnostic methods for the detection of Mycoplasma genitalium, Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis. Lett Appl Microbiol 2023; 76:6887826. [PMID: 36688743 DOI: 10.1093/lambio/ovac002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/28/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023]
Abstract
The AnyPlexTM II STI-7e panel assay (Seegene) detects seven sexually transmitted organisms (Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, M. hominis, Ureaplasma urealyticum, U. parvum, and Trichomonas vaginalis). This study compared the performance of AnyPlexTM II STI-7e with standard-of-care diagnostic methods. Samples (cervical or vaginal swabs, or urine) from 1330 women were tested on standard-of-care assays; 83/1318 (6.3%) tested positive for M. genitalium (ResistancePlus® MG), 99/1317 (7.5%) positive for C. trachomatis and 11/1316 (0.8%) positive for N. gonorrhoeae (Hologic® Aptima Combo 2®), and 6/689 (0.9%) positive for T. vaginalis (wet mount microscopy). AnyPlexTM II STI-7e had good agreement for the detection of M. genitalium [Cohen's kappa of 0.80, 95% confidence intervals (CI) 0.74-0.87] and C. trachomatis (kappa of 0.87, 95% CI 0.82-0.92), with positive and negative % agreement >96% for both infections. There was lower agreement for the detection of N. gonorrhoeae (kappa of 0.37, 95%CI 0.19-0.55) and T. vaginalis (kappa of 0.521, 95%CI 0.25-0.80). In summary, the test performed well in this comparison for M. genitalium and C. trachomatis detection, but results were less conclusive for N. gonorrhoeae and T. vaginalis due to low prevalence in the population.
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Affiliation(s)
- Kaveesha Bodiybadu
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, VIC 3052, Australia.,Murdoch Children's Research Institute, Parkville, VIC 3052, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jennifer Danielewski
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, VIC 3052, Australia.,Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Erica Plummer
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, VIC 3052, Australia.,Murdoch Children's Research Institute, Parkville, VIC 3052, Australia.,Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC 3053, Australia.,Central Clinical School, Monash University, Melbourne, VIC 3800, Australia
| | - Catriona S Bradshaw
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC 3053, Australia.,Central Clinical School, Monash University, Melbourne, VIC 3800, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Dorothy A Machalek
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, VIC 3052, Australia.,The Kirby Institute, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | - Suzanne M Garland
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, VIC 3052, Australia.,Murdoch Children's Research Institute, Parkville, VIC 3052, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Lenka A Vodstrcil
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC 3053, Australia.,Central Clinical School, Monash University, Melbourne, VIC 3800, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gerald L Murray
- Centre for Women's Infectious Diseases, The Royal Women's Hospital, Parkville, VIC 3052, Australia.,Murdoch Children's Research Institute, Parkville, VIC 3052, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC 3010, Australia
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12
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Yip CCY, Sridhar S, Chan WM, Ip JD, Chu AWH, Leung KH, Cheng VCC, Yuen KY, To KKW. Development and Validation of a Novel COVID-19 nsp8 One-Tube RT-LAMP-CRISPR Assay for SARS-CoV-2 Diagnosis. Microbiol Spectr 2022; 10:e0196222. [PMID: 36445095 PMCID: PMC9769742 DOI: 10.1128/spectrum.01962-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
Accurate and simple diagnostic tests for coronavirus disease 2019 (COVID-19) are essential components of the pandemic response. In this study, we evaluated a one-tube reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay coupled with clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-mediated endpoint detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in clinical samples. RT-LAMP-CRISPR is fast and affordable, does not require bulky thermocyclers, and minimizes carryover contamination risk. Results can be read either visually or with a fluorometer. RT-LAMP-CRISPR assays using primers targeting a highly expressed nsp8 gene and previously described nucleocapsid (N) gene primers were designed. The analytical characteristics and diagnostic performance of RT-LAMP-CRISPR assays were compared to those of a commercial real-time RT-PCR E gene assay. The limits of detection (LODs) of the nsp8 and N RT-LAMP-CRISPR assays were 750 and 2,000 copies/mL, which were higher than that of the commercial real-time RT-PCR assay (31.3 copies/mL). Despite the higher LOD, RT-LAMP-CRISPR assays showed diagnostic sensitivity and specificity of 98.6% and 100%, respectively, equivalent to those of the real-time RT-PCR assay (P = 0.5). The median fluorescence reading from the nsp8 assay (378.3 raw fluorescence unit [RFU] [range, 215.6 to 592.6]) was significantly higher than that of the N gene assay (342.0 RFU [range, 143.0 to 576.6]) (P < 0.0001). In conclusion, we demonstrate that RT-LAMP-CRISPR assays using primers rationally designed from highly expressed gene targets are highly sensitive, specific, and easy to perform. Such assays are a valuable asset in resource-limited settings. IMPORTANCE Accurate tests for the diagnosis of SARS-CoV-2, the virus causing coronavirus disease 2019 (COVID-19), are important for timely treatment and infection control decisions. Conventional tests such as real-time reverse transcription-PCR (RT-PCR) require specialized equipment and are expensive. On the other hand, rapid antigen tests suffer from a lack of sensitivity. In this study, we describe a novel assay format for the diagnosis of COVID-19 that is based on principles of loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas chemistry. A major advantage of this assay format is that it does not require expensive equipment to perform, and results can be read visually. This method proved to be fast, easy to perform, and inexpensive. The test compared well against an RT-PCR assay in terms of the ability to detect SARS-CoV-2 RNA in clinical samples. No false-positive test results were observed. The new assay format is ideal for SARS-CoV-2 diagnosis in resource-limited settings.
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Grants
- Health@InnoHK, Innovation and Technology Commission of Hong Kong
- Donations from Richard Yu and Carol Yu, the Shaw Foundation Hong Kong, Michael Seak-Kan Tong, The Hui Ming, Chan Yin Chuen Memorial Charitable Foundation
- Donations from Marina Man-Wai Lee, the Jessie & George Ho Charitable Foundation, Kai Chong Tong, Tse Kam Ming Laurence, Foo Oi Foundation Limited, Betty Hing-Chu Lee, and Ping Cham So
- Hui Hoy and Chow Sin Lan Charity Fund (許海周倩蘭慈善基金有限公司)
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Affiliation(s)
- Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Sha Tin, Hong Kong Special Administrative Region, China
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13
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Kao YF, Spainhour R, Cowan SR, Nafe L, Birkenheuer A, Reichard MV, Miller CA. A Serodiagnostic IgM ELISA to Detect Acute Cytauxzoonosis. Pathogens 2022; 11:pathogens11101183. [PMID: 36297239 PMCID: PMC9611129 DOI: 10.3390/pathogens11101183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
Cytauxzoonosis is a tick-borne infectious disease affecting domestic cats with high mortality and limited treatment modalities. Because early diagnosis and therapeutic intervention are crucial to survival of infected cats, the objective of this study was to develop an ELISA capable of detecting cytauxzoonosis and differentiating acute vs. chronic infection in clinical feline blood samples. A microsphere immunoassay (MIA) was developed to evaluate the production of Cytauxzoon felis-specific IgM and IgG antibodies in serial plasma samples from cats with experimental C. felis infection by targeting a C. felis-specific transmembrane protein (c88). Recombinant c88 protein was utilized to develop indirect ELISAs to detect IgM and IgG antibodies in clinical plasma samples from: PCR-positive cats with acute C. felis infection (n = 36), C. felis-negative cats with pyrexia (n = 10), healthy C. felis-negative cats (n = 22), and chronic C. felis carriers (n = 4). Anti-c88 IgM antibodies were detectable at day 12 post-tick infestation in cats with experimental C. felis infection (within 24 hours of developing clinical signs), while anti-c88 IgG was detectable at day 15 post-tick infestation - indicating IgM could be used to detect early infection. Using a cut-off value of 19.85 percent positive, the C. felis IgM ELISA detected acute cytauxzoonosis in 94.44% (34/36) of cats presented with clinical signs of acute cytauxzoonosis with 100% specificity (indicating a "Strong Positive" result). When a lower cutoff of 8.60 percent positive was used, cytauxzoonosis was detected in the 2 remaining PCR-positive cats with 87.88% specificity (indicating of a "Weak Positive" result). One C. felis-negative, febrile cat had high IgG, and chronic carriers had variable IgM and IgG results. Combined interpretation of IgM and IgG ELISAs did not reliably differentiate acute vs. chronic infection. While further validation on assay performance is needed, the C. felis IgM ELISA is a promising test to detect acute cytauxzoonosis and can be utilized to develop a point-of-care test for clinical use.
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Affiliation(s)
- Yun-Fan Kao
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74075, USA
| | - Rebecca Spainhour
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74075, USA
| | - Shannon R. Cowan
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74075, USA
| | - Laura Nafe
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Adam Birkenheuer
- Department of Clinical Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Mason V. Reichard
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74075, USA
| | - Craig A. Miller
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74075, USA
- Correspondence:
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14
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Erster O, Mendelson E, Kabat A, Levy V, Mannasse B, Assraf H, Azar R, Ali Y, Bucris E, Bar-Ilan D, Mor O, Elul M, Mandelboim M, Sofer D, Fleishon S, Zuckerman NS, Bar-Or I. Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Microbiol Spectr 2022;:e0217621. [PMID: 35285705 DOI: 10.1128/spectrum.02176-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In this report, we describe the development of a reverse transcription-quantitative PCR (RT-qPCR) assay, termed Alpha-Delta assay, which can detect all severe acute respiratory syndrome coronavirus 2 (SC-2) variants and distinguish between the Alpha (B.1.1.7) and Delta (B.1.617.2) variants. The Alpha- and Delta-specific reactions in the assay target mutations that are strongly linked to the target variant. The Alpha reaction targets the D3L substitution in the N gene, and the Delta reaction targets the spike gene 156 to 158 mutations. Additionally, we describe a second Delta-specific assay that we use as a confirmatory test for the Alpha-Delta assay that targets the 119 to 120 deletion in the Orf8 gene. Both reactions have similar sensitivities of 15 to 25 copies per reaction, similar to the sensitivity of commercial SC-2 detection tests. The Alpha-Delta assay and the Orf8119del assay were successfully used to classify clinical samples that were subsequently analyzed by whole-genome sequencing. Lastly, the capability of the Alpha-Delta assay and Orf8119del assay to identify correctly the presence of Delta RNA in wastewater samples was demonstrated. This study provides a rapid, sensitive, and cost-effective tool for detecting and classifying two worldwide dominant SC-2 variants. It also highlights the importance of a timely diagnostic response to the emergence of new SC-2 variants with significant consequences on global health. IMPORTANCE The new assays described herein enable rapid, straightforward, and cost-effective detection of severe acute respiratory syndrome coronavirus 2 (SC-2) with immediate classification of the examined sample as Alpha, Delta, non-Alpha, or non-Delta variant. This is highly important for two main reasons: (i) it provides the scientific and medical community with a novel diagnostic tool to rapidly detect and classify any SC-2 sample of interest as Alpha, Delta, or none and can be applied to both clinical and environmental samples, and (ii) it demonstrates how to respond to the emergence of new variants of concern by developing a variant-specific assay. Such assays should improve our preparedness and adjust the diagnostic capacity to serve clinical, epidemiological, and research needs.
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15
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Litchfield M, Brookes P, Ojrzynska A, Kavi J, Dawood R. Comparison of the clinical sensitivity and specificity of two commercial RNA SARS-CoV-2 assays. Int J Infect Dis 2022; 118:194-196. [PMID: 35217170 PMCID: PMC8863925 DOI: 10.1016/j.ijid.2022.02.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/01/2022] Open
Abstract
Objectives This study aimed to compare the performance of the NeuMoDx™ SARS-CoV-2 Assay, implemented on the NeuMoDx 96 Molecular System, with that of the ThermoFisher TaqPath™ COVID-19 CE-IVD RT-PCR Kit (reference method). Methods Overall, 450 nasopharyngeal swab samples, previously tested using the reference method, were tested by the NeuMoDx Assay, and the clinical sensitivity and specificity of the assay were analyzed. Results By retrospective statistical analysis of all valid results, the NeuMoDx Assay had a clinical specificity of 100% (95% confidence interval [CI]: 98.65–100.00) and a clinical sensitivity of 98.73% (95% CI: 95.47–99.85). Conclusions The NeuMoDx SARS-CoV-2 Assay demonstrated comparable analytical and clinical performance to the ThermoFisher TaqPath COVID-19 CE-IVD RT-PCR Kit. The NeuMoDx 96 Molecular System is well suited for automating medium-throughput routine SARS-CoV-2 testing or as an addition to high-throughput systems to allow fast-tracking for highly urgent clinical samples.
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Affiliation(s)
- Mark Litchfield
- Fleet Street Clinic, 29 Fleet Street, London, EC4Y 1AA, United Kingdom.
| | - Paul Brookes
- Royal Brompton and Harefield Hospital, 250 King's Road, London, SW3 5UE, United Kingdom.
| | - Agnieszka Ojrzynska
- Royal Brompton and Harefield Hospital, 250 King's Road, London, SW3 5UE, United Kingdom.
| | - Janki Kavi
- Fleet Street Clinic, 29 Fleet Street, London, EC4Y 1AA, United Kingdom.
| | - Richard Dawood
- Fleet Street Clinic, 29 Fleet Street, London, EC4Y 1AA, United Kingdom.
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16
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Miller S, Lee T, Merritt A, Pryce T, Levy A, Speers D. Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Microbiol Spectr 2021; 9:e0149421. [PMID: 34787486 DOI: 10.1128/Spectrum.01494-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Accurate and rapid diagnostic tests are a critical component for the early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and of the overall control strategy for the current pandemic. Nucleic acid amplification tests are the gold standard for diagnosis of acute SARS-CoV-2 infection, and many real-time PCR diagnostic assays have been developed. Mutations that occur within the primer/probe binding regions of the SARS-CoV-2 genome can negatively impact the performance of diagnostic assays. Here, we report two single-point mutations in the N gene of SARS-CoV-2 associated with N gene target detection failures in the Cepheid Xpert Xpress SARS-CoV-2 assay, the first a C to T mutation at position 29197, found in five patients, and the second a C to T mutation at position 29200, found in eight patients. By sequencing the Xpert amplicons, we showed both mutations to be located within the amplified region of the Xpert N gene target. This report highlights the necessity for multiple genetic targets and the continual monitoring and evaluation of diagnostic assay performance. IMPORTANCE This paper reports the identification of single-point mutations in the N gene of SARS-CoV-2 associated with a gene target failure by the Cepheid Xpert commercial system. In order to determine the mutation(s) responsible for the N gene detection failures, the genomic products from the Cepheid Xpert system were sequenced and compared to whole genomes of SARS-CoV-2 from clinical cases. This report is the first to our knowledge which characterizes the amplified PCR products of the Xpert system, confirming the mutations associated with the gene target failure. The mutations identified have previously been reported.
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17
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Niederwerder MC, Hefley TJ. Diagnostic sensitivity of porcine biological samples for detecting African swine fever virus infection after natural consumption in feed and liquid. Transbound Emerg Dis 2021; 69:2727-2734. [PMID: 34914859 DOI: 10.1111/tbed.14424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/04/2021] [Accepted: 12/12/2021] [Indexed: 01/12/2023]
Abstract
African swine fever virus (ASFV) is a global threat to swine production and sustainable pork supply. Without a commercially available vaccine, prevention of ASFV entry and spread is reliant on biosecurity and early detection of infection. Although ASFV ingestion in swill or feed by naïve pigs is a likely route of initial introduction, controlled experimental studies rarely utilize natural consumption as the infection route. In the current study, we utilized biological samples collected from pigs 5 days after natural consumption of ASFV in feed and liquid to assess diagnostic sensitivity for early detection of virus infection. Biological samples (serum, spleen, lymph nodes, tonsils, and faeces) were assessed for the presence of ASFV using quantitative PCR and virus isolation. Statistical methods modelled the detection sensitivity of each sample type with each diagnostic assay in individual samples. Our results provide important information that can be incorporated into ASFV surveillance programs.
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Affiliation(s)
- Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Trevor J Hefley
- Department of Statistics, College of Arts and Sciences, Kansas State University, Manhattan, Kansas, USA
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18
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Kaur H, Singh R, Doyle V, Valverde R. A Diagnostic TaqMan Real-Time PCR Assay for In Planta Detection and Quantification of Colletotrichum theobromicola, Causal Agent of Boxwood Dieback. Plant Dis 2021; 105:2395-2401. [PMID: 33630686 DOI: 10.1094/pdis-11-20-2439-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Boxwood dieback, caused by Colletotrichum theobromicola, is spreading at an alarming rate in the boxwood industry in the United States. Although C. theobromicola has been accepted as a distinct species within the C. gloeosporioides species complex, it is difficult to distinguish it from other closely related species based on morphology. Moreover, molecular identification of C. theobromicola requires amplification and sequencing of multiple loci, which can be expensive and time consuming. Therefore, a diagnostic TaqMan real-time PCR assay was developed for early and accurate detection and quantification of C. theobromicola in boxwood. The study involved the design of species-specific primers and a TaqMan probe to differentiate C. theobromicola from other closely related Colletotrichum species. The primers and probe discriminate between C. theobromicola and other species in the C. gloeosporioides species complex and can detect C. theobromicola at very low concentrations, illustrating the high specificity and sensitivity of the assay. This TaqMan real-time PCR assay accurately and rapidly distinguishes boxwood dieback from other diseases with similar symptomatology, including Macrophoma blight, Phytophthora root rot, and Volutella blight, as well as some disorders produced by abiotic agents.
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Affiliation(s)
- Harleen Kaur
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
| | - Raghuwinder Singh
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
| | - Vinson Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
| | - Rodrigo Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
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John G, Sahajpal NS, Mondal AK, Ananth S, Williams C, Chaubey A, Rojiani AM, Kolhe R. Next-Generation Sequencing (NGS) in COVID-19: A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology. Curr Issues Mol Biol 2021; 43:845-867. [PMID: 34449545 PMCID: PMC8929009 DOI: 10.3390/cimb43020061] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/24/2022] Open
Abstract
This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.
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Affiliation(s)
- Goldin John
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA 30912, USA; (G.J.); (N.S.S.); (A.K.M.); (S.A.); (C.W.); (A.C.)
| | - Nikhil Shri Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA 30912, USA; (G.J.); (N.S.S.); (A.K.M.); (S.A.); (C.W.); (A.C.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA 30912, USA; (G.J.); (N.S.S.); (A.K.M.); (S.A.); (C.W.); (A.C.)
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA 30912, USA; (G.J.); (N.S.S.); (A.K.M.); (S.A.); (C.W.); (A.C.)
| | - Colin Williams
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA 30912, USA; (G.J.); (N.S.S.); (A.K.M.); (S.A.); (C.W.); (A.C.)
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA 30912, USA; (G.J.); (N.S.S.); (A.K.M.); (S.A.); (C.W.); (A.C.)
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | - Amyn M. Rojiani
- Department of Pathology, Penn State University College of Medicine, Hershey, PA 16802, USA;
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, BAE 2576, 1120 15th Street, Augusta, GA 30912, USA; (G.J.); (N.S.S.); (A.K.M.); (S.A.); (C.W.); (A.C.)
- Correspondence: ; Tel.: +1-(706)-721-2771; Fax: +1-(706)-434-6053
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Diaz-Lara A, Stevens KA, Klaassen V, Hwang MS, Al Rwahnih M. Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays. Viruses 2021; 13:v13081442. [PMID: 34452308 PMCID: PMC8402890 DOI: 10.3390/v13081442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 11/21/2022] Open
Abstract
Viruses are considered of major importance in strawberry (Fragaria × ananassa Duchesne) production given their negative impact on plant vigor and growth. Strawberry accessions from the National Clonal Germplasm Repository were screened for viruses using high throughput sequencing (HTS). Analyses of sequence information from 45 plants identified multiple variants of 14 known viruses, comprising strawberry mottle virus (SMoV), beet pseudo yellows virus (BPYV), strawberry pallidosis-associated virus (SPaV), tomato ringspot virus (ToRSV), strawberry mild yellow edge virus (SMYEV), strawberry vein banding virus (SVBV), strawberry crinkle virus (SCV), strawberry polerovirus 1 (SPV-1), apple mosaic virus (ApMV), strawberry chlorotic fleck virus (SCFaV), strawberry crinivirus 4 (SCrV-4), strawberry crinivirus 3 (SCrV-3), Fragaria chiloensis latent virus (FClLV) and Fragaria chiloensis cryptic virus (FCCV). Genetic diversity of sequenced virus isolates was investigated via sequence homology analysis, and partial-genome sequences were deposited into GenBank. To confirm the HTS results and expand the detection of strawberry viruses, new reverse transcription quantitative PCR (RT-qPCR) assays were designed for the above-listed viruses. Further in silico and in vitro validation of the new diagnostic assays indicated high efficiency and reliability. Thus, the occurrence of different viruses, including divergent variants, among the strawberries was verified. This is the first viral metagenomic survey in strawberry, additionally, this study describes the design and validation of multiple RT-qPCR assays for strawberry viruses, which represent important detection tools for clean plant programs.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA;
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Kristian A. Stevens
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (K.A.S.); (V.K.); (M.S.H.)
- Department of Computer Science, University of California-Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Vicki Klaassen
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (K.A.S.); (V.K.); (M.S.H.)
| | - Min Sook Hwang
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (K.A.S.); (V.K.); (M.S.H.)
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA;
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (K.A.S.); (V.K.); (M.S.H.)
- Correspondence:
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21
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Khanal P, Olcha M, Niederwerder MC. Detection of African swine fever virus in feed dust collected from experimentally inoculated complete feed using quantitative PCR and virus titration assays. Transbound Emerg Dis 2021; 69:97-102. [PMID: 34132048 DOI: 10.1111/tbed.14176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 12/01/2022]
Abstract
African swine fever virus (ASFV) is a current threat to global pork production due to its high case fatality rate, lack of efficacious vaccine and recent transboundary spread into new regions of the world. Preventing introduction and further spread of ASFV is critical for countries currently negative for the virus. ASFV is stable in feed ingredients subjected to transoceanic conditions and transmission occurs through the natural consumption of contaminated feed. In this study, we investigated the use of feed dust collected from experimentally inoculated feed as a novel diagnostic sample type for ASFV detection. Moist swabs were used to collect dust from creep feeders after natural consumption of feed inoculated with 3.1-5.4 log10 TCID50 /g ASFV Georgia 2007 in the presence and absence of antimicrobial feed additives. Results validate the potential use of feed dust swabs as a novel diagnostic surveillance tool for detection and quantification of viral nucleic acid and infectious virus titre in ASFV-contaminated feed.
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Affiliation(s)
- Pratiksha Khanal
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Matthew Olcha
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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22
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Cattel J, Haberkorn C, Laporte F, Gaude T, Cumer T, Renaud J, Sutherland IW, Hertz JC, Bonneville J, Arnaud V, Fustec B, Boyer S, Marcombe S, David J. A genomic amplification affecting a carboxylesterase gene cluster confers organophosphate resistance in the mosquito Aedes aegypti: From genomic characterization to high-throughput field detection. Evol Appl 2021; 14:1009-1022. [PMID: 33897817 PMCID: PMC8061265 DOI: 10.1111/eva.13177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 01/06/2023] Open
Abstract
By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterize a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito Aedes aegypti and to develop a molecular assay to monitor the associated resistance alleles in the field. An experimental evolution experiment using a composite population from Laos supported the association between the over-transcription of multiple contiguous carboxylesterase genes on chromosome 2 and resistance to multiple organophosphate insecticides. Combining whole genome sequencing and qPCR on specific genes confirmed the presence of a ~100-Kb amplification spanning at least five carboxylesterase genes at this locus with the co-existence of multiple structural duplication haplotypes. Field data confirmed their circulation in South-East Asia and revealed high copy number polymorphism among and within populations suggesting a trade-off between this resistance mechanism and associated fitness costs. A dual-color multiplex TaqMan assay allowing the rapid detection and copy number quantification of this amplification event in Ae. aegypti was developed and validated on field populations. The routine use of this novel assay will improve the tracking of resistance alleles in this major arbovirus vector.
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Affiliation(s)
- Julien Cattel
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
- Present address:
Symbiosis Technologies for Insect Control (SymbioTIC)Plateforme de Recherche CyroiSte ClotildeFrance
| | - Chloé Haberkorn
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Fréderic Laporte
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Thierry Gaude
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Tristan Cumer
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Julien Renaud
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Ian W. Sutherland
- United States Navy Entomology. Center of ExcellenceNAS JacksonvilleJacksonvilleFLUSA
| | | | - Jean‐Marc Bonneville
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Victor Arnaud
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
| | - Bénédicte Fustec
- Department of MicrobiologyKhon Kaen UniversityKhon KaenThailand
- Institut de Recherche pour le DéveloppementUMR IRD 224‐CNRS 5290‐Université MontpellierMontpellier Cedex 5France
| | - Sébastien Boyer
- Medical and Veterinary EntomologyInstitut Pasteur du CambodgePhnom PenhCambodia
| | - Sébastien Marcombe
- Medical Entomology and Vector‐Borne Disease LaboratoryInstitut Pasteur du LaosVientianeLaos
| | - Jean‐Philippe David
- Laboratoire d'Ecologie Alpine (LECA)UMR 5553 CNRS – Université Grenoble‐AlpesGrenobleFrance
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23
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Elaswad A, Fawzy M. Mutations in Animal SARS-CoV-2 Induce Mismatches with the Diagnostic PCR Assays. Pathogens 2021; 10:371. [PMID: 33808783 PMCID: PMC8003424 DOI: 10.3390/pathogens10030371] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was detected in several animal species. After transmission to animals, the virus accumulates mutations in its genome as adaptation to the new animal host progresses. Therefore, we investigated whether these mutations result in mismatches with the diagnostic PCR assays and suggested proper modifications to the oligo sequences accordingly. A comprehensive bioinformatic analysis was conducted using 28 diagnostic PCR assays and 793 publicly available SARS-CoV-2 genomes isolated from animals. Sixteen out of the investigated 28 PCR assays displayed at least one mismatch with their targets at the 0.5% threshold. Mismatches were detected in seven, two, two, and six assays targeting the ORF1ab, spike, envelope, and nucleocapsid genes, respectively. Several of these mismatches, such as the deletions and mismatches at the 3' end of the primer or probe, are expected to negatively affect the diagnostic PCR assays resulting in false-negative results. The modifications to the oligo sequences should result in stronger template binding by the oligos, better sensitivity of the assays, and higher confidence in the result. It is necessary to monitor the targets of diagnostic PCR assays for any future mutations that may occur as the virus continues to evolve in animals.
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Affiliation(s)
- Ahmed Elaswad
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Mohamed Fawzy
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
- Middle East for Vaccines (ME VAC®), Sharquia 44813, Egypt
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24
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Leitner M, Büchold C, Pasternack R, Binder NB, Moore GW. Clinical Validation of an Automated Fluorogenic Factor XIII Activity Assay Based on Isopeptidase Activity. Int J Mol Sci 2021; 22:1002. [PMID: 33498248 DOI: 10.3390/ijms22031002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 02/06/2023] Open
Abstract
Hereditary factor XIII (FXIII) deficiency is a rare autosomal bleeding disorder which can cause life-threatening bleeding. Acquired deficiency can be immune-mediated or due to increased consumption or reduced synthesis. The most commonly used screening test is insensitive, and widely used quantitative assays have analytical limitations. The present study sought to validate Technofluor FXIII Activity, the first isopeptidase-based assay available on a routine coagulation analyser, the Ceveron s100. Linearity was evidenced throughout the measuring range, with correlation coefficients of >0.99, and coefficients of variation for repeatability and reproducibility were <5% and <10%, respectively. A normally distributed reference range of 47.0–135.5 IU/dL was derived from 154 normal donors. Clinical samples with Technofluor FXIII Activity results between 0 and 167.0 IU/dL were assayed with Berichrom® FXIII Activity, a functional ammonia release assay, and the HemosIL™ FXIII antigen assay, generating correlations of 0.950 and 0.980, respectively. Experiments with a transglutaminase inhibitor showed that Technofluor FXIII Activity can detect inhibition of enzymatic activity. No interference was exhibited by high levels of haemolysis and lipaemia, and interference by bilirubin was evident at 18 mg/dL, a level commensurate with severe liver disease. Technofluor FXIII Activity is a rapid, accurate and precise assay suitable for routine diagnostic use with fewer interferents than ammonia release FXIII activity assays.
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Affiliation(s)
- Matthew W McCarthy
- Weill Cornell Medical College, Division of General Internal Medicine, New York-Presbyterian Hospital, New York, NY, USA
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26
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Okda FA, Griffith E, Sakr A, Nelson E, Webby R. New Diagnostic Assays for Differential Diagnosis Between the Two Distinct Lineages of Bovine Influenza D Viruses and Human Influenza C Viruses. Front Vet Sci 2020; 7:605704. [PMID: 33363244 PMCID: PMC7759653 DOI: 10.3389/fvets.2020.605704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
Influenza D virus (IDV), a novel orthomyxovirus, is currently emerging in cattle worldwide. It shares >50% sequence similarity with the human influenza C virus (HICV). Two clades of IDV are currently co-circulating in cattle herds in the U.S. New assays specific for each lineage are needed for accurate surveillance. Also, differential diagnosis between zoonotic human influenza C virus and the two clades of IDV are important to assess the zoonotic potential of IDV. We developed an enzyme-linked immunosorbent assay (ELISA) based on two different epitopes HEF and NP and four peptides, and fluorescent focus neutralization assay to differentiate between IDV bovine and swine clades. Calf sera were obtained, and bovine samples underwent surveillance. Our results highlight the importance of position 215 with 212 in determining the heterogeneity between the two lineages. We needed IFA and FFN for tissue culture-based analysis and a BSL2 facility for analyzing virus interactions. Unfortunately, these are not available in many veterinary centers. Hence, our second aim was to develop an iELISA using specific epitopes to detect two lineages of IDVs simultaneously. Epitope-iELISA accurately detects neutralizing and non-neutralizing antibodies against the IDV in non-BSL2 laboratories and veterinary clinics and is cost-effective and sensitive. To differentiate between IDVs and HICVs, whole antigen blocking, polypeptides, and single-peptide ELISAs were developed. A panel of ferret sera against both viruses was used. Results suggested that both IDV and ICV had a common ancestor, and IDV poses a zoonotic risk to individuals with prior or current exposure to cattle. IDV peptides IANAGVK (286-292 aa), KTDSGR (423-428 aa), and RTLTPAT (448-455 aa) could differentiate between the two viruses, whereas peptide AESSVNPGAKPQV (203-215 aa) detected the presence of IDV in human sera but could not deny that it could be ICV, because the only two conserved influenza C peptides shared 52% sequence similarity with IDV and cross-reacted with IDV. However, blocking ELISAs differentiated between the two viruses. Diagnostic tools and assays to differentiate between ICV and IDV are required for serological and epidemiological analysis to clarify the complexity and evolution and eliminate misdiagnosis between ICV and IDV in human samples.
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Affiliation(s)
- Faten A Okda
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States.,Veterinary Division, National Research Center, Cairo, Egypt
| | - Elizabeth Griffith
- Department of Chemical and Therapeutic, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Ahmed Sakr
- Department of Business Administration and Management, Dakota State University, Madison, SD, United States
| | - Eric Nelson
- Veterinary & Biomedical Sciences Department, Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD, United States
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States
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27
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Yip CC, Chan WM, Ip JD, Seng CW, Leung KH, Poon RW, Ng AC, Wu WL, Zhao H, Chan KH, Siu GK, Ng TT, Cheng VC, Kok KH, Yuen KY, To KK. Nanopore Sequencing Reveals Novel Targets for Detection and Surveillance of Human and Avian Influenza A Viruses. J Clin Microbiol 2020; 58:e02127-19. [PMID: 32132187 DOI: 10.1128/JCM.02127-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Accurate detection of influenza A virus (IAV) is crucial for patient management, infection control, and epidemiological surveillance. The World Health Organization and the Centers for Disease Control and Prevention have recommended using the M gene as the diagnostic gene target for reverse-transcription-PCR (RT-PCR). However, M gene RT-PCR has reduced sensitivity for recent IAV due to novel gene mutations. Here, we sought to identify novel diagnostic targets for the molecular detection of IAV using long-read third-generation sequencing. Direct nanopore sequencing from 18 nasopharyngeal specimens and one saliva specimen showed that the 5' and 3' ends of the PB2 gene and the entire NS gene were highly abundant. Primers selected for PB2 and NS genes were well matched with seasonal or avian IAV gene sequences. Our novel PB2 and NS gene real-time RT-PCR assays showed limits of detection similar to or lower than that of M gene RT-PCR and achieved 100% sensitivity and specificity in the detection of A(H1N1), A(H3N2), and A(H7N9) in nasopharyngeal and saliva specimens. For 10 patients with IAV detected by M gene RT-PCR conversion in sequentially collected specimens, NS and/or PB2 gene RT-PCR was positive in 2 (20%) of the initial specimens that were missed by M gene RT-PCR. In conclusion, we have shown that PB2 or NS gene RT-PCRs are suitable alternatives to the recommended M gene RT-PCR for diagnosis of IAV. Long-read nanopore sequencing facilitates the identification of novel diagnostic targets.
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28
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Petiti J, Rosso V, Croce E, Franceschi V, Andreani G, Dragani M, De Gobbi M, Lunghi M, Saglio G, Fava C, Lo Iacono M, Cilloni D. Highly Sensitive Detection of IDH2 Mutations in Acute Myeloid Leukemia. J Clin Med 2020; 9:jcm9010271. [PMID: 31963812 PMCID: PMC7019902 DOI: 10.3390/jcm9010271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 11/16/2022] Open
Abstract
Background: Acute myeloid leukemia is a heterogeneous hematological disease, characterized by karyotypic and molecular alterations. Mutations in IDH2 have a role in diagnosis and as a minimal residue disease marker. Often the variant allele frequency during follow up is less than 20%, which represents the limit of detection of Sanger sequencing. Therefore, the development of sensitive methodologies to identify IDH2 mutations might help to monitor patients’ response to therapy. We compared three different methods to identify and monitor IDH2 mutations in patients’ specimens. Methods: Performances of PNA-PCR clamping, droplet digital PCR and Sanger for IDH2 status identification were evaluated and compared in 96 DNA patients’ specimens. Results: In contrast with Sanger sequencing, our results highlighted the concordance between PNA clamping and digital PCR. Furthermore, PNA-PCR clamping was able to detect more mutated DNA with respect to Sanger sequencing that showed several false negatives independently from the allelic frequency. Conclusions: We found that PNA-PCR clamping and digital PCR identified IDH2 mutations in DNA samples with comparable results in a percentage significantly higher compared to Sanger sequencing. PNA-PCR clamping can be used even in laboratories not equipped for sophisticated analyses, decreasing cost and time for IDH2 characterization.
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Affiliation(s)
- Jessica Petiti
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
- Correspondence: (J.P.); (D.C.); Tel.: +39-011-9026800 (J.P.); +39-011-9026610 (D.C.); Fax: +39-11-9038636 (J.P. & D.C.)
| | - Valentina Rosso
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Eleonora Croce
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Vanessa Franceschi
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Giacomo Andreani
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Matteo Dragani
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Marco De Gobbi
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Monia Lunghi
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale, Corso Giuseppe Mazzini, 18, 28100 Novara, Italy;
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Carmen Fava
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Marco Lo Iacono
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences of the University of Turin, San Luigi Gonzaga Hospital, Regione Gonzole 10, 10043 Orbassano (Turin), Italy; (V.R.); (E.C.); (V.F.); (G.A.); (M.D.); (M.D.G.); (G.S.); (C.F.); (M.L.I.)
- Correspondence: (J.P.); (D.C.); Tel.: +39-011-9026800 (J.P.); +39-011-9026610 (D.C.); Fax: +39-11-9038636 (J.P. & D.C.)
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29
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Saxena D, Sheikh S, Kao G, Binder ZA, Alonso-Basanta M, O'Rourke DM, Nasrallah MP, Dorsey JF. Rapid and ultrasensitive digital PCR (dPCR) profiling of EGFRvIII in tumor cells and tissues. Neurooncol Adv 2019; 1:vdz030. [PMID: 31807732 PMCID: PMC6881905 DOI: 10.1093/noajnl/vdz030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Amplification of the epidermal growth factor receptor (EGFR) gene is commonly found in glioblastoma (GBM). About 57% GBM overexpresses EGFR and are associated with tumor progression, poor prognosis, and shorter life expectancy. Molecular profiling of solid tumors usually takes several weeks and may be biased by intrinsic tumor heterogeneity. Methods The unique sequence created by the fusion of exon 1 and exon 8 in EGFRvIII was used to guide the design of primers and a Minor Groove Binder (MGB) probe. Extracted total RNA was reverse transcribed and pre-amplified by PCR, followed by detection of the EGFRvIII mutation by dPCR. Results The lowest limit of quantification of our EGFRvIII assay was 0.003%. The EGFRvIII variant was identified in patient-derived glioma neurosphere cell lines, xenograft mouse model, and patient-derived tumor specimens. The overall workflow can be accomplished within 24 hours. In certain samples, EGFRvIII was detected when next-generation sequencing was unable to identify the variant. This finding highlights the ability of the dPCR assay to identify EGFRvIII mutations in heterogeneous solid tumors such as GBM in a rapid fashion by profiling samples from spatially distinct areas of tumors from the same patient. Conclusions In this study, we developed a highly sensitive digital PCR (dPCR) platform and leveraged our assay to detect the variant III alteration of EGFR (EGFRvIII) and amplified EGFR in patient-derived glioma neurosphere cell lines, orthotopic xenograft GBM mouse models, and patient-derived tumor specimens in less than 24 hours from minute quantities of starting material.
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Affiliation(s)
- Deeksha Saxena
- Department of Radiation Oncology.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
| | | | - Gary Kao
- Department of Radiation Oncology
| | - Zev A Binder
- Department of Neurosurgery.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
| | | | - Donald M O'Rourke
- Department of Neurosurgery.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
| | - MacLean P Nasrallah
- Department of Pathology and Laboratory Medicine, Division of Neuropathology.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
| | - Jay F Dorsey
- Department of Radiation Oncology.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Cancer Center Glioblastoma Translational Center of Excellence, Penn Medicine, Philadelphia, PA
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Desoubeaux G, Rodriguez M, Bronson E, Sirpenski G, Cray C. APPLICATION OF 3-HYDROXYBUTYRATE MEASUREMENT AND PLASMA PROTEIN ELECTROPHORESIS IN THE DIAGNOSIS OF ASPERGILLOSIS IN AFRICAN PENGUINS ( SPHENISCUS DEMERSUS). J Zoo Wildl Med 2018; 49:696-703. [PMID: 30212328 DOI: 10.1638/2017-0172.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
New alternative laboratory means are needed to improve the options for antemortem diagnosis of avian aspergillosis. In this study, 3-hydroxybutyrate was measured in plasma samples collected from a cohort of African penguins ( Spheniscus demersus) maintained under human care. Results were interpreted in combination with those of protein electrophoresis and compared with anti- Aspergillus antibody and galactomannan antigen detection. Overall, 3-hydroxybutyrate levels were found significantly increased in Aspergillus-diseased cases versus the control penguin group ( P = 0.002). Mean absolute concentration of β-globulins was increased >20% in samples from infected birds, and α2-globublins were also found to be significantly increased versus clinically normal controls ( P < 0.001 and P = 0.001 respectively). Of note, the α2-globulins were also significantly increased versus penguins with inflammatory (non-aspergillosis) diseases ( P = 0.001). The specificity of 3-hydroxybutyrate, β-globulins, and α2-globulins for aspergillosis was 78.6%, 79.6%, and 92.2%, respectively. Using these measures in tandem resulted in high specificity (>90%) and negative predictive value (≥80%). In contrast, anti- Aspergillus antibody and galactomannan antigen did not distinguish between infected cases and controls ( P > 0.05). This study demonstrates that basic testing in tandem with the new biomarker 3-hydroxybutyrate may provide reliable evidence for the diagnosis of aspergillosis in penguins.
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O'Brien O, Wright MC, O'Brien C, Geoghegan O, Leonard N, Nicholson S, Cuffe S, Fabre A, Jochum W, Joerger M, Gray SG, Finn SP. Cost-Efficient and Easy to Perform PCR-Based Assay to Identify Met Exon 14 Skipping in Formalin-Fixed Paraffin-Embedded (FFPE) Non-Small Cell Lung Cancer (NSCLC) Samples. Diagnostics (Basel) 2019; 9:diagnostics9010013. [PMID: 30669306 PMCID: PMC6468531 DOI: 10.3390/diagnostics9010013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 01/03/2023] Open
Abstract
MET is a receptor tyrosine kinase (RTK) that plays important roles in carcinogenesis. Despite being frequently overexpressed in cancer, clinical responses to targeting this receptor have been limited. Recently novel splicing mutations involving the loss of exon 14 (called METex14 skipping) have emerged as potential biomarkers to predict for responsiveness to targeted therapies with Met inhibitors in non-small cell lung cancer (NSCLC). Currently, the diverse genomic alterations responsible for METex14 skipping pose a challenge for routine clinical diagnostic testing. In this report, we examine three different methodologies to detect METex14 and assess their potential utility for use as a diagnostic assay for both the identification of METex14 and intra-tumoural distribution in NSCLC.
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Affiliation(s)
- Odharnaith O'Brien
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Mark C Wright
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Cathal O'Brien
- Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Orla Geoghegan
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
| | - Niamh Leonard
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Sinéad Cuffe
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- HOPE Directorate, St. James's Hospital, D08 RT2X Dublin, Ireland.
| | - Aurelie Fabre
- Department of Pathology, St. Vincent's University Hospital, University College Dublin School of Medicine, D04 T6F4 Dublin, Ireland.
| | - Wolfram Jochum
- Department of Pathology, Cantonal Hospital, 9007 St. Gallen, Switzerland.
| | - Markus Joerger
- Department of Medical Oncology & Hematology, Cantonal Hospital, 9007 St. Gallen, Switzerland.
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Clinical Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, D08 NF82 Dublin, Ireland.
| | - Stephen P Finn
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
- Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D08 X4RX Dublin, Ireland.
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Perry SM, Muldoon S, Michaelson LP, Bunger R, Kasper CE. Effect of Norepinephrine on Intracellular Ca 2+ Levels in Malignant Hyperthermia-Susceptible B Cells: Pilot Study in the Search for a New Diagnostic Test for Malignant Hyperthermia. AANA J 2018; 86:383-392. [PMID: 31584408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Malignant hyperthermia (MH) crises may induce morbidity or death in MH-susceptible (MHS) individuals. The only sensitive method of determining susceptibility is the caffeine-halothane contracture test, requiring muscle biopsy. Early research on MH demonstrated an abnormal response to catecholamines in MHS individuals. The purpose of this study was to determine whether MHS B lymphocytes would demonstrate an increased sensitivity to norepinephrine as indicated by an adrenergic augmentation of intracellular calcium ion (Ca2+) accumulation, to possibly develop a less invasive laboratory assay for determining MH susceptibility. The fluorescent Ca2+ indicator dye fura-2 acetoxymethyl was used to identify Ca2+ flux within Epstein-Barr virus- immortalized MH-negative (MHN) and MHS B cells exposed to the RyR1 agonist 4-chloro-m-cresol (4-CmC) before and after administration of 1 μM of norepinephrine. In the presence of 4-CmC and norepinephrine, the area under the curve dose responses were significantly elevated in MHS B cells compared with MHN B cells (F[1,10] = 27.37; P < .01). Epstein-Barr virus-immortalized B cells from MHS humans displayed an increased sensitivity to norepinephrine compared with those from MHN individuals. These data suggest that an abnormal response to exogenous norepinephrine could potentially be used to develop a diagnostic laboratory assay to determine MH susceptibility.
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Affiliation(s)
- Susan M Perry
- is the vice dean for Faculty and Community Affairs at the University of South Florida College of Nursing in Tampa, Florida
| | - Sheila Muldoon
- is professor emeritus at the F. Edward Hebert School of Medicine in the Uniformed Services University of the Health Sciences (USUHS) in Bethesda, Maryland
| | - Luke P Michaelson
- is a research assistant professor, Department of Anesthesiology, School of Medicine, at the Uniformed Services University
| | - Rolf Bunger
- is an emeritus member of the American Physiological Society. He is professor of physiology, molecular biology and anesthesiology at USUHS
| | - Christine E Kasper
- is dean, University of New Mexico College of Nursing, Albuquerque, New Mexico
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Smolak A, Rowley J, Nagelkerke N, Kassebaum NJ, Chico RM, Korenromp EL, Abu-Raddad LJ. Trends and Predictors of Syphilis Prevalence in the General Population: Global Pooled Analyses of 1103 Prevalence Measures Including 136 Million Syphilis Tests. Clin Infect Dis 2018; 66:1184-1191. [PMID: 29136161 PMCID: PMC5888928 DOI: 10.1093/cid/cix975] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022] Open
Abstract
Background This study assessed levels, trends, and associations of observed syphilis prevalence in the general adult population using global pooled analyses. Methods A standardized database of syphilis prevalence was compiled by pooling systematically gathered data. Random-effects meta-analyses and meta-regressions were conducted using data from the period 1990-2016 to estimate pooled measures and assess predictors and trends. Countries were classified by World Health Organization region. Sensitivity analyses were conducted. Results The database included 1103 prevalence measures from 136 million syphilis tests across 154 countries (85% from women in antenatal care). Global pooled mean prevalence (weighted by region population size) was 1.11% (95% confidence interval [CI], .99-1.22). Prevalence predictors were region, diagnostic assay, sample size, and calendar year interacting with region. Compared to the African Region, the adjusted odds ratio (AOR) was 0.42 (95% CI, .33-.54) for the Region of the Americas, 0.13 (95% CI, .09-.19) for the Eastern Mediterranean Region, 0.05 (95% CI, .03-.07) for the European Region, 0.21 (95% CI, .16-.28) for the South-East Asia Region, and 0.41 (95% CI, .32-.53) for the Western Pacific Region. Treponema pallidum hemagglutination assay (TPHA) only or rapid plasma reagin (RPR) only, compared with dual RPR/TPHA diagnosis, produced higher prevalence (AOR >1.26), as did smaller sample-size studies (<500 persons) (AOR >2.16). Prevalence declined in all regions; the annual AORs ranged from 0.84 (95% CI, .79-.90) in the Eastern Mediterranean to 0.97 (95% CI, .97-1.01) in the Western Pacific. The pooled mean male-to-female prevalence ratio was 1.00 (95% CI, .89-1.13). Sensitivity analyses confirmed robustness of results. Conclusions Syphilis prevalence has declined globally over the past 3 decades. Large differences in prevalence persist among regions, with the African Region consistently the most affected.
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Affiliation(s)
- Alex Smolak
- Infectious Disease Epidemiology Group, Weill Cornell Medicine–Qatar, Cornell University, Doha, Qatar
| | | | | | - Nicholas J Kassebaum
- Institute for Health Metrics and Evaluation, University of Washington, Washington
- Division of Pediatric Anesthesiology, Seattle Children’s Hospital, Washington
| | - R Matthew Chico
- London School of Hygiene and Tropical Medicine, United Kingdom
| | | | - Laith J Abu-Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine–Qatar, Cornell University, Doha, Qatar
- Department of Healthcare Policy and Research, Weill Cornell Medicine, Cornell University, New York, New York
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Wood JB, Jones LS, Soper NR, Xu M, Torres VJ, Buddy Creech C, Thomsen IP. Serologic Detection of Antibodies Targeting the Leukocidin LukAB Strongly Predicts Staphylococcus aureus in Children With Invasive Infection. J Pediatric Infect Dis Soc 2018. [PMID: 29538707 PMCID: PMC6510946 DOI: 10.1093/jpids/piy017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Staphylococcus aureus is among the most commonly identified causes of invasive bacterial infection in children; however, reliable results from cultures of sterile-site samples often cannot be obtained, which necessitates prescription of a broad empiric antimicrobial agent(s). Children with invasive S aureus infection rapidly generate high antibody titers to the cytotoxin LukAB; therefore, the aim of this study was to assess the diagnostic utility of an anti-LukAB antibody assay for children with musculoskeletal infection (MSKI). METHODS We conducted a 2-year prospective study of all eligible children admitted to Vanderbilt Children's Hospital with an MSKI. Acute and convalescent sera were obtained, and antibodies that target LukAB were measured by an enzyme-linked immunosorbent assay. RESULTS Forty-two children were enrolled. The median concentrations of LukAB antibodies for children with S aureus infection were 130.3 U/mL in the acute phase and 455 U/mL in the convalescent phase (P < .001). The median concentrations of LukAB antibodies in children with a non-S aureus MSKI were 8.6 U/mL in the acute phase and 9.7 U/mL in the convalescent phase. The assay discriminated between S aureus and non-S aureus infection with areas under the receiver operating characteristic curve of 0.81 (95% confidence interval, 0.67-0.95; P < .001) and 0.95 (95% confidence interval, 0.86-1; P < .001) for samples tested in the acute and follow-up periods, respectively. With no false-negative results, the assay accurately ruled out S aureus in samples obtained during the convalescent phase. CONCLUSION Culture-independent diagnostics have the potential to improve care by narrowing antimicrobial therapy on the basis of the likelihood of S aureus infection. The results of this proof-of-concept study suggest that a LukAB serologic assay might be useful in the diagnosis of invasive bacterial infections, and larger-scale validation studies are warranted.
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Affiliation(s)
- James B Wood
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Nashville, Tennessee,Correspondence: J. B. Wood, Vanderbilt University Medical Center, Division of Pediatric Infectious Diseases, 1161 21st Ave South, D-7235 MCN, Nashville, TN 37232 ()
| | - Lauren S Jones
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Nashville, Tennessee
| | - Nicole R Soper
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Nashville, Tennessee
| | - Meng Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Victor J Torres
- Department of Microbiology, New York University School of Medicine, New York
| | - C Buddy Creech
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Nashville, Tennessee
| | - Isaac P Thomsen
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Nashville, Tennessee
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Rosso V, Petiti J, Bracco E, Pedrola R, Carnuccio F, Signorino E, Carturan S, Calabrese C, Bot-Sartor G, Ronconi M, Serra A, Saglio G, Frassoni F, Cilloni D. A novel assay to detect calreticulin mutations in myeloproliferative neoplasms. Oncotarget 2018; 8:6399-6405. [PMID: 28031530 PMCID: PMC5351640 DOI: 10.18632/oncotarget.14113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/15/2016] [Indexed: 11/27/2022] Open
Abstract
The myeloproliferative neoplasms are chronic myeloid cancers divided in Philadelphia positive (Ph+), chronic myeloid leukemia, or negative: polycythemia vera (PV) essential thrombocythemia (ET), and primary myelofibrosis (PMF). Most Ph negative cases have an activating JAK2 or MPL mutation. Recently, somatic mutations in the calreticulin gene (CALR) were detected in 56–88% of JAK2/MPL-negative patients affected by ET or PMF. The most frequent mutations in CARL gene are type-1 and 2. Currently, CALR mutations are evaluated by sanger sequencing. The evaluation of CARL mutations increases the diagnostic accuracy in patients without other molecular markers and could represent a new therapeutic target for molecular drugs. We developed a novel detection assay in order to identify type-1 and 2 CALR mutations by PNA directed PCR clamping. Seventy-five patients affected by myeloproliferative neoplasms and seven controls were examined by direct DNA sequencing and by PNA directed PCR clamping. The assay resulted to be more sensitive, specific and cheaper than sanger sequencing and it could be applied even in laboratory not equipped for more sophisticated analysis. Interestingly, we report here a case carrying both type 1 and type2 mutations in CALR gene.
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Affiliation(s)
- Valentina Rosso
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Jessica Petiti
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Enrico Bracco
- Department of Oncology, University of Turin, Turin, Italy
| | - Roberto Pedrola
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Francesca Carnuccio
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Elisabetta Signorino
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Sonia Carturan
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Chiara Calabrese
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Giada Bot-Sartor
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Michela Ronconi
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Anna Serra
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Francesco Frassoni
- Department of Pediatric Hemato-Oncology and Stem Cell, Cellular Therapy Laboratory, Institute G. Gaslini, Genova, Italy
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
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Gerloff N, Sun H, Mandelbaum M, Maher C, Nix WA, Zaidi S, Shaukat S, Seakamela L, Nalavade UP, Sharma DK, Oberste MS, Vega E. Diagnostic Assay Development for Poliovirus Eradication. J Clin Microbiol 2018; 56:e01624-17. [PMID: 29212703 DOI: 10.1128/JCM.01624-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/01/2017] [Indexed: 02/07/2023] Open
Abstract
With poliovirus eradication nearing, few pockets of active wild poliovirus (WPV) transmission remain in the world. Intratypic differentiation (ITD) plays a crucial part in laboratory surveillance as the molecular detection method that can identify and distinguish wild and vaccine-like polioviruses isolated from acute flaccid paralysis cases or environmental sources. The need to detect new variants of WPV serotype 1 (WPV1) and the containment of all serotype 2 polioviruses (PV2) in 2015 required changes to the previous version of the method. The ITD version 5.0 is a set of six real-time reverse transcription-PCR (rRT-PCR) assays that serve as accurate diagnostic tools to easily detect and differentiate PV serotypes and genotypes. We describe the creation and properties of quantitation standards, including 16 control RNA transcripts and nine plaque-isolated viruses. All ITD rRT-PCR assays were validated using these standards, and the limits of detection were determined for each assay. We designed and pilot tested two new assays targeting recently circulating WPV1 genotypes and all PV2 viruses. The WPV1 assay had 99.1% specificity and 100% sensitivity, and the PV2 assay had 97.7% specificity and 92% sensitivity. Before proceeding to the next step in the global poliovirus eradication program, we needed to gain a better understanding of the performance of the ITD 5.0 suite of molecular assays and their limits of detection and specificities. The findings and conclusions in this evaluation serve as building blocks for future development work.
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Watanabe S, Melzer MJ. A Multiplex PCR Assay for Differentiating Coconut Rhinoceros Beetle (Coleoptera: Scarabaeidae) From Oriental Flower Beetle (Coleoptera: Scarabaeidae) in Early Life Stages and Excrement. J Econ Entomol 2017; 110:678-682. [PMID: 28115497 DOI: 10.1093/jee/tow299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Indexed: 06/06/2023]
Abstract
The coconut rhinoceros beetle, Oryctes rhinoceros (L.), is a major pest of coconut and other palm trees. An incipient coconut rhinoceros beetle population was recently discovered on the island of Oahu, Hawaii and is currently the target of a large, mutiagency eradication program. Confounding this program is the widespread presence of another scarab beetle on Oahu, the oriental flower beetle, Protaetia orientalis (Gory and Percheron 1833). Eggs, early life stages, and fecal excrement of coconut rhinoceros beetle and oriental flower beetle are morphologically indistinguishable, thereby creating uncertainty when such specimens are discovered in the field. Here, we report the development of a multiplex PCR assay targeting cytochrome oxidase I of coconut rhinoceros beetle and oriental flower beetle that can rapidly detect and distinguish between these insects. This assay also features an internal positive control to ensure DNA of sufficient quantity and quality is used in the assay, increasing its reliability and reducing the chances of false negative results.
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Affiliation(s)
- S Watanabe
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, 3190 Maile Way, St. John 205, Honolulu, HI 96822 (; )
| | - M J Melzer
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, 3190 Maile Way, St. John 205, Honolulu, HI 96822 (; )
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Orsaria M, Marzinotto S, De Marchi L, Giacomarra V, Boria S, Rubini C, Londero AP, Di Loreto C, Mariuzzi L. HPV-related Oropharyngeal Squamous Cell Carcinoma: p16INK4A Immunohistochemistry or HPV Genotyping? Anticancer Res 2015; 35:4733-4739. [PMID: 26254363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND Infection with high-risk human papillomavirus (HPV) is linked to a sub-group of squamous cell oropharyngeal tumors (OPSCC). Our aim was to compare an HPV Polymerase Chain Reaction (PCR) assay and p16(INK4A) expression status by immunohistochemistry (IHC) as a surrogate marker. MATERIALS AND METHODS This was a retrospective study considering patients affected by squamous cell oropharyngeal tumors. All included samples were processed for IHC for p16(INK4A) and tested by PCR for detection of HPV DNA and HPV genotyping. RESULTS A total of 84 patients affected by squamous cell oropharyngeal tumors were included and tested. A significant positive correlation was found between HPV PCR and p16(INK4A) IHC but the agreement was poor (k coefficient of 0.25). In fact, the sensitivity of p16(INK4A) IHC positivity in detecting HPV PCR positivity was low (28.21%, 95% confidence interval=16.54% - 43.78%). CONCLUSION Positivity of p16(INK4A) by IHC had a low sensitivity in detecting HPV DNA and our results suggest the need at least to test p16(INK4A) IHC- negative samples using HPV PCR to increase detection accuracy and provide valuable information for the clinical management of these patients.
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Affiliation(s)
- Maria Orsaria
- Department of Medical and Biological Science, Institute of Anatomic Pathology, University Hospital of Udine, Udine, Italy
| | - Stefania Marzinotto
- Department of Medical and Biological Science, Institute of Anatomic Pathology, University Hospital of Udine, Udine, Italy
| | - Luca De Marchi
- Department of Medical and Biological Science, Institute of Anatomic Pathology, University Hospital of Udine, Udine, Italy
| | - Vittorio Giacomarra
- Division of Otorhinolaryngology, Sant' Antonio Abate Hospital, Tolmezzo, Italy
| | - Silvio Boria
- Division of Otorhinolaryngology, Sant' Antonio Abate Hospital, Tolmezzo, Italy
| | - Corrado Rubini
- Department of Pathologic Anatomy and Histopathology, Marche Polytechnic University, Ancona, Italy
| | | | - Carla Di Loreto
- Department of Medical and Biological Science, Institute of Anatomic Pathology, University Hospital of Udine, Udine, Italy
| | - Laura Mariuzzi
- Department of Medical and Biological Science, Institute of Anatomic Pathology, University Hospital of Udine, Udine, Italy
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Ghannam A, Sellier P, Defendi F, Favier B, Charignon D, López-Lera A, López-Trascasa M, Ponard D, Drouet C. C1 inhibitor function using contact-phase proteases as target: evaluation of an innovative assay. Allergy 2015; 70:1103-11. [PMID: 26010015 DOI: 10.1111/all.12657] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Controlling prekallikrein activation by C1 inhibitor (C1Inh) represents the most essential mechanism for angioedema patient protection. C1Inh function in the plasma is usually measured based on the residual activity of the C1s protease not involved in the pathological process. We have hereby proposed an alternative enzymatic measurement of C1Inh function based on contact-phase activation and correlation with angioedema diagnostic requirements. METHODS The contact phase was reconstituted using the purified components, with C1Inh standard or plasma sample. The kinetics of the amidase activity were monitored using Pro-Phe-Arg-pNA, independently of alpha2-macroglobulin. We prevented any interference from a possible high plasma kininogenase activity by preincubating the samples with protease inhibitor. Receiver operating characteristics (ROC) were used to calculate the assay's diagnostic performance. RESULTS The calibration curve was built using C1Inh standard (threshold limit 0.10 × 10(-3) U, i.e., 0.2 pmol), and C1Inh function was quantified in the sample, with a reference interval established based on healthy individuals (n = 281; men: 0.61-1.10 U/ml, median: 0.85 U/ml; women: 0.42-1.08 U/ml, median: 0.74 U/ml). The median values of female donors were lower than those of the others due to estrogen, yet C1Inh function remained within the reference interval. The ROC curve calculation provided the following optimum diagnostic cutoff values: women 0.36 U/ml (area under curve [AUC]: 0.99; sensitivity: 93.48%; specificity: 99.37%); and men 0.61 U/ml (AUC: 1; sensitivity: 100.0%; specificity: 100.0%). CONCLUSION The performance outcome provided features suitable for angioedema diagnostic or follow-up. Established by means of the kinin formation process, this assay should be preferred over the method based on a C1s protease target.
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Affiliation(s)
- A. Ghannam
- GREPI/AGIM CNRS FRE 3405; Université Joseph Fourier; Grenoble France
- KininX SAS; Grenoble France
| | - P. Sellier
- GREPI/AGIM CNRS FRE 3405; Université Joseph Fourier; Grenoble France
- KininX SAS; Grenoble France
| | - F. Defendi
- GREPI/AGIM CNRS FRE 3405; Université Joseph Fourier; Grenoble France
- Centre de Référence des Angioedèmes CREAK; CHU Grenoble; Grenoble France
| | - B. Favier
- GREPI/AGIM CNRS FRE 3405; Université Joseph Fourier; Grenoble France
| | - D. Charignon
- GREPI/AGIM CNRS FRE 3405; Université Joseph Fourier; Grenoble France
- Centre de Référence des Angioedèmes CREAK; CHU Grenoble; Grenoble France
| | - A. López-Lera
- Unidad de Inmunología; Hospital Universitario La Paz/IdiPAZ; Madrid Spain
- Centro de Investigación Biomédica en Red (CIBERER U-754); Madrid Spain
| | - M. López-Trascasa
- Unidad de Inmunología; Hospital Universitario La Paz/IdiPAZ; Madrid Spain
- Centro de Investigación Biomédica en Red (CIBERER U-754); Madrid Spain
| | - D. Ponard
- Centre de Référence des Angioedèmes CREAK; CHU Grenoble; Grenoble France
| | - C. Drouet
- GREPI/AGIM CNRS FRE 3405; Université Joseph Fourier; Grenoble France
- Centre de Référence des Angioedèmes CREAK; CHU Grenoble; Grenoble France
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Xia L, Zhang J, Cui C, Bi X, Xiong J, Yu H, An Z, Luo W, Xia N. In vitro affinity maturation and characterization of anti-P24 antibody for HIV diagnostic assay. J Biochem 2015; 158:531-8. [PMID: 26163519 DOI: 10.1093/jb/mvv070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 06/06/2015] [Indexed: 11/13/2022] Open
Abstract
P24 antigen is the main structural protein of HIV-1, its detection provide a means to aid the early diagnosis of HIV-1 infection. The aim of this study was to improve the selectivity and sensitivity of the HIV P24 diagnostic assay by developing a cohort of 9E8 affinity-matured antibodies through in vitro phage affinity maturation which was performed by complementarity determining region (CDR)-hot spot mutagenesis strategy. Antibody 9E8-491 had an affinity constant of 5.64 × 10(-11) M, which was 5.7-fold higher than that of the parent antibody (9E8). Furthermore, the affinity, sensitivity and specificity of 9E8-491 were higher than those of 9E8, which indicate that 9E8-491 is a good candidate detection antibody for HIV P24 assay. Structure analysis of matured variants revealed that most hydrogen bonds resided in HCDR3. Among the antibody-antigen predicted binding residues, Tyr(100A/100B) was the original conserved residue that was commonly present in HCDR3 of 9E8 and variants. Arg(100)/Asp(100C) was the major variant substitution that most likely influenced the binding differences among variants and 9E8 monoclonal antibody. Both efficient library panning and predicted structural data were in agreement that the binding residues were mostly located in HCDR3 and enabled identification of key residues that influence antibody affinity.
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Affiliation(s)
- Lin Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and
| | - Juan Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and
| | - Chuanjia Cui
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and
| | - Xingjian Bi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and
| | - Junhui Xiong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and
| | - Zhiqiang An
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and Texas Therapeutics Institute, The Brown Foundation of Molecular Medicine, University of Texas Health Science Center at Houston, Houston TX 77030, USA
| | - Wenxin Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, Xiamen University, Xiamen 361105, China and
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Abstract
In Alzheimer's disease (AD) transgenic mice, activation of synaptogenic protein kinase C ε (PKCε) was found to prevent synaptotoxic amyloid-β (Aβ)-oligomer elevation, PKCε deficits, early synaptic loss, cognitive deficits, and amyloid plaque formation. In humans, to study the role of PKCε in the pathophysiology of AD and to evaluate its possible use as an early AD-biomarker, we examined PKCε and Aβ in the brains of autopsy-confirmed AD patients (n = 20) and age-matched controls (AC, n = 19), and in skin fibroblast samples from AD (n = 14), non-AD dementia patients (n = 14), and AC (n = 22). Intraneuronal Aβ levels were measured immunohistochemically (using an Aβ-specific antibody) in hippocampal pyramidal cells of human autopsy brains. PKCε was significantly lower in the hippocampus and temporal pole areas of AD brains, whereas Aβ levels were significantly higher. The ratio of PKCε to Aβ in individual CA1 pyramidal cells was markedly lower in the autopsy AD brains versus controls. PKCε was inversely correlated with Aβ levels in controls, whereas in AD patients, PKCε showed no significant correlation with Aβ. In autopsy brains, PKCε decreased as the Braak score increased. Skin fibroblast samples from AD patients also demonstrated a deficit in PKCε compared to controls and an AD-specific change in the Aβ-oligomer effects on PKCε. Together, these data demonstrate that the relationship between Aβ levels and PKCε is markedly altered in AD patients' brains and skin fibroblasts, reflecting a loss of protective effect of PKCε against toxic Aβ accumulation. These changes of PKCε levels in human skin fibroblasts may provide an accurate, non-invasive peripheral AD biomarker.
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Affiliation(s)
- Tapan K Khan
- Blanchette Rockefeller Neurosciences Institute, Morgantown, WV, USA
| | - Abhik Sen
- Blanchette Rockefeller Neurosciences Institute, Morgantown, WV, USA
| | - Jarin Hongpaisan
- Blanchette Rockefeller Neurosciences Institute, Morgantown, WV, USA
| | - Chol S Lim
- Blanchette Rockefeller Neurosciences Institute, Morgantown, WV, USA
| | - Thomas J Nelson
- Blanchette Rockefeller Neurosciences Institute, Morgantown, WV, USA
| | - Daniel L Alkon
- Blanchette Rockefeller Neurosciences Institute, Morgantown, WV, USA
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Karasawa K, Sano Y, Arakawa H. Development of a novel telomerase assay using the PPDK-luciferin-luciferase detection system. LUMINESCENCE 2013; 29:52-7. [PMID: 23554164 DOI: 10.1002/bio.2501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/15/2012] [Accepted: 01/26/2013] [Indexed: 11/06/2022]
Abstract
Telomerase participates in malignant transformation or immortalization of cells, and has attracted attention as an anticancer drug screening and diagnostic tumor marker. We developed a novel telomerase assay called the PPDK-luciferin-luciferase system bioluminescence assay (PLLBA) using pyruvate phosphate dikinase (PPDK). In this assay, pyrophosphate produced by the telomerase reaction and polymerase chain reaction (PCR) is converted to ATP by PPDK, and ATP is detected by the firefly luciferin-luciferase reaction. In this work, telomerase substrate was obtained in accordance with the telomeric repeat amplification protocol (TRAP). Telomerase-positive (500 cells/assay), -inactive (heated for 10 min at 85 °C) and -negative (only Chaps lysis buffer) samples were used. As a result, the findings clearly showed that the signal-to-noise (S/N) ratio of the positive cells was 39.5. After the telomerase reaction and PCR, PLLBA was completed ~ 120 s later. A high level of reproducibility was obtained with - coefficient of variation (CV) of 4.1% (positive cells). The detection limit for cells using telomerase was one cell per assay. This assay for telomerase activity was also shown to be adaptable to human cancer-derived cell lines.
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Affiliation(s)
- K Karasawa
- Department of Analytical Biochemistry, School of Pharmacy, Showa University, Tokyo, Japan
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