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Torii S, Furumai H, Katayama H. Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143067. [PMID: 33131851 PMCID: PMC7568484 DOI: 10.1016/j.scitotenv.2020.143067] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 05/05/2023]
Abstract
The primary concentration and molecular process are critical to implement wastewater-based epidemiology for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the previously developed methods were optimized for nonenveloped viruses. Few studies evaluated if the methods are applicable to the efficient recovery of enveloped viruses from various types of raw sewage. This study aims (1) to compare the whole process recovery of Pseudomonas phage φ6, a surrogate for enveloped viruses, among combinations of primary concentration [ultrafiltration (UF), electronegative membrane vortex (EMV), and polyethylene glycol precipitation (PEG)] and RNA extraction methods (spin column-based method using QIAamp Viral RNA Mini Kit and acid guanidinium thiocyanate-phenol-chloroform extraction using TRIzol reagent) for three types of raw sewage and (2) to test the applicability of the method providing the highest φ6 recovery to the detection of SARS-CoV-2 RNA. Among the tested combinations, PEG+TRIzol provided the highest φ6 recovery ratio of 29.8% to 49.8% (geometric mean). UF + QIAamp Viral RNA Mini Kit provided the second highest φ6 recovery of 6.4% to 35.8%. The comparable φ6 recovery was observed for UF + TRIzol (13.8-30.0%). PEG + QIAamp Viral RNA Mini Kit provided only 1.4% to 3.0% of φ6 recovery, while coliphage MS2, a surrogate for nonenveloped viruses, was recovered comparably with PEG + TRIzol. This indicated that the nonenveloped surrogate (MS2) did not necessarily validate the efficient recovery for enveloped viruses. EMV + QIAamp Viral RNA Mini Kit provided significantly different φ6 recovery (1.6-21%) among the types of raw sewage. Then, the applicability of modified PEG + TRIzol was examined for the raw sewage collected in Tokyo, Japan. Of the 12 grab samples, 4 were positive for SARS-CoV-2 CDC N1 and N3 assay. Consequently, PEG + TRIzol provided the highest φ6 recovery and allowed for the detection of SARS-CoV-2 RNA from raw sewage.
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Affiliation(s)
- Shotaro Torii
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Furumai
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
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Kang SJ, Jang CS, Son JM, Hong KW. Comparison of Seven Commercial TaqMan Master Mixes and Two Real-Time PCR Platforms Regarding the Rapid Detection of Porcine DNA. Food Sci Anim Resour 2021; 41:85-94. [PMID: 33506219 PMCID: PMC7810389 DOI: 10.5851/kosfa.2020.e80] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/19/2020] [Accepted: 09/11/2020] [Indexed: 12/23/2022] Open
Abstract
A pig-specific real-time PCR assay based on the mitochondrial ND5 gene was developed to detect porcine material in food and other products. To optimize the performance of assay, seven commercial TaqMan master mixes and two real-time PCR platforms (Applied Biosystems StepOnePlus and Bio-rad CFX Connect) were used to evaluate the limit of detection (LOD) as well as the PCR efficiency and specificity. The LODs and PCR efficiencies for the seven master mixes on two platforms were 0.5-5 pg/reaction and 84.96%-108.80%, respectively. Additionally, non-specific amplifications of DNA from other animal samples (human, dog, cow, and chicken) were observed for four master mixes. These results imply that the sensitivity and specificity of a real-time PCR assay may vary depending on master mix and platform used. The best combination of master mix and real-time PCR platform can accurately detect 0.5 pg porcine DNA, with a PCR efficiency of 100.49%.
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Affiliation(s)
- Soo Ji Kang
- Department of Food Science and Biotechnology, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Korea
| | - Chan Song Jang
- Department of Food Science and Biotechnology, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Korea
| | - Ji Min Son
- Department of Food Science and Biotechnology, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Korea
| | - Kwang Won Hong
- Department of Food Science and Biotechnology, College of Life Science and Biotechnology, Dongguk University, Goyang 10326, Korea
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Li H, Han X, Qiu W, Xu D, Wang Y, Yu M, Hu X, Zhuo R. Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress. PeerJ 2019; 7:e6741. [PMID: 31024765 PMCID: PMC6474334 DOI: 10.7717/peerj.6741] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/07/2019] [Indexed: 12/30/2022] Open
Abstract
Background The herb Sedum alfredii (S. alfredii) Hance is a hyperaccumulator of heavy metals (cadmium (Cd), zinc (Zn) and lead (Pb)); therefore, it could be a candidate plant for efficient phytoremediation. The GDSL esterase/lipase protein (GELP) family plays important roles in plant defense and growth. Although the GELP family members in a variety of plants have been cloned and analyzed, there are limited studies on the family's responses to heavy metal-stress conditions. Methods Multiple sequence alignments and phylogenetic analyses were performed according to the criteria described. A WGCNA was used to construct co-expression regulatory networks. The roots of S. alfredii seedlings were treated with 100 µM CdCl2 for qRT-PCR to analyze expression levels in different tissues. SaGLIP8 was transformed into the Cd sensitive mutant strain yeast Δycf1 to investigate its role in resistance and accumulation to Cd. Results We analyzed GELP family members from genomic data of S. alfredii. A phylogenetic tree divided the 80 identified family members into three clades. The promoters of the 80 genes contained certain elements related to abiotic stress, such as TC-rich repeats (defense and stress responsiveness), heat shock elements (heat stress) and MYB-binding sites (drought-inducibility). In addition, 66 members had tissue-specific expression patterns and significant responses to Cd stress. In total, 13 hub genes were obtained, based on an existing S. alfredii transcriptome database, that control 459 edge genes, which were classified into five classes of functions in a co-expression subnetwork: cell wall and defense function, lipid and esterase, stress and tolerance, transport and transcription factor activity. Among the hub genes, Sa13F.102 (SaGLIP8), with a high expression level in all tissues, could increase Cd tolerance and accumulation in yeast when overexpressed. Conclusion Based on genomic data of S. alfredii, we conducted phylogenetic analyses, as well as conserved domain, motif and expression profiling of the GELP family under Cd-stress conditions. SaGLIP8 could increase Cd tolerance and accumulation in yeast. These results indicated the roles of GELPs in plant responses to heavy metal exposure and provides a theoretical basis for further studies of the SaGELP family's functions.
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Affiliation(s)
- He Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China.,State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Wenmin Qiu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Dong Xu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Ying Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Miao Yu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Xianqi Hu
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
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4
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Picard-Meyer E, Peytavin de Garam C, Schereffer JL, Robardet E, Cliquet F. Evaluation of six TaqMan RT-rtPCR kits on two thermocyclers for the reliable detection of rabies virus RNA. J Vet Diagn Invest 2018; 31:47-57. [PMID: 30541405 DOI: 10.1177/1040638718818223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rabies is diagnosed postmortem in animals, based on tests prescribed by the World Organization for Animal Health (OIE), such as the fluorescent antibody test, the direct rapid immunohistochemistry test, or pan-lyssavirus PCR assays. Several reverse-transcription real-time PCR (RT-rtPCR) methods have been developed and validated for rapid and accurate detection of lyssaviruses. We evaluated the performance of 6 TaqMan RT-rtPCR kits using different commercial master mixes and 2 real-time thermocyclers. Changing the master mix overall did not influence the TaqMan RT-rtPCR performance, regardless of the thermocycler used. The limits of detection at the 95% confidence level were 18.1-25.8 copies/µL for the Rotor-Gene Q MDx thermocycler and 16.7-21.5 for the Mx3005P thermocycler. Excellent repeatability was demonstrated for rabies virus (RABV) RNA samples of 100, 50, and 25 copies/µL regardless of the thermocycler used. RABV field samples ( n = 35) isolated worldwide gave positive results using the most efficient of the 6 kits tested, with a copy number of 6.03 × 102 to 6.78 × 107 RNA copies per reaction. The TaqMan RT-rtPCR assay provides sensitive and rapid amplification of RABV RNA.
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Affiliation(s)
| | | | | | | | - Florence Cliquet
- ANSES Nancy Laboratory for Rabies and Wildlife, Malzéville, France
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Singh RK, Dhama K, Malik YS, Ramakrishnan MA, Karthik K, Khandia R, Tiwari R, Munjal A, Saminathan M, Sachan S, Desingu PA, Kattoor JJ, Iqbal HMN, Joshi SK. Ebola virus - epidemiology, diagnosis, and control: threat to humans, lessons learnt, and preparedness plans - an update on its 40 year's journey. Vet Q 2017; 37:98-135. [PMID: 28317453 DOI: 10.1080/01652176.2017.1309474] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 03/17/2017] [Indexed: 02/08/2023] Open
Abstract
Ebola virus (EBOV) is an extremely contagious pathogen and causes lethal hemorrhagic fever disease in man and animals. The recently occurred Ebola virus disease (EVD) outbreaks in the West African countries have categorized it as an international health concern. For the virus maintenance and transmission, the non-human primates and reservoir hosts like fruit bats have played a vital role. For curbing the disease timely, we need effective therapeutics/prophylactics, however, in the absence of any approved vaccine, timely diagnosis and monitoring of EBOV remains of utmost importance. The technologically advanced vaccines like a viral-vectored vaccine, DNA vaccine and virus-like particles are underway for testing against EBOV. In the absence of any effective control measure, the adaptation of high standards of biosecurity measures, strict sanitary and hygienic practices, strengthening of surveillance and monitoring systems, imposing appropriate quarantine checks and vigilance on trade, transport, and movement of visitors from EVD endemic countries remains the answer of choice for tackling the EBOV spread. Herein, we converse with the current scenario of EBOV giving due emphasis on animal and veterinary perspectives along with advances in diagnosis and control strategies to be adopted, lessons learned from the recent outbreaks and the global preparedness plans. To retrieve the evolutionary information, we have analyzed a total of 56 genome sequences of various EBOV species submitted between 1976 and 2016 in public databases.
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Affiliation(s)
- Raj Kumar Singh
- a ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Kuldeep Dhama
- b Division of Pathology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Yashpal Singh Malik
- c Division of Biological Standardization, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | | | - Kumaragurubaran Karthik
- e Divison of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Rekha Khandia
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Ruchi Tiwari
- g Department of Veterinary Microbiology and Immunology , College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura , India
| | - Ashok Munjal
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Mani Saminathan
- b Division of Pathology, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Swati Sachan
- h Immunology Section, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | | | - Jobin Jose Kattoor
- c Division of Biological Standardization, ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Hafiz M N Iqbal
- i School of Engineering and Science, Tecnologico de Monterrey , Monterrey , Mexico
| | - Sunil Kumar Joshi
- j Cellular Immunology Lab , Frank Reidy Research Center for Bioelectrics , School of Medical Diagnostics & Translational Sciences, Old Dominion University , Norfolk , VA , USA
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6
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Meli ML, Berger A, Willi B, Spiri AM, Riond B, Hofmann-Lehmann R. Molecular detection of feline calicivirus in clinical samples: A study comparing its detection by RT-qPCR directly from swabs and after virus isolation. J Virol Methods 2017; 251:54-60. [PMID: 28986291 DOI: 10.1016/j.jviromet.2017.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 08/31/2017] [Accepted: 10/01/2017] [Indexed: 10/18/2022]
Abstract
Feline caliciviruses (FCVs) are non-enveloped RNA viruses that exhibit high genetic variation. Two reverse transcription quantitative polymerase chain reaction (RT-qPCR) FCV assays (S1 and S2) were evaluated using samples from 300 field cats. The direct detection of FCV in swabs and after propagation in cell culture, as well as the influence of storage conditions, was assessed. FCV-RNA detectability on dry swabs was similar after storage at either 4°C or -20°C, but viral burdens were maintained for a longer time period when viral transport medium was used. A total of 97 (32%) samples was considered FCV PCR-positive. Of these, 81% and 77% tested positive directly from swabs using S1 and S2, respectively; 84% and 81% tested positive after enrichment in cell culture, respectively. Combined detection by RT-PCR directly from swabs and after VI was most sensitive (up to 96%). Neither of the methods alone were able to detect all FCV-positive samples. In conclusion, clinical samples should be collected in viral transport medium, stored at ≤4°C and processed as soon as possible. The combination of cell culture with RT-qPCR or detection directly from swabs using a combination of different RT-qPCR assays is recommended to reach a high sensitivity of FCV detection.
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Affiliation(s)
- Marina L Meli
- Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland; Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Alice Berger
- Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland; Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Barbara Willi
- Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland; Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Andrea M Spiri
- Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland; Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Barbara Riond
- Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland; Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
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7
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Liu L, Luo Y, Accensi F, Ganges L, Rodríguez F, Shan H, Ståhl K, Qiu HJ, Belák S. Pre-Clinical Evaluation of a Real-Time PCR Assay on a Portable Instrument as a Possible Field Diagnostic Tool: Experiences from the Testing of Clinical Samples for African and Classical Swine Fever Viruses. Transbound Emerg Dis 2016; 64:e31-e35. [PMID: 27311689 DOI: 10.1111/tbed.12538] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Indexed: 02/06/2023]
Abstract
African swine fever (ASF) and classical swine fever (CSF) are two highly infectious transboundary animal diseases (TADs) that are serious threats to the pig industry worldwide, including in China, the world's largest pork producer. In this study, a duplex real-time PCR assay was developed for the rapid detection and differentiation of African swine fever virus (ASFV) and classical swine fever virus (CSFV). The assay was performed on a portable, battery-powered PCR thermocycler with a low sample throughput (termed as 'T-COR4 assay'). The feasibility and reliability of the T-COR4 assay as a possible field method was investigated by testing clinical samples collected in China. When evaluated with reference materials or samples from experimental infections, the assay performed in a reliable manner, producing results comparable to those obtained from stationary PCR platforms. Of 59 clinical samples, 41 had results identical to a two-step CSFV real-time PCR assay. No ASFV was detected in these samples. The T-COR4 assay was technically easy to perform and produced results within 3 h, including sample preparation. In combination with a simple sample preparation method, the T-COR4 assay provides a new tool for the field diagnosis and differentiation of ASF and CSF, which could be of particular value in remote areas.
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Affiliation(s)
- L Liu
- National Veterinary Institute (SVA), Uppsala, Sweden.,The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden.,Joint Laboratory for Veterinary Microbiology between SVA and HVRI, Uppsala, Sweden
| | - Y Luo
- Joint Laboratory for Veterinary Microbiology between SVA and HVRI, Uppsala, Sweden.,Division of High-consequence Swine Viral Diseases, Harbin Veterinary Research Institute (HVRI), Chinese Academy of Agricultural Sciences, Harbin, China
| | - F Accensi
- Centre de Recerca en Sanitat Animal (CReSA) - Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain.,Departament de Sanitat i Anatomia Animals, Facultat de Veterinària (UAB), Barcelona, Spain
| | - L Ganges
- Centre de Recerca en Sanitat Animal (CReSA) - Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - F Rodríguez
- Centre de Recerca en Sanitat Animal (CReSA) - Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain.,Departament de Sanitat i Anatomia Animals, Facultat de Veterinària (UAB), Barcelona, Spain
| | - H Shan
- Qingdao Agricultural University, Qingdao, China
| | - K Ståhl
- National Veterinary Institute (SVA), Uppsala, Sweden.,The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden
| | - H-J Qiu
- Joint Laboratory for Veterinary Microbiology between SVA and HVRI, Uppsala, Sweden.,Division of High-consequence Swine Viral Diseases, Harbin Veterinary Research Institute (HVRI), Chinese Academy of Agricultural Sciences, Harbin, China
| | - S Belák
- National Veterinary Institute (SVA), Uppsala, Sweden.,The OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden.,Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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Ribeiro EL, Oliveira AG, Laguardia-Nascimento M, Mata CPSMD, Reis JKD, Fonseca Júnior AA. Estudo comparativo e validação de três técnicas de PCR em tempo real (qPCR) para diagnóstico de Peste Suína Africana. PESQUISA VETERINARIA BRASILEIRA 2016. [DOI: 10.1590/s0100-736x2016000600003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Resumo: Este estudo verificou o desempenho de três técnicas de PCR quantitativa (Real-Time) para o diagnóstico de Peste Suína Africana, uma doença exótica no Brasil, a partir de amostras de tecidos. As três técnicas escolhidas baseiam-se na amplificação de sequências do gene da proteína viral VP72 e são preconizadas, cada uma, por laboratórios oficiais da OIE (PSA-OIE), dos Estados Unidos (PSA-USDA) e da União Europeia (PSA-EU), respectivamente. Oligonucleotídeos iniciadores e sondas de hidrólise marcadas com fluoróforos foram sintetizados conforme a literatura de referência consultada. Sequências-alvo do DNA viral foram inseridos em plasmídeo sintético, os quais serviram de controle positivo para a padronização das técnicas e otimização de reagentes, determinação dos limites de detecção e testes de verificação de desempenho. Para aferição de repetibilidade e reprodutibilidade das técnicas, as técnicas padronizadas foram repetidas em dias diferentes, por um segundo analista, com alteração no mix comercial de reagentes utilizado e em um equipamento diferente, e também por outro laboratório. Realizaram-se, ainda, provas de sensibilidade analítica com amostras de DNA viral de referência e especificidade analítica e diagnóstica, com amostras negativas. As técnicas de PSA-EU e PSA-USDA apresentaram-se mais vantajosas quanto ao consumo de iniciadores. Não houve diferenças significativas nos resultados quantitativos variando-se os dias dos ensaios, os analistas, os equipamentos e o mix de reagentes. As três técnicas apresentaram alta especificidade analítica e diagnóstica e sensibilidade diagnóstica. As três técnicas de qPCR mostraram-se eficazes para serem adotadas por um mesmo laboratório para emissão de diagnósticos oficiais de Peste Suína Africana.
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9
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Leal CAG, Carvalho AF, Leite RC, Figueiredo HCP. Development of duplex real-time PCR for the detection of WSSV and PstDV1 in cultivated shrimp. BMC Vet Res 2014; 10:150. [PMID: 24996437 PMCID: PMC4110376 DOI: 10.1186/1746-6148-10-150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/30/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The White spot syndrome virus (WSSV) and Penaeus stylirostris penstyldensovirus 1 (previously named Infectious hypodermal and hematopoietic necrosis virus-IHHNV) are two of the most important viral pathogens of penaeid shrimp. Different methods have been applied for diagnosis of these viruses, including Real-time PCR (qPCR) assays. A duplex qPCR method allows the simultaneous detection of two viruses in the same sample, which is more cost-effective than assaying for each virus separately. Currently, an assay for the simultaneous detection of the WSSV and the PstDV1 in shrimp is unavailable. The aim of this study was to develop and standardize a duplex qPCR assay for the simultaneous detection of the WSSV and the PstDV1 in clinical samples of diseased L. vannamei. In addition, to evaluate the performance of two qPCR master mixes with regard to the clinical sensitivity of the qPCR assay, as well as, different methods for qPCR results evaluation. RESULTS The duplex qPCR assay for detecting WSSV and PstDV1 in clinical samples was successfully standardized. No difference in the amplification of the standard curves was observed between the duplex and singleplex assays. Specificities and sensitivities similar to those of the singleplex assays were obtained using the optimized duplex qPCR. The analytical sensitivities of duplex qPCR were two copies of WSSV control plasmid and 20 copies of PstDV1 control plasmid. The standardized duplex qPCR confirmed the presence of viral DNA in 28 from 43 samples tested. There was no difference for WSSV detection using the two kits and the distinct methods for qPCR results evaluation. High clinical sensitivity for PstDV1 was obtained with TaqMan Universal Master Mix associated with relative threshold evaluation. Three cases of simultaneous infection by the WSSV and the PstDV1 were identified with duplex qPCR. CONCLUSION The standardized duplex qPCR was shown to be a robust, highly sensitive, and feasible diagnostic tool for the simultaneous detection of the WSSV and the PstDV1 in whiteleg shrimp. The use of the TaqMan Universal Master Mix and the relative threshold method of data analysis in our duplex qPCR method provided optimal levels of sensitivity and specificity.
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Affiliation(s)
| | | | | | - Henrique C P Figueiredo
- AQUAVET, Laboratory of Aquatic Animal Diseases, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil.
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10
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Li L, Jin C, Ye L, Shao G, Wang L, Lin M. Argininosuccinate synthetase gene is silenced by CpG methylation in children with phenylketonuria. Clin Biochem 2013; 46:1793-7. [PMID: 24192130 DOI: 10.1016/j.clinbiochem.2013.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/16/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
Abstract
OBJECTIVES The concentration of tyrosine and the ratio of branch-amino acid to the aromatic amino acid in phenylketonuria (PKU) patients are much lower than that of normal people, which reveal that PKU patients have amino acid metabolism disorder. The aim of the present study was to investigate the arginine level in blood, the expression of argininosuccinate synthetase (ASS), the rate-limiting enzyme in arginine synthesis pathway, and the methylation of ASS in patients with PKU. DESIGN AND METHODS Twenty-five children with PKU and 65 healthy controls were investigated in this study. Blood concentration of arginine was analyzed by automatic amino acid analyzer. The methylation of ASS gene promoter was evaluated by using methylation-specific polymerase chain reaction (MSP) and bisulfite sequencing PCR (BSP) methods, and the mRNA level of ASS was evaluated by semi-quantitative RT-PCR. RESULTS Blood concentration of arginine in PKU patients without dietary control was 0.017±0.009mmol/L while in normal persons was 0.129±0.007mmol/L, which is statistically significant (P<0.001). The promoter of ASS was methylated in PKU (15/15, 100%) but not in normal persons (0/15). The mRNA level of ASS in PKU patients was lower than that of normal people, which was well correlated with its methylation status. CONCLUSIONS The silencing of ASS due to aberrant promoter CpG methylation may be an important mechanism for arginine biosynthesis disorders in PKU. High levels of phenylalanine and low levels of arginine are common characteristics in PKU patients. These findings would extend the current understanding of arginine, ASS in the development of PKU disease.
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Affiliation(s)
- Li Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
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Luque-Perez E, Mazzara M, Weber TP, Foti N, Grazioli E, Munaro B, Pinski G, Bellocchi G, Van den Eede G, Savini C. Testing the Robustness of Validated Methods for Quantitative Detection of GMOs Across qPCR Instruments. FOOD ANAL METHOD 2013. [DOI: 10.1007/s12161-012-9445-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Cuevas-Romero S, Blomström AL, Alvarado A, Hernández-Jauregui P, Rivera-Benitez F, Ramírez-Mendoza H, Berg M. Development of a real-time RT-PCR method for detection of porcine rubulavirus (PoRV-LPMV). J Virol Methods 2013; 189:1-6. [PMID: 23305816 PMCID: PMC7113651 DOI: 10.1016/j.jviromet.2012.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 11/16/2012] [Accepted: 12/17/2012] [Indexed: 11/25/2022]
Abstract
In order to provide a rapid and sensitive method for detection of the Porcine rubulavirus La Piedad-Michoacan-Mexico Virus (PoRV-LPMV), we have developed a specific real-time reverse transcriptase polymerase chain reaction assay. The detection of PoRV-LPMV, represents a diagnostic challenge due to the viral RNA being present in very small amounts in tissue samples. In this study, a TaqMan(®) real-time PCR assay was designed based on the phosphoprotein gene of PoRV-LPMV, to allow specific amplification and detection of viral RNA in clinical samples. Assay conditions for the primers and probe were optimized using infected PK15 cells and ten-fold serial dilutions of a plasmid containing the whole P-gene. The sensitivity of the developed TaqMan(®) assay was approximately 10 plasmid copies per reaction, and was shown to be 1000 fold better than a conventional nested RT-PCR. The performance of this real-time RT-PCR method enables studies of various aspects of PoRV-LPMV infection. Finally, the assay detects all current known variants of the virus.
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Affiliation(s)
- Sandra Cuevas-Romero
- Division of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Optimization of a combined human parechovirus-enterovirus real-time reverse transcription-PCR assay and evaluation of a new parechovirus 3-specific assay for cerebrospinal fluid specimen testing. J Clin Microbiol 2012; 51:452-8. [PMID: 23175256 DOI: 10.1128/jcm.01982-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human parechoviruses (HPeVs), particularly type 3 (HPeV3), are known central nervous system (CNS) pathogens, causing serious infections in infants similar to those caused by enteroviruses (EVs). The primary aim of this study was to combine and validate HPeV and EV real-time reverse transcription-PCR (RT-PCR) detection assays with the best available RT-PCR reagents and conditions for parallel detection of HPeV and EV on a single platform. The secondary aim was to develop and validate a newly developed HPeV3-specific real-time RT-PCR assay. Five commercially available RT-PCR kits were evaluated with the pan-HPeV and EV assays in one-step and two-step RT-PCRs. Two-step RT-PCR with the AgPath ID RT-PCR (AGP) kit performed best for both pan-HPeV and EV assays. The pan-HPeV-specific assay performed best with the AGP kit in a one-step RT-PCR. Frozen aliquots of 145 (for HPeV, n = 70; for EV, n = 75) previously characterized cerebrospinal fluid (CSF) specimens were tested by EV-, pan-HPeV-, and HPeV3-specific (HPeV specimens only) assays. The pan-HPeV and EV assays demonstrated 100% analytical sensitivity and specificity compared to historic results, while the HPeV3-specific assay demonstrated 97% sensitivity and 100% specificity. We propose a real-time pan-HPeV, EV two-step RT-PCR algorithm for simultaneous detection of HPeV and EV from CSF specimens on a single platform. The HPeV3-specific one-step RT-PCR assay can be used as a rapid and cost-effective assay to detect and identify HPeV3 in pan-HPeV RT-PCR assay-positive CSF specimens.
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Buzard GS, Baker D, Wolcott MJ, Norwood DA, Dauphin LA. Multi-platform comparison of ten commercial master mixes for probe-based real-time polymerase chain reaction detection of bioterrorism threat agents for surge preparedness. Forensic Sci Int 2012; 223:292-7. [PMID: 23107058 DOI: 10.1016/j.forsciint.2012.10.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 08/14/2012] [Accepted: 10/03/2012] [Indexed: 01/18/2023]
Abstract
The Centers for Disease Control and Prevention and United States Army Research Institute for Infectious Diseases have developed real-time PCR assays for the detection of bioterrorism threat agents. These assays all rely on a limited number of approved real-time PCR master mixes. Because the availability of these reagents is a critical element of bioterrorism preparedness, we undertook a joint national preparedness exercise to address the potential surge needs resulting from a large-scale bio-emergency. We identified 9 commercially-available potential alternatives to an existing approved master mix (LightCycler FastStart DNA Master HybProbes): the TaqMan Fast Universal PCR master mix, OmniMix HS, FAST qPCR master mix, EXPRESS qPCR SuperMix kit, QuantiFast Probe PCR kit, LightCycler FastStart DNA Master(PLUS) HybProbe, Brilliant II FAST qPCR master mix, ABsolute Fast QPCR Mix and the HotStart IT Taq master mix. The performances of these kits were evaluated by the use of real-time PCR assays for four bioterrorism threat agents: Bacillus anthracis, Brucella melitensis, Burkholderia mallei and Francisella tularensis. The master mixes were compared for target-specific detection levels, as well as consistency of results among three different real-time PCR platforms (LightCycler, SmartCycler and 7500 Fast Dx). Real-time PCR analysis revealed that all ten kits performed well for agent detection on the 7500 Fast Dx instrument; however, the QuantiFast Probe PCR kit yielded the most consistently positive results across multiple real-time PCR platforms. We report that certain combinations of commonly used master mixes and instruments are not as reliable as others at detecting low concentrations of target DNA. Furthermore, our study provides laboratories the option to select from the commercial kits we evaluated to suit their preparedness needs.
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Affiliation(s)
- Gregory S Buzard
- Bioterrorism Rapid Response and Advanced Technology (BRRAT) Laboratory, Division of Preparedness and Emerging Infections (DPEI), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA 30333, United States
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