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Fan J, Yuan L, Liu Q, Tong C, Wang W, Xiao F, Liu B, Liu X. An ultrasensitive and simple assay for the Hepatitis C virus using a reduced graphene oxide-assisted hybridization chain reaction. Analyst 2019; 144:3972-3979. [DOI: 10.1039/c9an00179d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hepatitis C virus (HCV) is a major cause of chronic liver disease, which affects 2–3% of the world population.
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Affiliation(s)
- Jialong Fan
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Liqun Yuan
- People's Hospital of Hunan Province
- Changsha
- China
| | - Qingxin Liu
- Jiangsu Vocational College of Agriculture and Forestry
- China; College of Veterinary Medicine
- Nanjing Agricultural University
- Jurong
- Nanjing
| | - Chunyi Tong
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Wenmiao Wang
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Feng Xiao
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Bin Liu
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
| | - Xuanming Liu
- College of Biology
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation
- Hunan University
- Changsha
- China
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A Multiplex PCR/LDR Assay for Viral Agents of Diarrhea with the Capacity to Genotype Rotavirus. Sci Rep 2018; 8:13215. [PMID: 30181651 PMCID: PMC6123451 DOI: 10.1038/s41598-018-30301-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Rotavirus and noroviruses are major causes of diarrhea. Variable rotavirus vaccination efficacy in Africa and Asia is multifactorial, including the diversity of circulating strains and viral co-infection. We describe a multiplexed assay that detects and genotypes viruses from stool specimens. It includes a one-step reverse transcriptase PCR reaction, a ligase detection reaction (LDR), then hybridization of fluorescent products to micro-beads. In clinical samples it detects rotavirus, caliciviruses (sapovirus and norovirus), mixed infections, and genotypes or genogroups of rotaviruses and noroviruses, respectively. The assay also has the capacity to detect hepatitis A. The assay was validated on reference isolates and 296 stool specimens from the US and Ghana. The assay was 97% sensitive and 100% specific. The genogroup was concordant in 100% of norovirus, and the genotype in 91% and 89% of rotavirus G- and P-types, respectively. Two rare rotavirus strains, G6P[6] and G6P[8], were detected in stool specimens from Ghana. The high-throughput assay is sensitive, specific, and may be of utility in the epidemiological surveillance for rare and emerging viral strains post-rotavirus vaccine implementation.
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Gibriel AA, Adel O. Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:66-90. [PMID: 28927538 PMCID: PMC7108312 DOI: 10.1016/j.mrrev.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/24/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023]
Abstract
Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.
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Affiliation(s)
- Abdullah A Gibriel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt.
| | - Ola Adel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
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Babu B, Jeyaprakash A, Jones D, Schubert TS, Baker C, Washburn BK, Miller SH, Poduch K, Knox GW, Ochoa-Corona FM, Paret ML. Development of a rapid, sensitive TaqMan real-time RT-PCR assay for the detection of Rose rosette virus using multiple gene targets. J Virol Methods 2016; 235:41-50. [PMID: 27210549 DOI: 10.1016/j.jviromet.2016.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 05/02/2016] [Accepted: 05/15/2016] [Indexed: 12/30/2022]
Abstract
Rose rosette virus (RRV), belonging to the genus Emaravirus, is a highly destructive pathogen that causes rose rosette disease. The disease is a major concern for the rose industry in the U.S. due to the lack of highly sensitive methods for early detection of RRV. This is critical, as early identification of the infected plants and eradication is necessary in minimizing the risks associated with the spread of the disease. A highly reliable, specific and sensitive detection assay is thus required to test and confirm the presence of RRV in suspected plant samples. In this study a TaqMan real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for the detection of RRV from infected roses, utilizing multiple gene targets. Four pairs of primers and probes; two of them (RRV_2-1 and RRV_2-2) based on the consensus sequences of the glycoprotein gene (RNA2) and the other two (RRV_3-2 and RRV_3-5) based on the nucleocapsid gene (RNA3) were designed. The specificity of the primers and probes was evaluated against other representative viruses infecting roses, belonging to the genera Alfamovirus, Cucumovirus, Ilarvirus, Nepovirus, Tobamovirus, and Tospovirus and one Emaravirus (Wheat mosaic virus). Dilution assays using the in vitro transcripts (spiked with total RNA from healthy plants, and non-spiked) showed that all the primers and probes are highly sensitive in consistently detecting RRV with a detection limit of 1 fg. Testing of the infected plants over a period of time (three times in monthly intervals) indicated high reproducibility, with the primer/probe RRV_3-5 showing 100% positive detection, while RRV_2-1, RRV_2-2 and RRV_3-2 showed 90% positive detection. The developed real-time RT-PCR assay is reliable, highly sensitive, and can be easily used in diagnostic laboratories for testing and confirmation of RRV.
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Affiliation(s)
- Binoy Babu
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States.
| | - Ayyamperumal Jeyaprakash
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Debra Jones
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Timothy S Schubert
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Carlye Baker
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, United States
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Steven H Miller
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Kristina Poduch
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, United States
| | - Gary W Knox
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States
| | - Francisco M Ochoa-Corona
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States
| | - Mathews L Paret
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, United States.
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Das S, Rundell MS, Mirza AH, Pingle MR, Shigyo K, Garrison AR, Paragas J, Smith SK, Olson VA, Larone DH, Spitzer ED, Barany F, Golightly LM. A Multiplex PCR/LDR Assay for the Simultaneous Identification of Category A Infectious Pathogens: Agents of Viral Hemorrhagic Fever and Variola Virus. PLoS One 2015; 10:e0138484. [PMID: 26381398 PMCID: PMC4575071 DOI: 10.1371/journal.pone.0138484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 08/30/2015] [Indexed: 02/04/2023] Open
Abstract
CDC designated category A infectious agents pose a major risk to national security and require special action for public health preparedness. They include viruses that cause viral hemorrhagic fever (VHF) syndrome as well as variola virus, the agent of smallpox. VHF is characterized by hemorrhage and fever with multi-organ failure leading to high morbidity and mortality. Smallpox, a prior scourge, has been eradicated for decades, making it a particularly serious threat if released nefariously in the essentially non-immune world population. Early detection of the causative agents, and the ability to distinguish them from other pathogens, is essential to contain outbreaks, implement proper control measures, and prevent morbidity and mortality. We have developed a multiplex detection assay that uses several species-specific PCR primers to generate amplicons from multiple pathogens; these are then targeted in a ligase detection reaction (LDR). The resultant fluorescently-labeled ligation products are detected on a universal array enabling simultaneous identification of the pathogens. The assay was evaluated on 32 different isolates associated with VHF (ebolavirus, marburgvirus, Crimean Congo hemorrhagic fever virus, Lassa fever virus, Rift Valley fever virus, Dengue virus, and Yellow fever virus) as well as variola virus and vaccinia virus (the agent of smallpox and its vaccine strain, respectively). The assay was able to detect all viruses tested, including 8 sequences representative of different variola virus strains from the CDC repository. It does not cross react with other emerging zoonoses such as monkeypox virus or cowpox virus, or six flaviviruses tested (St. Louis encephalitis virus, Murray Valley encephalitis virus, Powassan virus, Tick-borne encephalitis virus, West Nile virus and Japanese encephalitis virus).
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Affiliation(s)
- Sanchita Das
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Mark S. Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aashiq H. Mirza
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Maneesh R. Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Kristi Shigyo
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jason Paragas
- Integrated Research Facility, Division of Clinical Research, NIAID, NIH, Fort Detrick, Maryland, United States of America
| | - Scott K. Smith
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victoria A. Olson
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Davise H. Larone
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, United States of America
| | - Eric D. Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York, United States of America
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Linnie M. Golightly
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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Rundell MS, Pingle M, Das S, Hussain A, Ocheretina O, Charles M, Larone DH, Spitzer ED, Golightly L, Barany F. A multiplex PCR/LDR assay for simultaneous detection and identification of the NIAID category B bacterial food and water-borne pathogens. Diagn Microbiol Infect Dis 2014; 79:135-40. [PMID: 24709368 DOI: 10.1016/j.diagmicrobio.2014.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/17/2014] [Accepted: 02/26/2014] [Indexed: 01/06/2023]
Abstract
Enteric pathogens that cause gastroenteritis remain a major global health concern. The goal of this study was to develop a multiplex PCR/ligation detection reaction (LDR) assay for the detection of all NIAID category B bacterial food and water-borne pathogens directly from stool specimens. To validate the PCR/LDR assay, clinical isolates of Campylobacter spp., Vibrio spp., Shigella spp., Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica, and diarrheagenic Escherichia coli were tested. The sensitivity and specificity of the assay were assessed using a large number of seeded culture-negative stool specimens and a smaller set of clinical specimens from Haiti. The overall sensitivity ranged from 91% to 100% (median 100%) depending on the species. For the majority of organisms, the sensitivity was 100%. The overall specificity based on initial testing ranged from 98% to 100% depending on the species. After additional testing of discordant samples, the lowest specificity was 99.4%. PCR/LDR detected additional category B agents (particularly diarrheagenic E. coli) in 11/40 specimens from Haiti that were culture-positive for V. cholerae and in approximately 1% of routine culture-negative stool specimens from a hospital in New York. This study demonstrated the ability of the PCR/LDR assay to detect a large comprehensive panel of category B enteric bacterial pathogens as well as mixed infections. This type of assay has the potential to provide earlier warnings of possible public health threats and more accurate surveillance of food and water-borne pathogens.
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Affiliation(s)
- Mark S Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Maneesh Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Sanchita Das
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Aashiq Hussain
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Oksana Ocheretina
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021; Groupe Haitien d'Étude du Sarcome de Kaposi et des Infections Opportunistes, Port-Au-Prince, Haiti
| | - Macarthur Charles
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021; Groupe Haitien d'Étude du Sarcome de Kaposi et des Infections Opportunistes, Port-Au-Prince, Haiti
| | - Davise H Larone
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Eric D Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, NY 11794
| | - Linnie Golightly
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021.
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Sambri V, Capobianchi MR, Cavrini F, Charrel R, Donoso-Mantke O, Escadafal C, Franco L, Gaibani P, Gould EA, Niedrig M, Papa A, Pierro A, Rossini G, Sanchini A, Tenorio A, Varani S, Vázquez A, Vocale C, Zeller H. Diagnosis of west nile virus human infections: overview and proposal of diagnostic protocols considering the results of external quality assessment studies. Viruses 2013; 5:2329-48. [PMID: 24072061 PMCID: PMC3814591 DOI: 10.3390/v5102329] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 08/28/2013] [Accepted: 09/09/2013] [Indexed: 01/14/2023] Open
Abstract
West Nile virus, genus Flavivirus, is transmitted between birds and occasionally other animals by ornithophilic mosquitoes. This virus also infects humans causing asymptomatic infections in about 85% of cases and <1% of clinical cases progress to severe neuroinvasive disease. The virus also presents a threat since most infections remain unapparent. However, the virus contained in blood and organs from asymptomatically infected donors can be transmitted to recipients of these infectious tissues. This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for ‘Imported’ Viral Diseases (ENIVD).
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Affiliation(s)
- Vittorio Sambri
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-331-8687352
| | - Maria R. Capobianchi
- National Institute for Infectious Diseases (INMI) “L. Spallanzani”, Rome 00149, Italy; E-Mail:
| | - Francesca Cavrini
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Rémi Charrel
- UMR_D 190 “Emergence des Pathologies Virales”, APHM Public Hospitals of Marseille, EHESP French School of Public Health & IHU Mediterranee Infection, IRD French Institute of Research for Development, Aix Marseille University, 13005, Marseille, France; E-Mail: (R.C.)
| | - Olivier Donoso-Mantke
- Centre for Biological Threats and Special Pathogens (ZBS-1), Robert Koch-Institut, Berlin 13353, Germany; E-Mails: (O.D.-M.); (C.E.); (M.N.); (A.S.)
| | - Camille Escadafal
- Centre for Biological Threats and Special Pathogens (ZBS-1), Robert Koch-Institut, Berlin 13353, Germany; E-Mails: (O.D.-M.); (C.E.); (M.N.); (A.S.)
| | - Leticia Franco
- National Microbiology Centre, Instituto de Salud Carlos III, Madrid 28220, Spain; E-Mails: (L.F.); (A.T.); (A.V.)
| | - Paolo Gaibani
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Ernest A. Gould
- UMR_D 190 “Emergence des Pathologies Virales”, APHM Public Hospitals of Marseille, EHESP French School of Public Health & IHU Mediterranee Infection, IRD French Institute of Research for Development, Aix Marseille University, 13005, Marseille, France; E-Mail: (R.C.)
- NERC Centre for Ecology and Hydrology, Wallingford, Oxon OX10 8BB, UK; E-Mail: (E.A.G.)
| | - Matthias Niedrig
- Centre for Biological Threats and Special Pathogens (ZBS-1), Robert Koch-Institut, Berlin 13353, Germany; E-Mails: (O.D.-M.); (C.E.); (M.N.); (A.S.)
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; E-Mail:
| | - Anna Pierro
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Giada Rossini
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Andrea Sanchini
- Centre for Biological Threats and Special Pathogens (ZBS-1), Robert Koch-Institut, Berlin 13353, Germany; E-Mails: (O.D.-M.); (C.E.); (M.N.); (A.S.)
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control, Stockholm 171 83, Sweden
| | - Antonio Tenorio
- National Microbiology Centre, Instituto de Salud Carlos III, Madrid 28220, Spain; E-Mails: (L.F.); (A.T.); (A.V.)
| | - Stefania Varani
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Ana Vázquez
- National Microbiology Centre, Instituto de Salud Carlos III, Madrid 28220, Spain; E-Mails: (L.F.); (A.T.); (A.V.)
| | - Caterina Vocale
- Operative Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, S. Orsola-Malpighi University Hospital, Bologna 40138, Italy; E-Mails: (V.S.); (F.C.); (P.G.); (A.P.); (G.R.); (S.V.); (C.V.)
| | - Herve Zeller
- European Centre for Disease Prevention and Control, Stockholm 171 83, Sweden; E-Mail:
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Yao J, Flack K, Ding L, Zhong W. Tagging the rolling circle products with nanocrystal clusters for cascade signal increase in the detection of miRNA. Analyst 2013; 138:3121-5. [DOI: 10.1039/c3an00398a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Chicken prolactin (PRL) is a physiological candidate gene for egg production. Variations of T8052C and G8113C in exon 5 of PRL gene may associate with chicken egg production. The objective of the study was to investigate the association of these two single nucleotide polymorphisms in PRL gene with egg production of Recessive White chickens and Qingyuan Partridge chickens. Genotyping was performed by polymerase chain reaction-ligase detection reaction (PCR-LDR) method. The T8052C and G8113C of PRL were significantly associated with age at first egg (AFE) and total egg number at 300 days of age (EN 300). A significant association was also found between T8052C-G8113C haplotypes and AFE as well as EN300, the H2H3 was the most advantageous diplotype for egg production. We putatively drew the conclusion that these two SNPs in PRL gene as well as their haplotypes could be used as the potential molecular markers for egg production traits in chicken.
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Armstrong PM, Prince N, Andreadis TG. Development of a multi-target TaqMan assay to detect eastern equine encephalitis virus variants in mosquitoes. Vector Borne Zoonotic Dis 2012; 12:872-6. [PMID: 22835151 DOI: 10.1089/vbz.2012.1008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Disease outbreaks caused by eastern equine encephalitis virus (EEEV; Togaviridae, Alphavirus) may be prevented by implementing effective surveillance and intervention strategies directed against the mosquito vector. Methods for EEEV detection in mosquitoes include a real-time reverse transcriptase PCR technique (TaqMan assay), but we report its failure to detect variants isolated in Connecticut in 2011, due to a single base-pair mismatch in the probe-binding site. To improve the molecular detection of EEEV, we developed a multi-target TaqMan assay by adding a second primer/probe set to provide redundant targets for EEEV detection. The multi-target TaqMan assay had similar performance characteristics to the conventional assay, but also detected newly-evolving strains of EEEV. The approach described here increases the reliability of the TaqMan assay by creating back-up targets for virus detection without sacrificing sensitivity or specificity.
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Affiliation(s)
- Philip M Armstrong
- Center for Vector Biology and Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, Connecticut 06504, USA.
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Yi P, Lu W, Guo J, Liu Q, Chen Z, Han J, Li L. Development of a PCR/ligase detection reaction/nanogold-based universal array approach for the detection of low-abundant DNA point mutations. Cell Biochem Biophys 2012; 61:629-36. [PMID: 21847634 DOI: 10.1007/s12013-011-9248-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The aim of this study was to investigate the feasibility of combining PCR and ligase detection reaction (LDR) with a novel nano-gold-based universal array for the detection of low abundance point mutations from fetal DNA in maternal plasma samples. The sequence with the target point mutation was first amplified by PCR and then used as a template for LDR in which the upstream specific primer contains a tag sequence at the 5'-end. After hybridization to the probes of a universal array containing anti-tag sequences, the ligated products were bound to streptavidin-labeled nano-gold particles and the hybridization signals were amplified by silver staining. The PCR/LDR/universal array was first tested for sensitivity with nano-gold-based detection, and then this system was applied to detect the low abundance specific mutation IVS2 654(C→T) of the β-globin gene in a model using maternal plasma samples. The nano-gold-based method unambiguously identified a single mutation at a sensitivity of 1:1000. This approach was applied to detect the paternally inherited IVS2 654(C→T) mutation from thirty maternal plasma samples. The results were consistent with those obtained by PCR/reverse dot blot of amniotic fluid cell DNA. The PCR/LDR/nano-gold-based universal array is able to detect low-abundance point mutations with high sensitivity.
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Affiliation(s)
- Ping Yi
- Department of Obstetrics and Gynecology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, 10 Changjiangzhilu, Daping, Yuzhong District, Chongqing 400042, People's Republic of China
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12
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De Filette M, Ulbert S, Diamond M, Sanders NN. Recent progress in West Nile virus diagnosis and vaccination. Vet Res 2012; 43:16. [PMID: 22380523 PMCID: PMC3311072 DOI: 10.1186/1297-9716-43-16] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 03/01/2012] [Indexed: 01/22/2023] Open
Abstract
West Nile virus (WNV) is a positive-stranded RNA virus belonging to the Flaviviridae family, a large family with 3 main genera (flavivirus, hepacivirus and pestivirus). Among these viruses, there are several globally relevant human pathogens including the mosquito-borne dengue virus (DENV), yellow fever virus (YFV), Japanese encephalitis virus (JEV) and West Nile virus (WNV), as well as tick-borne viruses such as tick-borne encephalitis virus (TBEV). Since the mid-1990s, outbreaks of WN fever and encephalitis have occurred throughout the world and WNV is now endemic in Africa, Asia, Australia, the Middle East, Europe and the Unites States. This review describes the molecular virology, epidemiology, pathogenesis, and highlights recent progress regarding diagnosis and vaccination against WNV infections.
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Affiliation(s)
- Marina De Filette
- Laboratory of Gene Therapy, Faculty of Veterinary Sciences, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium.
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13
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Hasib L, Dilcher M, Hufert F, Meyer-König U, Weidmann M. Development of a flow-through [corrected] microarray based reverse transcriptase multiplex ligation-dependent probe amplification assay for the detection of European Bunyaviruses. [corrected]. Mol Biotechnol 2012; 49:176-86. [PMID: 21390485 PMCID: PMC3172416 DOI: 10.1007/s12033-011-9389-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is suspected that apart from tick-borne encephalitis virus several additional European Arboviruses such as the sandfly borne Toscana virus, sandfly fever Sicilian virus and sandfly fever Naples virus, mosquito-borne Tahyna virus, Inkoo virus, Batai virus and tick-borne Uukuniemi virus cause aseptic meningo-encephalitis or febrile disease in Europe. Currently, the microarray technology is developing rapidly and there are many efforts to apply it to infectious diseases diagnostics. In order to arrive at an assay system useful for high throughput analysis of samples from aseptic meningo-encephalitis cases the authors developed a combined multiplex ligation-dependent probe amplification and flow-through microarray assay for the detection of European Bunyaviruses. These results show that this combined assay indeed is highly sensitive, and specific for the accurate detection of multiple viruses.
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Affiliation(s)
- Lekbira Hasib
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57 37075, Göttingen, Germany.
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Jiang Y, Guo Y, Wang P, Dong Q, Opriessnig T, Cheng J, Xu H, Ding X, Guo J. A novel diagnostic platform based on multiplex ligase detection–PCR and microarray for simultaneous detection of swine viruses. J Virol Methods 2011; 178:171-8. [DOI: 10.1016/j.jviromet.2011.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 08/30/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
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15
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A multiplex nested PCR assay for the simultaneous detection of genetically modified soybean, maize and rice in highly processed products. Food Control 2011. [DOI: 10.1016/j.foodcont.2011.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Abstract
The genus Flavivirus includes major pathogens such as dengue, yellow fever, Japanese encephalitis, West Nile and tick-borne encephalitis viruses. Molecular amplification assays for the diagnosis of flaviviruses have been developed in the last decades. These assays were formerly based on reverse transcriptase PCR, while in recent years the real-time reverse transcriptase PCR format has taken a predominant role. In this article, we focus on the more recent developments for the molecular diagnosis of flaviviruses, with special attention to those based on new methodologies such as nucleic acid sequence-based amplification or loop-mediated isothermal amplification techniques. These new approaches may provide a good profile of sensitivity and specificity and offer a real chance to implement flavivirus molecular diagnosis in clinical and point-of-care settings.
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Affiliation(s)
| | - Pranav Patel
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Sonja Linke
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Katharina Achazi
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
| | - Matthias Niedrig
- Robert Koch-Institut, Center for Biological Security 1, Highly Pathogenic Viruses, Nordufer 20, 13353 Berlin, Germany
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17
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García-Cañas V, Mondello M, Cifuentes A. Combining ligation reaction and capillary gel electrophoresis to obtain reliable long DNA probes. J Sep Sci 2011; 34:1011-9. [PMID: 21404441 DOI: 10.1002/jssc.201000826] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 01/24/2011] [Accepted: 02/01/2011] [Indexed: 11/12/2022]
Abstract
New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target sequences hybridization. Depending on the molecular technique, the length of DNA probes ranges from 40 to 450 nucleotides, solid-phase chemical synthesis being the strategy generally used for their production. However, the fidelity of chemical synthesis of DNA decreases for larger DNA probes. Defects in the oligonucleotide sequence result in the loss of hybridization efficiency, affecting the sensitivity and selectivity of the amplification method. In this work, an enzymatic procedure has been developed as an alternative to solid-phase chemical synthesis for the production of long oligonucleotides. The enzymatic procedure for probe production was based on ligation of short DNA sequences. Long DNA probes were obtained from smaller oligonucleotides together with a short sequence that acts as bridge stabilizing the molecular complex for DNA ligation. The ligation reactions were monitored by capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) using a bare fused-silica capillary. The capillary gel electrophoresis-LIF method demonstrated to be very useful and informative for the characterization of the ligation reaction, providing important information about the nature of some impurities, as well as for the fine optimization of the ligation conditions (i.e. ligation cycles, oligonucleotide and enzyme concentration). As a result, the yield and quality of the ligation product were highly improved. The in-lab prepared DNA probes were used in a novel multiplex ligation-dependent genome amplification (MLGA) method for the detection of genetically modified maize in samples. The great possibilities of the whole approach were demonstrated by the specific and sensitive detection of transgenic maize at percentages lower than 1%.
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18
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Shin GW, Hwang HS, Chung B, Jung GY. Recent developments in CE-based detection methods for food-borne pathogens. Electrophoresis 2010; 31:2137-53. [DOI: 10.1002/elps.200900682] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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Yi P, Chen Z, Yu L, Zheng Y, Liu G, Xie H, Zhou Y, Zheng X, Han J, Li L. Development of a PCR/LDR/capillary electrophoresis assay with potential for the detection of a beta-thalassemia fetal mutation in maternal plasma. J Matern Fetal Neonatal Med 2010; 23:920-7. [DOI: 10.3109/14767050903387060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Yan J, Li Z, Liu C, Cheng Y. Simple and sensitive detection of microRNAs with ligase chain reaction. Chem Commun (Camb) 2010; 46:2432-4. [PMID: 20379549 DOI: 10.1039/b923521c] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and sensitive miRNA assay was developed with ligase chain reaction (LCR) based on specific ligation of DNA probes by using miRNAs as the templates.
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Affiliation(s)
- Jingli Yan
- Key Laboratory of Medical Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province, P. R. China
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Pingle M, Rundell M, Das S, Golightly LM, Barany F. PCR/LDR/universal array platforms for the diagnosis of infectious disease. Methods Mol Biol 2010; 632:141-57. [PMID: 20217576 DOI: 10.1007/978-1-60761-663-4_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections.
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Affiliation(s)
- Maneesh Pingle
- Department of Microbiology, Weill Medical College, Cornell University, New York, NY, USA.
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22
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Multiplex PCR-ligation detection reaction assay for simultaneous detection of drug resistance and toxin genes from Staphylococcus aureus, Enterococcus faecalis, and Enterococcus faecium. J Clin Microbiol 2009; 48:277-80. [PMID: 19864481 DOI: 10.1128/jcm.01411-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex PCR-ligation detection reaction (PCR-LDR) assay was developed for rapid detection of methicillin, tetracycline, and vancomycin resistance, as well as toxic shock toxin and Panton-Valentine leukocidin. The assay was tested on 470 positive blood culture bottles containing Staphylococcus aureus or enterococci. PCR-LDR exhibited a sensitivity and specificity of > or = 98% for all components except tetracycline resistance, which had a sensitivity of 94.7%. Rapid and sensitive detection of antimicrobial resistance and virulence genes could help guide therapy and appropriate infection control measures.
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Rapid and accurate in vitro assays for detection of West Nile virus in blood and tissues. Transfus Med Rev 2009; 23:146-54. [PMID: 19304115 DOI: 10.1016/j.tmrv.2008.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
West Nile virus (WNV) is a mosquito-borne single-stranded RNA virus, which has relatively recently emerged as a blood transfusion and organ transplantation transmissible pathogen. Low levels of WNV (viremia) are found in asymptomatic blood transfusion or cell/tissue donors with an infection, which poses a health threat to recipients. Since the introduction of nucleic acid testing (NAT) in 2003, many changes have occurred in the field of WNV detection and diagnosis. This review will focus on the recent progress in the in vitro assays for rapid and accurate detection of WNV in blood and tissues.
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Detection and serotyping of dengue virus in serum samples by multiplex reverse transcriptase PCR-ligase detection reaction assay. J Clin Microbiol 2008; 46:3276-84. [PMID: 18685000 DOI: 10.1128/jcm.00163-08] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The detection and successful typing of dengue virus (DENV) from patients with suspected dengue fever is important both for the diagnosis of the disease and for the implementation of epidemiologic control measures. A technique for the multiplex detection and typing of DENV serotypes 1 to 4 (DENV-1 to DENV-4) from clinical samples by PCR-ligase detection reaction (LDR) has been developed. A serotype-specific PCR amplifies the regions of genes C and E simultaneously. The two amplicons are targeted in a multiplex LDR, and the resultant fluorescently labeled ligation products are detected on a universal array. The assay was optimized using 38 DENV strains and was evaluated with 350 archived acute-phase serum samples. The sensitivity of the assay was 98.7%, and its specificity was 98.4%, relative to the results of real-time PCR. The detection threshold was 0.017 PFU for DENV-1, 0.004 PFU for DENV-2, 0.8 PFU for DENV-3, and 0.7 PFU for DENV-4. The assay is specific; it does not cross-react with the other flaviviruses tested (West Nile virus, St. Louis encephalitis virus, Japanese encephalitis virus, Kunjin virus, Murray Valley virus, Powassan virus, and yellow fever virus). All but 1 of 26 genotypic variants of DENV serotypes in a global DENV panel from different geographic regions were successfully identified. The PCR-LDR assay is a rapid, sensitive, specific, and high-throughput technique for the simultaneous detection of all four serotypes of DENV.
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