151
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Loreck K, Mitrenga S, Meemken D, Heinze R, Reissig A, Mueller E, Ehricht R, Engemann C, Greiner M. Development of a miniaturized protein microarray as a new serological IgG screening test for zoonotic agents and production diseases in pigs. PLoS One 2019; 14:e0217290. [PMID: 31116794 PMCID: PMC6530865 DOI: 10.1371/journal.pone.0217290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022] Open
Abstract
In order to monitor the occurrence of zoonotic agents in pig herds as well as to improve herd health management, the development of new cost-effective diagnostic methods for pigs is necessary. In this study, a protein microarray-based assay for the simultaneous detection of immunoglobulin G (IgG) antibodies against different zoonotic agents and pathogens causing production diseases in pigs was developed. Therefore, antigens of ten different important swine pathogens (Toxoplasma gondii, Yersinia enterocolitica, Salmonella spp., Trichinella spp., Mycobacterium avium, Hepatitis E virus, Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, the porcine reproductive and respiratory syndrome virus, Influenza A virus) were spotted and covalently immobilized as 'antigen-spots' on microarray chips in order to test pig serum for the occurrence of antibodies. Pig serum was sampled at three German abattoirs and ELISA tests for the different pathogens were conducted with the purpose of creating a panel of reference samples for microarray analysis. To evaluate the accuracy of the antigens on the microarray, receiver operating characteristic (ROC) curve analysis using the ELISA test results as reference was performed for the different antigens. High area under curve values were achieved for the antigens of two zoonotic agents: Toxoplasma gondii (0.91), Yersinia enterocolitica (0.97) and for three production diseases: Actinobacillus pleuropneumoniae (0.77), Mycoplasma hyopneumoniae (0.94) and the porcine reproductive and respiratory syndrome virus (0.87). With the help of the newly developed microarray assay, collecting data on the occurrence of antibodies against zoonotic agents and production diseases in pig herds could be minimized to one measurement, resulting in an efficient screening test.
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Affiliation(s)
- Katharina Loreck
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Sylvia Mitrenga
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Diana Meemken
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Berlin, Germany
| | | | - Annett Reissig
- Leibniz-Institute of Photonic Technology (IPHT), Department for Optical Molecular Diagnostics and Systems Technology, Jena, Germany
- InfectoGnostics Research Campus, Centre for Applied Research, Jena, Germany
| | - Elke Mueller
- Leibniz-Institute of Photonic Technology (IPHT), Department for Optical Molecular Diagnostics and Systems Technology, Jena, Germany
- InfectoGnostics Research Campus, Centre for Applied Research, Jena, Germany
| | - Ralf Ehricht
- Leibniz-Institute of Photonic Technology (IPHT), Department for Optical Molecular Diagnostics and Systems Technology, Jena, Germany
- InfectoGnostics Research Campus, Centre for Applied Research, Jena, Germany
| | | | - Matthias Greiner
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Exposure, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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152
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Wagner S, Roberson D, Boland J, Yeager M, Cullen M, Mirabello L, Dunn ST, Walker J, Zuna R, Schiffman M, Wentzensen N. Development of the TypeSeq Assay for Detection of 51 Human Papillomavirus Genotypes by Next-Generation Sequencing. J Clin Microbiol 2019; 57:e01794-18. [PMID: 30814267 PMCID: PMC6498001 DOI: 10.1128/jcm.01794-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/20/2019] [Indexed: 01/11/2023] Open
Abstract
We have developed a new human papillomavirus (HPV) genotyping assay for detection of 51 HPV genotypes by next-generation sequencing (NGS). The TypeSeq assay consists of 3 PCR steps that equalize viral load and each type's amplicon copies prior to genotyping by NGS, thereby maximizing multiple-type sensitivity with minimal sequencing reads. The analytical sensitivity of the TypeSeq assay is 10 copies per reaction for 49 of the 51 types, including 13 high-risk (HR) types. We tested 863 clinical cervical specimens previously evaluated with the Roche Linear Array HPV genotyping test (LA). TypeSeq achieved 94.4% positive agreement with LA for detection of any HR type. Positive agreement was 91.4% and 85.5% for HPV16 and HPV18, respectively. Low-risk (LR) types ranged from 40.0% positive agreement (HPV83) to 90.9% (HPV69). Our unique approach to HPV amplification achieved a multiple-type sensitivity comparable to that of LA, with 83.9% and 84.2% of specimens positive for multiple HPV types by TypeSeq or LA, respectively. A total of 48.2% of specimens showed perfect agreement for all 37 types common to both assays. The simplicity of our open-source TypeSeq assay allows for high-throughput yet scalable processing, with a single technician able to process up to 768 specimens within 3 days. By leveraging NGS sample multiplexing capabilities, the per-sample labor requirements are greatly reduced compared to those of traditional genotyping methods. These features and the broad spectrum of detectable types make TypeSeq highly suitable for a wide range of applications.
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Affiliation(s)
- Sarah Wagner
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Joseph Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - S Terence Dunn
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Joan Walker
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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153
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Fu K, Xu W, Hu J, Lopez A, Bohn PW. Microscale and Nanoscale Electrophotonic Diagnostic Devices. Cold Spring Harb Perspect Med 2019; 9:a034249. [PMID: 30104197 PMCID: PMC6417966 DOI: 10.1101/cshperspect.a034249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Detecting and identifying infectious agents and potential pathogens in complex environments and characterizing their mode of action is a critical need. Traditional diagnostics have targeted a single characteristic (e.g., spectral response, surface receptor, mass, intrinsic conductivity, etc.). However, advances in detection technologies have identified emerging approaches in which multiple modes of action are combined to obtain enhanced performance characteristics. Particularly appealing in this regard, electrophotonic devices capable of coupling light to electron translocation have experienced rapid recent growth and offer significant advantages for diagnostics. In this review, we explore three specific promising approaches that combine electronics and photonics: (1) assays based on closed bipolar electrochemistry coupling electron transfer to color or fluorescence, (2) sensors based on localized surface plasmon resonances, and (3) emerging nanophotonics approaches, such as those based on zero-mode waveguides and metamaterials.
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Affiliation(s)
- Kaiyu Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Wei Xu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jiayun Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Arielle Lopez
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556
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154
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Elsayed MSAE, Amer A. The rapid detection and differentiation of Mycobacterium tuberculosis complex members from cattle and water buffaloes in the delta area of Egypt, using a combination of real-time and conventional PCR. Mol Biol Rep 2019; 46:3909-3919. [PMID: 31041672 DOI: 10.1007/s11033-019-04834-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/24/2019] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis complex (MTBC) has the potential to cause infections in animals and human beings. The combination of real-time PCR targeting atpE or lpqT and RD1, and conventional PCR targeting regions of difference (RD) was rigorously evaluated as a descriptive molecular epidemiology tool. A total of 2100 cattle and buffaloes from the Menoufia, Sharkia, Gharbia, Dakahlia, Elbuhaira, and Cairo Governorates were tested by single intradermal comparative cervical tuberculin test (SICCT). The frequency was 74/2100 (3.5%); thereafter, on post-mortem examination (PM), 49/74 (66.21%) showed visible lesions, while only 25/74 (33.78%) were non-visible with a significant difference of (p < .0001). Real-time PCR using atpE or lpqT and RD1 similarly detected the frequency of infection, sensitivity, specificity, positive predictive value, negative predictive value, and accuracy, which represented 73/74 (98.65%), 98.65, 100, 100, 90.91, and 98.81%, respectively. Multiplex conventional PCR targeting RD1, 4, 9, and 12 confirmed that 49/74 (66.21%) were M.bovis, while the simplex conventional PCR targeting RD4 and RD9 confirmed mycobacteria in 71/74 (95.94%) samples, which included 61/74 (82.4%) M.bovis and 2/74 (2.7%) M.tuberculosis. Additionally, 8/74 (10.8%) exhibited mixed patterns of M.bovis and M.tuberculosis, and 3/74 (4.05%) were negative. There was a significant difference between the results of simplex and multiplex conventional PCR (p < .0001). Moreover, simplex conventional PCR targeting RD4 and RD9 proved higher sensitivity, specificity, positive predictive value, negative predictive value, and accuracy, which were 95.95, 100, 100, 76.92, and 96.43%, respectively, when compared with the values of multiplex conventional PCR targeting RD1,4,9, and 12 which were 66.22, 100, 100, 28.57, and 70.24%, respectively. The repeatability results of real-time PCR using atpE or lpqT and RD1, and simplex conventional PCR targeting RD4 and RD9 were acceptable. In conclusion, a combination of real-time PCR using atpE or lpqT and RD1 as the first step with simplex conventional PCR targeting RD4 and RD9 as the second step was reliable as a diagnostic tool.
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Affiliation(s)
- Mohamed Sabry Abd Elraheam Elsayed
- Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Menoufia, 32897, Egypt.
| | - Ali Amer
- Animal Health Research Institute, Dokki-Giza, Egypt
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155
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Zhao Y, Liu F, Li Q, Wu M, Lei L, Pan Z. A multiplex RT-PCR assay for rapid and simultaneous detection of four RNA viruses in swine. J Virol Methods 2019; 269:38-42. [PMID: 30951787 PMCID: PMC7113762 DOI: 10.1016/j.jviromet.2019.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 11/17/2022]
Abstract
A multiplex reverse transcription polymerase chain rection (mRT-PCR) was developed for simultaneous detection of four RNA viruses in swine. The conserved target sequences directed to classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis coronavirus (TGEV) were selected based on alignments of genomic sequences and then specific primers were designed. The mRT-PCR assay was developed and evaluated for its specificity and sensitivity. The expected product from the single viral template was amplified by mRT-PCR and no spurious PCR amplification occurred from the genomic RNA or DNA of other pathogens. For single virus or different combinations of two viruses the detection limit of mRT-PCR was consistent with a single RT-PCR wtith 1 × 103 copies. For different combinations of the three viruses or four viruses, sensitivity of PEDV detection partially decreased. All of positive clinical specimens by the mRT-PCR were identically confirmed using Taqman RT-qPCR. Therefore, the mRT-PCR is a useful tool for epidemiological studies and laboratory diagnosis of single virus and/or mixed infections in swine.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Feifei Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qingmei Li
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Mengfan Wu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lei Lei
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zishu Pan
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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156
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Abstract
Multiplex detection of biomolecules is important in bionanotechnology and clinical diagnostics. Multiplexing using engineered solutions such as microarrays, synthetic nanopores, and DNA barcodes is promising, but they require sophisticated design/engineering and typically yield semiquantitative information. Single-molecule fluorescence resonance energy transfer (smFRET) is an attractive tool in this regard as it enables both sensitive and quantitative detection. However, multiplexing with smFRET remains a great challenge as it requires either multiple excitation sources, an antenna system created by multiple FRET pairs, or multiple acceptors of the donor fluorophore, which complicates not only the labeling schemes but also data analysis, due to overlapping of FRET efficiencies ( EFRET). Here, we address these currently outstanding issues by designing interconvertible hairpin-based sensors (iHabSs) with nonoverlapping EFRET utilizing a single donor/acceptor pair and demonstrate a high-confidence multiplex detection of unlabeled nucleic acid sequences. We validated the reliability of our approach by systematically omitting one target at a time. Further, we demonstrate that these iHabSs are fully recyclable, sensitive with a limit of detection of ∼200 pM, and able to discriminate against single base mismatches. The multiplexed approach developed here has the potential to benefit the fields of biosensing and diagnostics by allowing simultaneous and quantitative detection of unlabeled nucleic acid biomarkers.
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Affiliation(s)
- Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
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157
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Tomkowiak A, Skowrońska R, Weigt D, Kwiatek M, Nawracała J, Kowalczewski PŁ, Pluta M. Identification of Powdery Mildew Blumeria graminis f. sp. tritici Resistance Genes in Selected Wheat Varieties and Development of Multiplex PCR. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractThe aim of the study was to identify thePm2, Pm3a, Pm4bandPm6genes and to develop multiplex PCR reaction conditions to reduce time and limit analysis costs. The following molecular markers were used for gene identification:Xcfd81, Whs350andXgwm205(forPm2),Pm3a(forPm3a),STS_241andXgwm382(forPm4b),NAU/BCDSTS 135-2(forPm6). Plant material consisted of 7 popular European wheat varieties from the wheat collection at the Department of Genetics and Plant Breeding of the Poznań University of Life Sciences. The field experiment was established in 2017 and 2018 on 10 m2plots in a randomized complete block design in three replicates in the Dłoń Agricultural Experimental Farm of the Poznań University of Life Sciences (51°41’23.835”N 017°4’1.414”E). The analyses demonstrated that the accumulation of all identifiedPmgenes was found in the Assosan variety. The accumulation of thePm2, Pm4bandPm6genes was found in Atomic, Bussard, Lear, Sparta, Tonacja and Ulka varieties. The work also involved developing multiplex PCR conditions forXcfd81andSTS_241andXcfd81andXgwm382primer pairs, allowing the simultaneous identification of thePm2andPm4bgenes.
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Affiliation(s)
- Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Roksana Skowrońska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Michał Kwiatek
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
| | - Przemysław Łukasz Kowalczewski
- Institute of Food Technology of Plant Origin, Faculty of Food Science and Nutrition, Poznań, University of Life Sciences, 31 Wojska Polskiego Str, 60-624 Poznań, Poznań, Poland
| | - Mateusz Pluta
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań, University of Life Sciences, 11 Dojazd Str, 60-632 Poznań, Poznań, Poland
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158
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Hao X, Liu R, He Y, Xiao X, Xiao W, Zheng Q, Lin X, Tao P, Zhou P, Li S. Multiplex PCR methods for detection of several viruses associated with canine respiratory and enteric diseases. PLoS One 2019; 14:e0213295. [PMID: 30830947 PMCID: PMC6398926 DOI: 10.1371/journal.pone.0213295] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/18/2019] [Indexed: 11/23/2022] Open
Abstract
Viral respiratory and intestinal infections are the most common causes of canine viral illness. Infection with multiple pathogens occurs in many cases. Rapid diagnosis of these multiple infections is important for providing timely and effective treatment. To improve diagnosis, in this study, two new multiplex polymerase chain reactions (mPCRs) were developed for simultaneous detection of canine respiratory viruses (CRV) and canine enteric viruses (CEV) using two separate primer mixes. The viruses included canine adenovirus type 2 (CAV-2), canine distemper virus (CDV), canine influenza virus (CIV), canine parainfluenza virus (CPIV), canine circovirus (CanineCV), canine coronavirus (CCoV) and canine parvovirus (CPV). The sensitivity of the mPCR results showed that the detection limit of both mPCR methods was 1×104 viral copies. Twenty nasal swabs (NS) and 20 anal swabs (AS) collected from dogs with symptoms of respiratory disease or enteric disease were evaluated using the novel mPCR methods as a clinical test. The mPCR protocols, when applied to these respiratory specimens and intestinal samples, could detect 7 viruses simultaneously, allowing rapid investigation of CRV (CAV-2, CDV, CIV and CPIV) and CEV (CAV-2, CanineCV, CCoV and CPV) status and prompt evaluation of coinfection. Our study provides an effective and accurate tool for rapid differential diagnosis and epidemiological surveillance in dogs.
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Affiliation(s)
- Xiangqi Hao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
| | - Ruohan Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
| | - Yuwei He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
| | - Xiangyu Xiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
| | - Weiqi Xiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
| | - Qingxu Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
| | - Xi Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
| | - Pan Tao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
| | - Pei Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
- * E-mail: (PZ); (SL)
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province, People’s Republic of China
- Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province, People’s Republic of China
- * E-mail: (PZ); (SL)
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159
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Taylor SC, Nadeau K, Abbasi M, Lachance C, Nguyen M, Fenrich J. The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time. Trends Biotechnol 2019; 37:761-774. [PMID: 30654913 DOI: 10.1016/j.tibtech.2018.12.002] [Citation(s) in RCA: 389] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/20/2022]
Abstract
Quantitative PCR (qPCR) is one of the most common techniques for quantification of nucleic acid molecules in biological and environmental samples. Although the methodology is perceived to be relatively simple, there are a number of steps and reagents that require optimization and validation to ensure reproducible data that accurately reflect the biological question(s) being posed. This review article describes and illustrates the critical pitfalls and sources of error in qPCR experiments, along with a rigorous, stepwise process to minimize variability, time, and cost in generating reproducible, publication quality data every time. Finally, an approach to make an informed choice between qPCR and digital PCR technologies is described.
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Affiliation(s)
- Sean C Taylor
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada.
| | - Katia Nadeau
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Meysam Abbasi
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Claude Lachance
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Marie Nguyen
- Bio-Rad Laboratories, 255 Linus Pauling Drive, Hercules, CA 94547, USA
| | - Joshua Fenrich
- Bio-Rad Laboratories, 255 Linus Pauling Drive, Hercules, CA 94547, USA
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160
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Bioinformatics and Microarray-Based Technologies to Viral Genome Sequence Analysis. MICROBIAL GENOMICS IN SUSTAINABLE AGROECOSYSTEMS 2019. [PMCID: PMC7121691 DOI: 10.1007/978-981-13-8739-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Identification of microbial pathogen is an important event which lead to diagnosis, treatment, and control of infections produce by them. The high-throughput technology like microarray and new-generation sequencing machine are able to generate huge amount of nucleotide sequences of viral and bacterial genome of both known and unknown pathogens. Few years ago it was the DNA microarrays which had great potential to screen all the known pathogens and yet to be identified pathogen simultaneously. But after the development of a new generation sequencing, technologies and advance computational approach researchers are looking forward for a complete understanding of microbes and host interactions. The powerful sequencing platform is rapidly transforming the landscape of microbial identification and characterization. As bioinformatics analysis tools and databases are easily available to researchers, the enormous amount of data generated can be meaningfully handled for better understanding of the microbial world. Here in this chapter, we present commentary on how the computational method incorporated with sequencing technique made easy for microbial detection and characterization.
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161
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Simultaneous Detection of Beta and Gamma Human Herpesviruses by Multiplex qPCR Reveals Simple Infection and Coinfection Episodes Increasing Risk for Graft Rejection in Solid Organ Transplantation. Viruses 2018; 10:v10120730. [PMID: 30572622 PMCID: PMC6316002 DOI: 10.3390/v10120730] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 12/16/2022] Open
Abstract
Herpesviruses are common components of the human microbiome that become clinically relevant when a competent immunosurveillance is compromised, such as in transplantation. Members of the beta and gamma subfamilies are associated with a wide diversity of pathologies, including end-organ disease and cancer. In this study, we developed a multiplex qPCR technique with high specificity, sensitivity, efficiency and predictability that allowed the simultaneous detection and quantification of beta and gamma human herpesviruses. The technique was tested in a cohort of 34 kidney- or liver-transplanted pediatric patients followed up for up to 12 months post-transplant. Viral load was determined in 495 leukocyte-plasma paired samples collected bi-weekly or monthly. Human herpesvirus (HHV) 7 was the herpesvirus most frequently found in positive samples (39%), followed by Epstein-Barr virus (EBV) (20%). Also, EBV and HHV7 were present in the majority of coinfection episodes (62%). The share of positive samples exclusively detected either in leukocytes or plasma was 85%, suggesting that these herpesviruses tended to take a latent or lytic path in an exclusive manner. Infection by human cytomegalovirus (HCMV) and HHV6, as well as coinfection by EBV/HHV7 and EBV/HHV6/HHV7, were associated with graft rejection (RR = 40.33 (p = 0.0013), 5.60 (p = 0.03), 5.60 (p = 0.03) and 17.64 (p = 0.0003), respectively). The routine monitoring of beta and gamma herpesviruses should be mandatory in transplant centers to implement preventive strategies.
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Alvarez-Díaz JC, Ortiz-Echeverry BA, Velásquez N. Duplex RT-PCR assay for simultaneous detection of TSWV and CSVd in chrysanthemum. J Virol Methods 2018; 266:41-48. [PMID: 30578896 DOI: 10.1016/j.jviromet.2018.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023]
Abstract
A novel duplex RT-PCR assay for simultaneous detection of TSWV and CSVd in chrysanthemums was developed. Previous reported primers for amplification of TSWV and CSVd were used and a novel pair of primers for CSVd was designed to improve duplex amplification compatibility. Sensitivity and efficiency of the previous reported and novel primers for CSVd were assessed. Then, the sensitivity of the combined primers to amplify both TSWV and CSVd cDNA were also evaluated. Both TSWV and CSVd were detected in preparations diluted up to 10-4 and 10-5 respectively, from total RNA extracts. This duplex RT-PCR method showed an estimated diagnostic sensitivity (DSe) of 97% and diagnostic specificity (DSp) of 99%. For combination of the primers TSWV L1/ L2 and CSVd UCO-1 F/ UCO-1R, the protocol could detect pathogen RNA from naturally infected plants until 0.1 ng and 1 ng respectively. This novel protocol for detection of TSWV/CSVd represents a useful diagnostic tool without the need of expensive probes and less extensive laboratory work. This method could be helpful to assist the selection and further propagation of healthy chrysanthemums on the field as well as to understand the dynamics and the interaction of this virus and viroid within farms.
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Affiliation(s)
- Juan C Alvarez-Díaz
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia.
| | - Bianor A Ortiz-Echeverry
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia
| | - Nubia Velásquez
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia
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163
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Liu Z, Zhang C, Shen H, Sun J, Zhang J. Duplex fluorescence melting curve analysis as a new tool for rapid detection and differentiation of genotype I, II and Bartha-K61 vaccine strains of pseudorabies virus. BMC Vet Res 2018; 14:372. [PMID: 30486818 PMCID: PMC6264625 DOI: 10.1186/s12917-018-1697-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/13/2018] [Indexed: 12/21/2022] Open
Abstract
Background Recently, pseudorabies (PR) outbreaks have been reported in a large number of swine herds vaccinated with the Bartha-K61 vaccine in China, the current pseudorabies virus (PRV) belonging to Genotype II is differential genetically from Bartha-K61 vaccine belonging to Genotype I. Furthermore, it has been proved that the Bartha-K61 vaccine cannot provide sufficient protection against the current PRVs in China. Therefore, the accurate and rapid identification of PRVs is essential. The objective of this study is to develop a duplex fluorescence melting curve analysis (FMCA) capable of rapid, simple, high-throughput differentiation of Chinese, European/American and Bartha-K61 vaccine strains of PRV. Results Primers 6F/6R and probes P1/P2, combined with three recombinant plasmids p-B (Bartha-K61), p-N (Genotype I), and p-H (Genotype II), were used to establish the Bicolor FMCA. FAM Tm values (probe P1) and HEX (probe P2) channels of p-B were used as reference values. Tm differences (ΔTm) between detected samples and reference plasmid p-B were calculated in each channel. Bartha-K61 vaccine samples had ΔTm values of ±1 °C in both FAM and HEX channels, Genotype I samples had ΔTm values of ±1 °C in the FAM channel and 4.38 ± 1 °C in the HEX channel, and Genotype II samples had ΔTm values of 6.52 ± 1 °C in the FAM channel and 4.38 ± 1 °C in the HEX channel. The minimum detection limit of the duplex FMCA was approximately 1 × 100 copies per reaction for p-B, p-N, and p-H. The duplex FMCA technique was used to detect and different 198 suspected clinical samples, of which 18 (9%) were positive for Genotype II strains and eight (4%) were positive for Bartha-K61 vaccine strains, and the results were compared with sequencing and phylogenetic analyses, which confirmed that the Bicolor FMCA worked correctly for all samples. Conclusions In this study, we developed a duplex FMCA of dual-labeled, self-quenched probes that was performed for rapid detection and differentiation of Genotype I, II and Bartha-K61 vaccine strains of PRV. The duplex FMCA was rapid, simple, and high-throughput, and will likely prove useful for molecular epidemiological investigations and pathogen surveillance of PRV. Electronic supplementary material The online version of this article (10.1186/s12917-018-1697-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhicheng Liu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province,Ministry of Agriculture, P.R.China, Guangzhou, 510640, Guangdong, China
| | - Chunhong Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province,Ministry of Agriculture, P.R.China, Guangzhou, 510640, Guangdong, China
| | - Haiyan Shen
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province,Ministry of Agriculture, P.R.China, Guangzhou, 510640, Guangdong, China
| | - Junying Sun
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province,Ministry of Agriculture, P.R.China, Guangzhou, 510640, Guangdong, China
| | - Jianfeng Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province,Ministry of Agriculture, P.R.China, Guangzhou, 510640, Guangdong, China.
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164
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Hu J, Huang R, Wang Y, Wei X, Wang Z, Geng Y, Jing J, Gao H, Sun X, Dong C, Jiang C. Development of duplex PCR-ELISA for simultaneous detection of Salmonella spp. and Escherichia coli O157: H7 in food. J Microbiol Methods 2018; 154:127-133. [PMID: 30393180 DOI: 10.1016/j.mimet.2018.10.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/26/2018] [Indexed: 11/28/2022]
Abstract
In the current study, a duplex PCR-ELISA method was developed targeting the specific genes, invA of Salmonella spp. and rfbE of Escherichia coli O157: H7, to detect one or both bacteria in food. In brief, PCR product amplified by PCR primer labeled with digoxin at the 5'-end and a probe labeled with biotin at the 3'-end can form dimer by nucleic acid hybridization which can be captured by binding of biotin to streptomycin coated in ELISA plate before using enzyme-labeled anti-digoxin antibody and substrate to develop color. Also, evaluation of the duplex PCR-ELISA method was conducted in different food samples including milk, juice, cabbage, shrimp, chicken, pork and beef. Results indicated that the duplex PCR-ELISA developed here was specific when using 25 non-target bacteria strains as controls and was sensitive with a limit of detection (LOD) of 1 CFU/mL, 1, 000 times higher than that of the duplex PCR method and was repeatable regardless of inter- and intra-batch variations. The duplex PCR-ELISA method established in the present study has proven to be highly specific, sensitive and repeatable. It has the potential to be applied in such fields as clinical diagnosis of food-borne diseases, food hygiene monitoring and pathogen detection in food.
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Affiliation(s)
- Jinqiang Hu
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China; Collaborative Innovation Center of Food Production and Safety, Zhengzhou 450000, Henan Province, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou 450000, Henan Province, China.
| | - Runna Huang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Yi Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Xiangke Wei
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Zhangcun Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Yao Geng
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Jianzhou Jing
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Hui Gao
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Xincheng Sun
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Caiwen Dong
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Chunpeng Jiang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
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165
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Lopes ATS, Albuquerque GR, Maciel BM. Multiplex Real-Time Polymerase Chain Reaction for Simultaneous Quantification of Salmonella spp., Escherichia coli, and Staphylococcus aureus in Different Food Matrices: Advantages and Disadvantages. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6104015. [PMID: 30356394 PMCID: PMC6176325 DOI: 10.1155/2018/6104015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/06/2018] [Indexed: 12/24/2022]
Abstract
Quantitative real-time polymerase chain reactions (qPCRs) of the most prevalent bacteria causing foodborne diseases worldwide, such as Salmonella spp., Escherichia coli, and Staphylococcus aureus, can be an important tool for quantitative microbial risk assessment, which requires numerical data to determine the level of contamination at a specific stage of food production. However, most of qPCR assays described in the literature for these pathogens are qualitative; their objective is pathogen detection and not pathogen quantification. Thus, the aim of our work was to develop a qPCR for the simultaneous quantification of Salmonella spp., E. coli, and S. aureus and to propose its use in the analysis of foods, as a tool for microbiological quality monitoring. For this, a multiplex qPCR was standardized for the simultaneous quantification of specific fragments of target genes (ssf, phoA, and nuc) corresponding to each one of the mentioned bacteria. The limit of detection of the technique was 13, 10, and 12 gene copies for ssf, phoA, and nuc, respectively; standard curves showed R2 > 0.99, with efficiencies ranging from 99 to 110%, and inter- and intraexperiment reproducibility presented a low coefficient of variation in all trials. This methodology was applied in different food matrices (milk, ground beef, and oyster meat), and the results were compared with official microbiological culture methodology and with ready-to-use test. Advantages and disadvantages of each methodology used in this study are pointed out. We suggest that this multiplex qPCR can be used as a rapid screening technique for the analysis of food microbiological quality.
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Affiliation(s)
| | - George Rêgo Albuquerque
- Graduation Program in Animal Science, Santa Cruz State University, Ilhéus (BA), Brazil
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus (BA), Brazil
| | - Bianca Mendes Maciel
- Graduation Program in Animal Science, Santa Cruz State University, Ilhéus (BA), Brazil
- Department of Biological Sciences, Santa Cruz State University, Ilhéus (BA), Brazil
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166
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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167
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Abstract
![]()
The compartmentalization of reactions
in monodispersed droplets
is valuable for applications across biology. However, the requirement
of microfluidics to partition the sample into monodispersed droplets
is a significant barrier that impedes implementation. Here, we introduce
particle-templated emulsification, a method to encapsulate samples
in monodispersed emulsions without microfluidics. By vortexing a mixture
of hydrogel particles and sample solution, we encapsulate the sample
in monodispersed emulsions that are useful for most droplet applications.
We illustrate the method with ddPCR and single cell culture. The ability
to encapsulate samples in monodispersed droplets without microfluidics
should facilitate the implementation of compartmentalized reactions
in biology.
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Affiliation(s)
- Makiko N Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States
| | - Samuel C Kim
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States.,Chan Zuckerberg Biohub , San Francisco , California 94158 , United States
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168
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Pan P, Jin W, Li X, Chen Y, Jiang J, Wan H, Yu D. Optimization of multiplex quantitative polymerase chain reaction based on response surface methodology and an artificial neural network-genetic algorithm approach. PLoS One 2018; 13:e0200962. [PMID: 30044832 PMCID: PMC6059488 DOI: 10.1371/journal.pone.0200962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/04/2018] [Indexed: 11/19/2022] Open
Abstract
Multiplex quantitative polymerase chain reaction (qPCR) has found an increasing range of applications. The construction of a reliable and dynamic mathematical model for multiplex qPCR that analyzes the effects of interactions between variables is therefore especially important. This work aimed to analyze the effects of interactions between variables through response surface method (RSM) for uni- and multiplex qPCR, and further optimize the parameters by constructing two mathematical models via RSM and back-propagation neural network-genetic algorithm (BPNN-GA) respectively. The statistical analysis showed that Mg2+ was the most important factor for both uni- and multiplex qPCR. Dynamic models of uni- and multiplex qPCR could be constructed using both RSM and BPNN-GA methods. But RSM was better than BPNN-GA on prediction performance in terms of the mean absolute error (MAE), the mean square error (MSE) and the Coefficient of Determination (R2). Ultimately, optimal parameters of uni- and multiplex qPCR were determined by RSM.
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Affiliation(s)
- Ping Pan
- Hangzhou First People’s Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Weifeng Jin
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Xiaohong Li
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yi Chen
- Hangzhou First People’s Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Jiahui Jiang
- Hangzhou First People’s Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Haitong Wan
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Daojun Yu
- Hangzhou First People’s Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Department of Clinical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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169
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Rios L, Perera CL, Coronado L, Relova D, Álvarez AM, Ganges L, Díaz de Arce H, Núñez JI, Pérez LJ. Multi-Target Strategy for Pan/Foot-and-Mouth Disease Virus (FMDV) Detection: A Combination of Sequences Analysis, in Silico Predictions and Laboratory Diagnostic Evaluation. Front Vet Sci 2018; 5:160. [PMID: 30050913 PMCID: PMC6052897 DOI: 10.3389/fvets.2018.00160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/25/2018] [Indexed: 12/29/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting cloven-hoofed animals that causes severe economic losses. The disease is characterized by a vesicular condition and it cannot be differentiated from other vesicular diseases. Therefore, laboratory confirmation of any suspected FMD case is compulsory. Despite viral isolation in cell cultures has been considered for many years as the gold standard for FMD diagnosis, the advantages of real-time reverse transcription polymerase chain reaction (rRT-PCR) technology have motivated its use directly in clinical specimens for FMD diagnosis. The current work was aimed to develop and validate a molecular multi-check strategy using rRT-PCR (mMulti-rRT-PCR) based on SYBR-Green I for pan/foot-and-mouth disease virus (pan/FMDV) diagnosis. From in silico approaches, different primer pairs previously reported were selected and modified to reduce the likelihood of viral escape as well as potential failures in the pan/FMDV detection. The analytical parameters were evaluated using a high number of representative viral strains. The repeatability of the assay and its performance on field samples were also assessed. The mMulti-rRT-PCR was able to detect emergent FMDV strains that circulated in South America between the years 2006–2010 and on which the single rRT-PCRs failed when they were applied independently. The results obtained here showed that the proposed system is an accurate and rapid diagnosis method for sensitive and specific detection of FMDV. Thus, a validated mMulti-rRT-PCR assay based on SYBR-Green I detection coupled to melting curves resolution for pan/FMDV diagnosis on clinical samples is proposed. This study also highlights the need to incorporate the multi-target detection principle in the diagnosis of highly variable agents, specially, of those listed by OIE like FMDV.
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Affiliation(s)
- Liliam Rios
- Reiman Cancer Research Laboratory, Faculty of Medicine, University of New Brunswick, Saint John, NB, Canada
| | - Carmen L Perera
- Centro Nacional de Sanidad Agropecuaria, OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribean Region, San José de las Lajas, Cuba
| | - Liani Coronado
- Centro Nacional de Sanidad Agropecuaria, OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribean Region, San José de las Lajas, Cuba
| | - Damarys Relova
- Centro Nacional de Sanidad Agropecuaria, OIE Collaborating Centre for Diagnosis and Risk Analysis of the Caribean Region, San José de las Lajas, Cuba
| | - Ana M Álvarez
- Instituto Nacional de Investigaciones Agricolas, Maracay, Venezuela
| | - Llilianne Ganges
- OIE Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, Spain.,IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autonoma de Barcelona, Barcelona, Spain
| | | | - José I Núñez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Lester J Pérez
- Dalhousie Medicine New Brunswick, Dalhousie University, Saint John, NB, Canada
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170
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Botti C, Micillo A, Ricci G, Russo A, Denisco A, Cantile M, Scognamiglio G, De Rosa A, Botti G. Characterization of respiratory infection viruses in hospitalized children from Naples province in Southern Italy. Exp Ther Med 2018; 15:4805-4809. [PMID: 29805499 PMCID: PMC5958661 DOI: 10.3892/etm.2018.6061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022] Open
Abstract
Most acute respiratory infections (ARIs) in children are due to viral etiology, and represent an important cause of mortality and morbidity in children <5 years old in developing countries. The pathogens that cause ARIs vary geographically and by season, and viruses serve a major role. In the present study, the distribution of the seven respiratory viruses that are more prevalent in Southern European countries were retrospectively analyzed in a Southern Italy Hospital, that centralizes pediatric diseases from the Naples province. Viruses were categorized by a FilmArray Respiratory Panel, and demonstrated no substantial differences in sex, age and seasonal viruses distribution. However, all the investigated viruses had a higher detection rate in the surrounding municipalities than in the metropolitan area of Naples. In recent years, the association between air pollution and respiratory infections has become an increasing public health concern. The data in this study support this association in the surrounding areas of Naples extensively contaminated by environmental toxic agents. In these areas, characterization of the epidemiology of ARIs is required to implement a prevention and control program.
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Affiliation(s)
- Chiara Botti
- Laboratory of Clinical Pathology, Santobono-Pausilipon Hospital, I-80129 Naples, Italy
| | - Alberto Micillo
- Laboratory of Clinical Pathology, Santobono-Pausilipon Hospital, I-80129 Naples, Italy
| | - Giuseppe Ricci
- Laboratory of Clinical Pathology, Santobono-Pausilipon Hospital, I-80129 Naples, Italy
| | - Adolfo Russo
- Laboratory of Clinical Pathology, Santobono-Pausilipon Hospital, I-80129 Naples, Italy
| | - Alberto Denisco
- Laboratory of Clinical Pathology, Santobono-Pausilipon Hospital, I-80129 Naples, Italy
| | - Monica Cantile
- Pathology Unit, National Cancer Institute ‘Pascale Foundation’, I-80131 Naples, Italy
| | - Giosuè Scognamiglio
- Pathology Unit, National Cancer Institute ‘Pascale Foundation’, I-80131 Naples, Italy
| | - Antonio De Rosa
- Laboratory of Clinical Pathology, Santobono-Pausilipon Hospital, I-80129 Naples, Italy
| | - Gerardo Botti
- Pathology Unit, National Cancer Institute ‘Pascale Foundation’, I-80131 Naples, Italy
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171
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Guswenrivo I, Tseng SP, Scotty Yang CC, Yoshimura T. Development of Multiplex Nested PCR for Simultaneous Detection of Ectoparasitic Fungi Laboulbeniopsis termitarius and Antennopsis gallica on Reticulitermes speratus (Blattodea: Rhinotermitidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2018; 111:1330-1336. [PMID: 29669024 DOI: 10.1093/jee/toy091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 06/08/2023]
Abstract
Laboulbeniopsis termitarius (Thaxt) and Antennopsis gallica (Buchli and Heim) are two of the most common ectoparasitic fungi found on the body surface of termites. While visual observation under a dissecting microscope is a common method used to screen for such fungi, it generally requires a large number of termites and is thus very time consuming. In this study, we develop a fast, efficient protocol to detect fungal infection on the termite Reticulitermes speratus (Kolbe). Species-specific primers were designed based on sequence data and amplified using a number of universal fungus primer pairs that target partial sequences of the 18s rRNA gene of the two fungi. To detect these fungi in a robust yet economic manner, we then developed a multiplex nested polymerase chain reaction assay using species-specific primers. Results suggested that both fungi could be successfully detected, even in cases where L. termitarius was at low titer (e.g., a single thallus per termite). The new method described here is recommended for future surveys of these two fungi, as it is more sensitive, species specific, and faster than visual observation, and is likely to facilitate a better understanding of these fungi and their dynamics in host populations.
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Affiliation(s)
- I Guswenrivo
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
- Research and Development Unit for Biomaterials, Indonesian Institute of Sciences, Cibinong Science Center, Cibinong-Bogor, Indonesia
| | - S P Tseng
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - C C Scotty Yang
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - T Yoshimura
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
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172
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Chen JW, Lau YY, Krishnan T, Chan KG, Chang CY. Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques. Front Microbiol 2018; 9:1104. [PMID: 29892277 PMCID: PMC5985333 DOI: 10.3389/fmicb.2018.01104] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.
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Affiliation(s)
- Jian-Woon Chen
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yin Yin Lau
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Thiba Krishnan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Chien-Yi Chang
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
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173
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Simultaneous Expression of GUS and Actin Genes by Using the Multiplex RT-PCR and Multiplex Gold Nanoparticle Probes. J Fluoresc 2018; 28:633-638. [PMID: 29687369 DOI: 10.1007/s10895-018-2225-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/27/2018] [Indexed: 12/31/2022]
Abstract
Gene expression analysis is considered to be extremely important in many different biological researches. DNA-based diagnostic test, which contributes to DNA identification, has higher specificity, cost, and speed than some biochemical and molecular methods. In this study, we try to use the novel nano technology approach with Multiplex RT-PCR and Gold nano particular probes (GNPs-probes) in order to get gene expression in Curcumas melons. We used Agrobacterium tumefactions for gene transfer and GUS reporter gene as a reporter. After cDNA synthesis, Multiplex PCR and Multiplex RT-PCR techniques were used. Finally, probes were designed for RNA of GUS and Actin genes, and then the analysis of the gene expression using the probes attached to GNPs was carried out and the color changes in the GNPs were applied. In the following, probes hybridization was checked with DNA between 400 to 700 nm wavelengths and the highest rate was observed in the 550 to 650 nm. The results show that the simultaneous use of GNP-attached detectors and Multiplex RT-PCRcan reduce time and costmore considerably than somelaboratory methods for gene expiration investigation. Additionally, it can be seen thatthere is an increase in sensitivity and specificity of our investigation. Based on our findings, this can bea novel study doneusingMultiplex RT-PCRand unmodified AuNPs for gene transfer and expression detection to plants. We can claim that this assay has a remarkable advantage including rapid, cost-effectiveness, specificity and accuracy to detect transfer and expression genes in plants. Also,we can use this technique from other gene expressionsin many different biology samples.
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174
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A multiplex PCR method for the simultaneous detection of three viruses associated with canine viral enteric infections. Arch Virol 2018; 163:2133-2138. [PMID: 29675651 PMCID: PMC7086948 DOI: 10.1007/s00705-018-3828-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/20/2018] [Indexed: 10/26/2022]
Abstract
The aim of this study was to establish a multiplex PCR (mPCR) method that can simultaneously detect canine parvovirus (CPV-2), canine coronavirus (CCoV) and canine adenovirus (CAV), thereby eliminating the need to detect these pathogens individually. Based on conserved regions in the genomes of these three viruses, the VP2 gene of CPV-2, the endoribonuclease nsp15 gene of CCoV, and the 52K gene of CAV were selected for primer design. The specificity of the mPCR results showed no amplification of canine distemper virus (CDV), canine parainfluenza virus (CPIV), or pseudorabies virus (PRV), indicating that the method had good specificity. A sensitivity test showed that the detection limit of the mPCR method was 1 × 104 viral copies. A total of 63 rectal swabs from dogs with diarrheal symptoms were evaluated using mPCR and routine PCR. The ratio of positive samples to total samples for CPV-2, CCoV, and CAV was 55.6% (35/63) for mPCR and 55.6% (35/63) for routine PCR. Thirty-five positive samples were detected by both methods, for a coincidence ratio of 100%. This mPCR method can simultaneously detect CCoV (CCoV-II), CAV (CAV-1, CAV-2) and CPV-2 (CPV-2a, CPV-2b, CPV-2c), which are associated with viral enteritis, thereby providing an efficient, inexpensive, specific, and accurate new tool for clinical diagnosis and laboratory epidemiological investigations.
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175
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Graham CB, Maes SE, Hojgaard A, Fleshman AC, Sheldon SW, Eisen RJ. A molecular algorithm to detect and differentiate human pathogens infecting Ixodes scapularis and Ixodes pacificus (Acari: Ixodidae). Ticks Tick Borne Dis 2018; 9:390-403. [PMID: 29258802 PMCID: PMC6452875 DOI: 10.1016/j.ttbdis.2017.12.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/21/2017] [Accepted: 12/06/2017] [Indexed: 12/23/2022]
Abstract
The incidence and geographic range of tick-borne illness associated with Ixodes scapularis and Ixodes pacificus have dramatically increased in recent decades. Anaplasmosis, babesiosis, and Borrelia spirochete infections, including Lyme borreliosis, account for tens of thousands of reported cases of tick-borne disease every year. Assays that reliably detect pathogens in ticks allow investigators and public health agencies to estimate the geographic distribution of human pathogens, assess geographic variation in their prevalence, and evaluate the effectiveness of prevention strategies. As investigators continue to describe new species within the Borrelia burgdorferi sensu lato complex and to recognize some Ixodes-borne Borrelia species as human pathogens, assays are needed to detect and differentiate these species. Here we describe an algorithm to detect and differentiate pathogens in unfed I. scapularis and I. pacificus nymphs including Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi sensu stricto, Borrelia mayonii, and Borrelia miyamotoi. The algorithm comprises 5 TaqMan real-time polymerase chain reaction assays and 3 sequencing protocols. It employs multiple targets for each pathogen to optimize specificity, a gene target for I. scapularis and I. pacificus to verify tick-derived DNA quality, and a pan-Borrelia target to detect Borrelia species that may emerge as human disease agents in the future. We assess the algorithm's sensitivity, specificity, and performance on field-collected ticks.
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Affiliation(s)
- Christine B Graham
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521, United States.
| | - Sarah E Maes
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521, United States
| | - Andrias Hojgaard
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521, United States
| | - Amy C Fleshman
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521, United States
| | - Sarah W Sheldon
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521, United States
| | - Rebecca J Eisen
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd., Fort Collins, CO 80521, United States
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176
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Laamiri N, Aouini R, Marnissi B, Ghram A, Hmila I. A multiplex real-time RT-PCR for simultaneous detection of four most common avian respiratory viruses. Virology 2017; 515:29-37. [PMID: 29223788 DOI: 10.1016/j.virol.2017.11.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022]
Abstract
A one-step multiplex real-time reverse transcription-PCR (rRT-PCR) assay was developed for simultaneous detection and quantification of four avian respiratory viruses: avian influenza virus (AIV), infectious bronchitis virus (IBV), Newcastle disease virus (NDV) and infectious laryngotracheitis virus (ILTV). In comparison with the singleplex rRT-PCR, the specificity, the sensitivity and the reproducibility of the new assay were evaluated and validated using 70 clinical samples. The optimal cutoff point, the corresponding limit of quantification (LoQ) and the limit of detection (LoD) were statistical established based on receiver operating characteristic (ROC) curve analysis. The results showed that the multiplex assay presents higher sensitivity and specificity. Correlation coefficients (R2) and amplification efficiencies (E) of all singleplex and multiplex rRT-PCR reactions are within the acceptable range. The 95% LoDs of multiplex assay were in the range [3-19] copies genomic/ µl, and its corresponding cutoff cycles were in the range [34.16-36.59]. No competitive inhibition for the detection of the four targets and no specific amplification or cross reactivity with other tested viruses was observed. Excellent results were attained in the inter-assay and intra-assay reproducibility evaluation. All identified samples by the multiplex rRT-PCR assay proved to be 100% concordant with the results of the singleplex assays. The results achieved showed that the multiplex assay is very suitable as a routine laboratory test for rapid and specific detection and quantification of co-infections in field samples.
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Affiliation(s)
- Nacira Laamiri
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia.; University of Carthage, Faculty of Sciences Bizerte, 7021 Zarzouna Bizerte, Tunisia.
| | - Rim Aouini
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia.; University of Carthage, Faculty of Sciences Bizerte, 7021 Zarzouna Bizerte, Tunisia
| | - Boutheina Marnissi
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia
| | - Abdeljelil Ghram
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia
| | - Issam Hmila
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia
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177
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Charlermroj R, Makornwattana M, Himananto O, Seepiban C, Phuengwas S, Warin N, Gajanandana O, Karoonuthaisiri N. An accurate, specific, sensitive, high-throughput method based on a microsphere immunoassay for multiplex detection of three viruses and bacterial fruit blotch bacterium in cucurbits. J Virol Methods 2017; 247:6-14. [DOI: 10.1016/j.jviromet.2017.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/30/2017] [Accepted: 05/09/2017] [Indexed: 11/29/2022]
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178
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Baccouche A, Okumura S, Sieskind R, Henry E, Aubert-Kato N, Bredeche N, Bartolo JF, Taly V, Rondelez Y, Fujii T, Genot AJ. Massively parallel and multiparameter titration of biochemical assays with droplet microfluidics. Nat Protoc 2017; 12:1912-1932. [PMID: 28837132 DOI: 10.1038/nprot.2017.092] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Biochemical systems in which multiple components take part in a given reaction are of increasing interest. Because the interactions between these different components are complex and difficult to predict from basic reaction kinetics, it is important to test for the effect of variations in the concentration for each reagent in a combinatorial manner. For example, in PCR, an increase in the concentration of primers initially increases template amplification, but large amounts of primers result in primer-dimer by-products that inhibit the amplification of the template. Manual titration of biochemical mixtures rapidly becomes costly and laborious, forcing scientists to settle for suboptimal concentrations. Here we present a droplet-based microfluidics platform for mapping of the concentration space of up to three reaction components followed by detection with a fluorescent readout. The concentration of each reaction component is read through its internal standard (barcode), which is fluorescent but chemically orthogonal. We describe in detail the workflow, which comprises the following: (i) production of the microfluidics chips, (ii) preparation of the biochemical mixes, (iii) their mixing and compartmentalization into water-in-oil emulsion droplets via microfluidics, (iv) incubation and imaging of the fluorescent barcode and reporter signals by fluorescence microscopy and (v) image processing and data analysis. We also provide recommendations for choosing the appropriate fluorescent markers, programming the pressure profiles and analyzing the generated data. Overall, this platform allows a researcher with a few weeks of training to acquire ∼10,000 data points (in a 1D, 2D or 3D concentration space) over the course of a day from as little as 100-1,000 μl of reaction mix.
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Affiliation(s)
- Alexandre Baccouche
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,Earth Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Shu Okumura
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,CIBIS, Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Rémi Sieskind
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Elia Henry
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Nathanaël Aubert-Kato
- Earth Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Information Science, Ochanomizu University, Tokyo, Japan.,Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institute of Intelligent Systems and Robotics (ISIR), Paris, France
| | - Nicolas Bredeche
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institute of Intelligent Systems and Robotics (ISIR), Paris, France
| | | | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Yannick Rondelez
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Teruo Fujii
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,CIBIS, Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Anthony J Genot
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan
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179
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Lee H, Lee D, Park JH, Song SH, Jeong IG, Kim CS, Searson PC, Lee KH. High throughput differential identification of TMPRSS2-ERG fusion genes in prostate cancer patient urine. Biomaterials 2017; 135:23-29. [DOI: 10.1016/j.biomaterials.2017.04.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 12/18/2022]
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180
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Wan W, Lu M, Wang D, Gao X, Hong J. High-fidelity de novo synthesis of pathways using microchip-synthesized oligonucleotides and general molecular biology equipment. Sci Rep 2017; 7:6119. [PMID: 28733633 PMCID: PMC5522410 DOI: 10.1038/s41598-017-06428-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/17/2017] [Indexed: 11/24/2022] Open
Abstract
Engineering and evaluation of synthetic routes for generating valuable compounds require accurate and cost-effective de novo synthesis of genetic pathways. Here, we present an economical and streamlined de novo DNA synthesis approach for engineering a synthetic pathway with microchip-synthesized oligonucleotides (oligo). The process integrates entire oligo pool amplification, error-removal, and assembly of long DNA molecules. We utilized this method to construct a functional lycopene biosynthetic pathway (11.9 kb encoding 10 genes) in Escherichia coli using a highly error-prone microchip-synthesized oligo pool (479 oligos) without pre-purification, and the error-frequency was reduced from 14.25/kb to 0.53/kb. This low-equipment-dependent and cost-effective method can be widely applied for rapid synthesis of biosynthetic pathways in general molecular biology laboratories.
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Affiliation(s)
- Wen Wan
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Min Lu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xiaolian Gao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
- Department of Biology and Biochemistry, University of Houston, Houston, TX77004-5001, USA
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China.
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181
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Tung HY, Chen WC, Ou BR, Yeh JY, Cheng YH, Tsng PH, Hsu MH, Tsai MS, Liang YC. Simultaneous detection of multiple pathogens by multiplex PCR coupled with DNA biochip hybridization. Lab Anim 2017; 52:186-195. [PMID: 28691600 DOI: 10.1177/0023677217718864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Traditional serological enzyme-linked immunosorbent assay (ELISA) is routinely used to monitor pathogens during quarantine in most animal facilities to prevent possible infection. However, the ELISA platform is a single-target assay, and screening all targeted pathogens is time-consuming and laborious. In this study, to increase sensitivity and to reduce diagnosis time for high-throughput processes, multiplex PCR and DNA biochip techniques were combined to develop a multi-pathogen diagnostic method for use instead of routine ELISA. Eight primer sets were designed for multiplex PCR to detect genes from seven targeted bacterial and viral pathogens. DNA-DNA hybridization was conducted on a biochip following the multiple PCR analysis. Using this method, a total of 24 clinical samples were tested, and the result showed that not only single infection but also co-infection by multi-pathogens can be detected. In conclusion, multiplex PCR coupled with a DNA biochip is an efficient method for detecting multi-pathogens in a reaction. This platform is a useful tool for quarantine services and disease prevention in animal facilities.
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Affiliation(s)
- Hsiang-Yun Tung
- 1 College of Biotechnology and Bioresources, Dayeh University, Changhua, Taiwan
| | - Wei-Chen Chen
- 2 Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Bor-Rung Ou
- 3 Department of Animal Science and Biotechnology, Tunghai University, Taichung, Taiwan
| | - Jan-Ying Yeh
- 4 Department of Post-Baccalaureate Veterinary Medicine, Asia University, Wufeng Taichung, Taiwan.,5 Food Safety and Inspection Center, Asia University, Wufeng Taichung, Taiwan
| | - Yeong-Hsiang Cheng
- 6 Department of Biotechnology and Animal Science, National I-Lan University, I-Lan, Taiwan
| | - Ping-Hua Tsng
- 7 GeneReach Biotechnology Corporation, Taichung, Taiwan
| | - Ming-Hua Hsu
- 8 Nuclear Science and Technology Development Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Shiun Tsai
- 1 College of Biotechnology and Bioresources, Dayeh University, Changhua, Taiwan
| | - Yu-Chuan Liang
- 2 Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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182
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Comparing Culture and Multiplex PCR Methods to Examine Fastidious Bacteria in Otitis Externa and Media. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.2.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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183
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Chen JQ, Healey S, Regan P, Laksanalamai P, Hu Z. PCR-based methodologies for detection and characterization of Listeria monocytogenes and Listeria ivanovii in foods and environmental sources. FOOD SCIENCE AND HUMAN WELLNESS 2017. [DOI: 10.1016/j.fshw.2017.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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184
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A qPCR-Based Tool to Diagnose the Presence of Harmful Cyanobacteria and Cyanotoxins in Drinking Water Sources. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14050547. [PMID: 28531121 PMCID: PMC5451997 DOI: 10.3390/ijerph14050547] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/14/2017] [Accepted: 05/17/2017] [Indexed: 11/30/2022]
Abstract
Harmful cyanobacteria have been an important concern for drinking water quality for quite some time, as they may produce cyanotoxins and odorants. Microcystis and Cylindrospermopsis are two common harmful cyanobacterial genera detected in freshwater lakes and reservoirs, with microcystins (MCs) and cylindrospermopsin (CYN) as their important metabolites, respectively. In this study, two sets of duplex qPCR systems were developed, one for quantifying potentially-toxigenic Microcystis and Microcystis, and the other one for cylindrospermopsin-producing cyanobacteria and Cylindrospermopsis. The duplex qPCR systems were developed and validated in the laboratory by using 338 samples collected from 29 reservoirs in Taiwan and her offshore islands. Results show that cell numbers of Microcystis and Cylindorspermopsis enumerated with microscopy, and MCs and CYN concentrations measured with the enzyme-linked immuno-sorbent assay method, correlated well with their corresponding gene copies determined with the qPCR systems (range of coefficients of determination R2 = 0.392−0.740). The developed qPCR approach may serve as a useful tool for the water industry to diagnose the presence of harmful cyanobacteria and the potential presence of cyanotoxins in source waters.
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185
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Chiquito-Almanza E, Acosta-Gallegos JA, García-Álvarez NC, Garrido-Ramírez ER, Montero-Tavera V, Guevara-Olvera L, Anaya-López JL. Simultaneous Detection of Both RNA and DNA Viruses Infecting Dry Bean and Occurrence of Mixed Infections by BGYMV, BCMV and BCMNV in the Central-West Region of Mexico. Viruses 2017; 9:E63. [PMID: 28358318 PMCID: PMC5408669 DOI: 10.3390/v9040063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 11/17/2022] Open
Abstract
A multiplex reverse transcription polymerase chain reaction (RT-PCR) assay was developed to simultaneously detect bean common mosaic virus (BCMV), bean common mosaic necrotic virus (BCMNV), and bean golden yellow mosaic virus (BGYMV) from common bean leaves dried with silica gel using a single total nucleic acid extraction cetyl trimethyl ammonium bromide (CTAB) method. A mixture of five specific primers was used to amplify three distinct fragments corresponding to 272 bp from the AC1 gene of BGYMV as well as 469 bp and 746 bp from the CP gene of BCMV and BCMNV, respectively. The three viruses were detected in a single plant or in a bulk of five plants. The multiplex RT-PCR was successfully applied to detect these three viruses from 187 field samples collected from 23 municipalities from the states of Guanajuato, Nayarit and Jalisco, Mexico. Rates of single infections were 14/187 (7.5%), 41/187 (21.9%), and 35/187 (18.7%), for BGYMV, BCMV, and BCMNV, respectively; 29/187 (15.5%) samples were co-infected with two of these viruses and 10/187 (5.3%) with the three viruses. This multiplex RT-PCR assay is a simple, rapid, sensitive, and cost-effective method for detecting these viruses in the common bean and can be used for routine molecular diagnosis and epidemiological studies.
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Affiliation(s)
- Elizabeth Chiquito-Almanza
- Instituto Tecnológico de Celaya, Departamento de Ingeniería Bioquímica, Celaya, Guanajuato, CP 38010, Mexico.
| | | | - Nadia C García-Álvarez
- INIFAP-Campo Experimental Santiago Ixcuintla, Santiago Ixcuintla, Nayarit, CP 63300, Mexico.
| | | | | | - Lorenzo Guevara-Olvera
- Instituto Tecnológico de Celaya, Departamento de Ingeniería Bioquímica, Celaya, Guanajuato, CP 38010, Mexico.
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186
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Giri S, Rajan AK, Kumar N, Dhanapal P, Venkatesan J, Iturriza-Gomara M, Taniuchi M, John J, Abraham AM, Kang G. Comparison of culture, single and multiplex real-time PCR for detection of Sabin poliovirus shedding in recently vaccinated Indian children. J Med Virol 2017; 89:1485-1488. [PMID: 28213965 PMCID: PMC6139431 DOI: 10.1002/jmv.24793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/30/2017] [Indexed: 11/30/2022]
Abstract
Although, culture is considered the gold standard for poliovirus detection from stool samples, real‐time PCR has emerged as a faster and more sensitive alternative. Detection of poliovirus from the stool of recently vaccinated children by culture, single and multiplex real‐time PCR was compared. Of the 80 samples tested, 55 (68.75%) were positive by culture compared to 61 (76.25%) and 60 (75%) samples by the single and one step multiplex real‐time PCR assays respectively. Real‐time PCR (singleplex and multiplex) is more sensitive than culture for poliovirus detection in stool, although the difference was not statistically significant.
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Affiliation(s)
- Sidhartha Giri
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Anand K Rajan
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Nirmal Kumar
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Pavithra Dhanapal
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Miren Iturriza-Gomara
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Jacob John
- Department of Community Medicine, Christian Medical College, Vellore, India
| | - Asha Mary Abraham
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Gagandeep Kang
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India
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187
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Ionică AM, Matei IA, D'Amico G, Bel LV, Dumitrache MO, Modrý D, Mihalca AD. Dirofilaria immitis and D. repens show circadian co-periodicity in naturally co-infected dogs. Parasit Vectors 2017; 10:116. [PMID: 28245837 PMCID: PMC5331712 DOI: 10.1186/s13071-017-2055-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/22/2017] [Indexed: 11/10/2022] Open
Abstract
Background Dirofilaria immitis and Dirofilaria repens are mosquito-borne zoonotic filarioids typically infecting dogs, causing a potentially fatal cardiopulmonary disease and dermatological conditions, respectively. The females are larviparous, releasing the larvae (microfilariae) into the bloodstream, which further develop in mosquito vectors. However, microfilaremia greatly fluctuates during a 24-h period. As the sampling time can greatly influence the accuracy of diagnosis, the aim of the present study was to assess the circadian periodicity of D. immitis and D. repens in naturally co-infected dogs in an endemic area of Romania and to investigate possible differences of periodicity between these two species. Methods Overall, four dogs harbouring natural co-infection with D. immitis and D. repens were selected and sampled every two hours for two consecutive days: two dogs in July 2014 and two in July 2015. At each sampling time, a 0.7 ml blood sample was taken. Modified Knott’s test was performed on 0.5 ml, and the remaining 0.2 ml were used for DNA extraction and molecular amplification, both in single and duplex PCR reactions. Microfilariae of both species were morphologically identified and counted in each collected sample, microfilaremia was calculated, and fluctuation was charted. Results The dynamics of microfilaremia showed similar patterns for both Dirofilaria species. In all four dogs, D. immitis was present at all sampling times, with several peak values of microfilaremia, of which one was common for all dogs (1 am), while minimum counts occurred between 5 and 9 am. Similarly, for D. repens, one of the peak values was recorded in all dogs at 1 am, while minimum counts (including zero) occurred at 9 and 11 am. Single species-specific PCR reactions were positive for both D. immitis and D. repens in all collected samples, while duplex PCR failed to amplify D. repens DNA in many cases. Conclusions Both Dirofilaria immitis and D. repens microfilariae are subperiodic, following a similar variation pattern, with peak values of microfilaremia registered during the night in Romania. Duplex PCR fails to identify the infection with D. repens in co-infected dogs when the ratio of microfilaremia is in favour of D. immitis. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2055-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angela Monica Ionică
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 335700, Cluj-Napoca, Romania
| | - Ioana Adriana Matei
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 335700, Cluj-Napoca, Romania
| | - Gianluca D'Amico
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 335700, Cluj-Napoca, Romania
| | - Lucia Victoria Bel
- Department of Anesthesiology and Surgical Techniques, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 335700, Cluj-Napoca, Romania
| | - Mirabela Oana Dumitrache
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 335700, Cluj-Napoca, Romania.
| | - David Modrý
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Andrei Daniel Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 335700, Cluj-Napoca, Romania
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Development of a Rapid Identification Method for the Differentiation of Enterococcus Species Using a Species-Specific Multiplex PCR Based on Comparative Genomics. Curr Microbiol 2017; 74:476-483. [PMID: 28229213 DOI: 10.1007/s00284-017-1210-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 02/02/2017] [Indexed: 10/20/2022]
Abstract
Enterococci are lactic acid bacteria that are commonly found in food and in animal gut. Since 16 S ribosomal RNA (rRNA) sequences, genetic markers for bacterial identification, are similar among several Enterococcus species, it is very difficult to determine the correct species based on only 16 S rRNA sequences. Therefore, we developed a rapid method for the identification of different Enterococcus species using comparative genomics. We compared 38 genomes of 13 Enterococcus species retrieved from the National Center of Biotechnology Information database and identified 25,623 orthologs. Among the orthologs, four genes were specific to four Enterococcus species (Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, and Enterococcus durans). We designed species-specific primer sets targeting the genes and developed a multiplex PCR using primer sets that could distinguish the four Enterococcus species among the nine strains of Enterococcus species that were available locally. The multiplex PCR method also distinguished the four species isolated from various environments, such as feces of chicken and cow, meat of chicken, cow, and pigs, and fermented soybeans (Cheonggukjang and Doenjang). These results indicated that our novel multiplex PCR using species-specific primers could identify the four Enterococcus species in a rapid and easy way. This method will be useful to distinguish Enterococcus species in food, feed, and clinical settings.
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Morozov VA, Heinrichs G, Denner J. Effective Detection of Porcine Cytomegalovirus Using Non-Invasively Taken Samples from Piglets. Viruses 2017; 9:v9010009. [PMID: 28085106 PMCID: PMC5294978 DOI: 10.3390/v9010009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/29/2016] [Accepted: 01/03/2017] [Indexed: 11/21/2022] Open
Abstract
Shortage of human organs forced the development of xenotransplantation using cells, tissues, and organs from pigs. Xenotransplantation may be associated with the transmission of porcine zoonotic microorganisms, among them the porcine cytomegalovirus (PCMV). To prevent virus transmission, pigs have to be screened using sensitive methods. In order to perform regular follow-ups and further breeding of the animals, samples for testing should be collected by low-invasive or non-invasive methods. Sera, ear biopsies, as well as oral and anal swabs were collected from ten 10-day-old Aachen minipigs (AaMP) and tested for PCMV using sensitive nested polymerase chain reaction (PCR) as well as uniplex and duplex real-time PCR. Porcine cytomegalovirus DNA was detected most frequently in oral and anal swabs. Comparison of duplex and uniplex real-time PCR systems for PCMV detection demonstrated a lower sensitivity of duplex real-time PCR when the copy numbers of the target genes were low (less 200). Therefore, to increase the efficacy of PCMV detection in piglets, early testing of oral and anal swabs by uniplex real-time PCR is recommended.
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190
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Sequence specific sorting of DNA molecules with FACS using 3dPCR. Sci Rep 2017; 7:39385. [PMID: 28051104 PMCID: PMC5209659 DOI: 10.1038/srep39385] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/22/2016] [Indexed: 12/04/2022] Open
Abstract
Genetic heterogeneity is an important feature of many biological systems, but introduces technical challenges to their characterization. Even with the best modern instruments, only a small fraction of DNA molecules present in a sample can be read, and they are recovered in the form of short, hundred-base reads. In this paper, we introduce 3dPCR, a method to sort DNA molecules with sequence specificity. 3dPCR allows heterogeneous populations of DNA to be sorted to recover long targets for deep sequencing. It is valuable whenever a target sequence is rare in a mixed population, such as for characterizing mutations in heterogeneous cancer cell populations or identifying cells containing a specific genetic sequence or infected with a target virus.
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191
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Kumar P, Medigeshi GR, Mishra VS, Islam M, Randev S, Mukherjee A, Chaudhry R, Kapil A, Ram Jat K, Lodha R, Kabra SK. Etiology of Acute Respiratory Infections in Infants: A Prospective Birth Cohort Study. Pediatr Infect Dis J 2017; 36:25-30. [PMID: 27753796 DOI: 10.1097/inf.0000000000001359] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND There is paucity of studies on etiology of acute respiratory infections (ARI) in infants. The objective of this study is to document incidence and etiology of ARI in infants, their seasonal variability and association of clinical profile with etiology. METHODS A birth cohort was followed for the first year of life; for each episode of ARI, nasopharyngeal aspirates were collected to identify the causative respiratory virus(es) using multiplex real-time polymerase chain reaction assay. For lower respiratory tract infections blood culture, serum procalcitonin, serum antibodies to Mycoplasma and Chlamydia and urinary Streptococcus pneumoniae antigen were also assayed. RESULTS A total of 503 ARI episodes were documented in 310 infants for an incidence rate of 1.8 episodes per infant per year. Of these, samples were processed in 395 episodes (upper respiratory tract infection: 377; lower respiratory tract infection: 18). One or more viruses were detected in 250 (63.3%) episodes and viral coinfections in 72 (18.2%) episodes. Rhinovirus was the most common virus [105 (42%)] followed by respiratory syncytial virus [50 (20%)], parainfluenza virus [42 (16.8%)] and coronavirus [44 (17.6%)]. In lower respiratory tract infections, viral infections were detected in 12 (66.7%) episodes, bacterial infections in 17 (94.4%) episodes and mixed bacterial-viral infections in 8 (44.4%) episodes. Peak incidence of viruses was observed during February-March and September-November. There was no significant difference in symptom duration with virus types. CONCLUSION In this cohort of infants, ARI incidence was 1.8 episodes per year per infant; 95% were upper respiratory tract infections. Viruses were identified in 63.3% episodes, and the most common viruses detected were rhinovirus, respiratory syncytial virus and parainfluenza virus.
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Affiliation(s)
- Prawin Kumar
- From the *Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India; †Department of Biotechnology, Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute (THSTI), Faridabad, India; and ‡Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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Zhang X, Peng Y, Wang Y, Zhang Z, Li D, Yu J, Han C. Simultaneous detection and differentiation of three genotypes of Brassica yellows virus by multiplex reverse transcription-polymerase chain reaction. Virol J 2016; 13:189. [PMID: 27876078 PMCID: PMC5120529 DOI: 10.1186/s12985-016-0647-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/10/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Brassica yellows virus (BrYV), proposed to be a new polerovirus species, three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) have been described. This study was to develop a simple, rapid, sensitive, cost-effective method for simultaneous detection and differentiation of three genotypes of BrYV. RESULTS In this study, a multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for simultaneous detection and differentiation of the three genotypes of BrYV. The three genotypes of BrYV and Tunip yellows virus (TuYV) could be differentiated simultaneously using six optimized specific oligonucleotide primers, including one universal primer for detecting BrYV, three BrYV genotype-specific primers, and a pair of primers for specific detection of TuYV. Primers were designed from conserved regions of each virus and their specificity was confirmed by sequencing PCR products. The mRT-PCR products were 278 bp for BrYV-A, 674 bp for BrYV-B, 505 bp for BrYV-C, and 205 bp for TuYV. Amplification of three target genotypes was optimized by increasing the PCR annealing temperatures to 62 °C. One to three fragments specific for the virus genotypes were simultaneously amplified from infected samples and identified by their specific molecular sizes in agarose gel electrophoresis. No specific products could be amplified from cDNAs of other viruses which could infect crucifer crops. Detection limits of the plasmids for multiplex PCR were 100 fg for BrYV-A and BrYV-B, 10 pg for BrYV-C, and 1 pg for TuYV, respectively. The mRT-PCR was applied successfully for detection of three BrYV genotypes from field samples collected in China. CONCLUSIONS The simple, rapid, sensitive, and cost-effective mRT-PCR was developed successfully for detection and differentiation of the three genotypes of BrYV.
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Affiliation(s)
- Xiaoyan Zhang
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Yanmei Peng
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Ying Wang
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Zongying Zhang
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Dawei Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jialin Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenggui Han
- State Key Laboratory for Agrobiotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
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193
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Xu L, You X, Zheng P, Zhang BM, Gupta PK, Lavori P, Meyer E, Zehnder JL. Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use. J Mol Diagn 2016; 19:72-83. [PMID: 27815002 DOI: 10.1016/j.jmoldx.2016.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/24/2016] [Accepted: 07/28/2016] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10-3. A single library could identify >93% of the clones with frequency ≥10-3 in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10-3 and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
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Affiliation(s)
- Liwen Xu
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Xiaoqing You
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - PingPing Zheng
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Puja K Gupta
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Philip Lavori
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, Stanford, California
| | - Everett Meyer
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California.
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194
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Nested PCR Assay for Eight Pathogens: A Rapid Tool for Diagnosis of Bacterial Meningitis. Mol Diagn Ther 2016; 20:45-54. [PMID: 26645831 DOI: 10.1007/s40291-015-0174-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE Bacterial meningitis is a dreadful infectious disease with a high mortality and morbidity if remained undiagnosed. Traditional diagnostic methods for bacterial meningitis pose a challenge in accurate identification of pathogen, making prognosis difficult. The present study is therefore aimed to design and evaluate a specific and sensitive nested 16S rDNA genus-based polymerase chain reaction (PCR) assay using clinical cerebrospinal fluid (CSF) for rapid diagnosis of eight pathogens causing the disease. METHODS The present work was dedicated to development of an in-house genus specific 16S rDNA nested PCR covering pathogens of eight genera responsible for causing bacterial meningitis using newly designed as well as literature based primers for respective genus. A total 150 suspected meningitis CSF obtained from the patients admitted to Central India Institute of Medical Sciences (CIIMS), India during the period from August 2011 to May 2014, were used to evaluate clinical sensitivity and clinical specificity of optimized PCR assays. RESULTS The analytical sensitivity and specificity of our newly designed genus-specific 16S rDNA PCR were found to be ≥92%. With such a high sensitivity and specificity, our in-house nested PCR was able to give 100% sensitivity in clinically confirmed positive cases and 100% specificity in clinically confirmed negative cases indicating its applicability in clinical diagnosis. CONCLUSIONS Our in-house nested PCR system therefore can diagnose the accurate pathogen causing bacterial meningitis and therefore be useful in selecting a specific treatment line to minimize morbidity. Results are obtained within 24 h and high sensitivity makes this nested PCR assay a rapid and accurate diagnostic tool compared to traditional culture-based methods.
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195
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Yaren O, Glushakova LG, Bradley KM, Hoshika S, Benner SA. Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus. J Virol Methods 2016; 236:54-61. [PMID: 27421627 PMCID: PMC5010982 DOI: 10.1016/j.jviromet.2016.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 06/17/2016] [Accepted: 07/12/2016] [Indexed: 11/21/2022]
Abstract
This paper combines two advances to detect MERS-CoV, the causative agent of Middle East Respiratory Syndrome, that have emerged over the past few years from the new field of "synthetic biology". Both are based on an older concept, where molecular beacons are used as the downstream detection of viral RNA in biological mixtures followed by reverse transcription PCR amplification. The first advance exploits the artificially expanded genetic information systems (AEGIS). AEGIS adds nucleotides to the four found in standard DNA and RNA (xNA); AEGIS nucleotides pair orthogonally to the A:T and G:C pairs. Placing AEGIS components in the stems of molecular beacons is shown to lower noise by preventing unwanted stem invasion by adventitious natural xNA. This should improve the signal-to-noise ratio of molecular beacons operating in complex biological mixtures. The second advance introduces a nicking enzyme that allows a single target molecule to activate more than one beacon, allowing "signal amplification". Combining these technologies in primers with components of a self-avoiding molecular recognition system (SAMRS), we detect 50 copies of MERS-CoV RNA in a multiplexed respiratory virus panel by generating fluorescence signal visible to human eye and/or camera.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Lyudmyla G Glushakova
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA; Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, USA.
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196
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Akhter A, Mughal MK, Elyamany G, Sinclair G, Azma RZ, Masir N, Shuib S, Rashid-Kolvear F, Shabani-Rad MT, Stewart DA, Mansoor A. Multiplexed automated digital quantification of fusion transcripts: comparative study with fluorescent in-situ hybridization (FISH) technique in acute leukemia patients. Diagn Pathol 2016; 11:89. [PMID: 27632978 PMCID: PMC5024455 DOI: 10.1186/s13000-016-0541-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 09/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The World Health Organization (WHO) classification system defines recurrent chromosomal translocations as the sole diagnostic and prognostic criteria for acute leukemia (AL). These fusion transcripts are pivotal in the pathogenesis of AL. Clinical laboratories universally employ conventional karyotype/FISH to detect these chromosomal translocations, which is complex, labour intensive and lacks multiplexing capacity. Hence, it is imperative to explore and evaluate some newer automated, cost-efficient multiplexed technologies to accommodate the expanding genetic landscape in AL. METHODS "nCounter® Leukemia fusion gene expression assay" by NanoString was employed to detect various fusion transcripts in a large set samples (n = 94) utilizing RNA from formalin fixed paraffin embedded (FFPE) diagnostic bone marrow biopsy specimens. This series included AL patients with various recurrent translocations (n = 49), normal karyotype (n = 19), or complex karyotype (n = 21), as well as normal bone marrow samples (n = 5). Fusion gene expression data were compared with results obtained by conventional karyotype and FISH technology to determine sensitivity/specificity, as well as positive /negative predictive values. RESULTS Junction probes for PML/RARA; RUNX1-RUNX1T1; BCR/ABL1 showed 100 % sensitivity/specificity. A high degree of correlation was noted for MLL/AF4 (85 sensitivity/100 specificity) and TCF3-PBX1 (75 % sensitivity/100 % specificity) probes. CBFB-MYH11 fusion probes showed moderate sensitivity (57 %) but high specificity (100 %). ETV6/RUNX1 displayed discordance between fusion transcript assay and FISH results as well as rare non-specific binding in AL samples with normal or complex cytogenetics. CONCLUSIONS Our study presents preliminary data with high correlation between fusion transcript detection by a throughput automated multiplexed platform, compared to conventional karyotype/FISH technique for detection of chromosomal translocations in AL patients. Our preliminary observations, mandates further vast validation studies to explore automated molecular platforms in diagnostic pathology.
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Affiliation(s)
- Ariz Akhter
- Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, Calgary, AB, Canada
| | - Muhammad Kashif Mughal
- Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, Calgary, AB, Canada
| | - Ghaleb Elyamany
- Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, Calgary, AB, Canada
| | - Gary Sinclair
- Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, Calgary, AB, Canada
| | - Raja Zahratul Azma
- Department of Pathology, University Kebangsaan Malaysia, Kuala Lumpur, Cheras, Malaysia
| | - Noraidah Masir
- Department of Pathology, University Kebangsaan Malaysia, Kuala Lumpur, Cheras, Malaysia
| | - Salwati Shuib
- Department of Pathology, University Kebangsaan Malaysia, Kuala Lumpur, Cheras, Malaysia
| | - Fariborz Rashid-Kolvear
- Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, Calgary, AB, Canada
| | - Meer-Taher Shabani-Rad
- Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, Calgary, AB, Canada
| | | | - Adnan Mansoor
- Department of Pathology and Laboratory Medicine, University of Calgary and Calgary Laboratory Services, Calgary, AB, Canada. .,Division of Haematology and Transfusion Medicine, University of Calgary/Calgary Laboratory Services, Room 7522, 7th floor, McCaig tower building; 3134 Hospital drive NW, Calgary, AB, T2N 5A1, Canada.
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Li J, Macdonald J. Multiplexed lateral flow biosensors: Technological advances for radically improving point-of-care diagnoses. Biosens Bioelectron 2016; 83:177-92. [DOI: 10.1016/j.bios.2016.04.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/22/2022]
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198
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Turchaninova MA, Davydov A, Britanova OV, Shugay M, Bikos V, Egorov ES, Kirgizova VI, Merzlyak EM, Staroverov DB, Bolotin DA, Mamedov IZ, Izraelson M, Logacheva MD, Kladova O, Plevova K, Pospisilova S, Chudakov DM. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat Protoc 2016; 11:1599-616. [DOI: 10.1038/nprot.2016.093] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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199
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Dale TD, Watts PC, Jones D, Pounder K, Everest DJ, Begon ME, Chantrey J. Enhancement of wildlife disease surveillance using multiplex quantitative PCR: development of qPCR assays for major pathogens in UK squirrel populations. EUR J WILDLIFE RES 2016; 62:589-599. [PMID: 32214943 PMCID: PMC7088385 DOI: 10.1007/s10344-016-1031-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/22/2016] [Accepted: 07/03/2016] [Indexed: 11/22/2022]
Abstract
Rapid development in polymerase chain reaction (PCR) technology has revolutionised the speed and accuracy of many diagnostic assays. However, comparatively few wildlife epidemiological studies use quantitative PCR (qPCR) for pathogen detection, even fewer employ an internal control, to ensure confidence in negative results, and PCR's ability to multiplex and therefore detect several targets in a single reaction is underutilised. Here, we describe the development of two multiplex qPCR assays for the red and grey squirrel that detect the pathogens squirrelpox virus (SQPV) and adenovirus in squirrels (SADV), both of which cause mortality in the red squirrel. Both assays use a section of the squirrel phosphoglycerate kinase gene as an endogenous internal control that identifies and compensates for both, inadequate sampling or PCR inhibition. Tests on infected squirrel tissue demonstrate that simple swab samples (particularly from distal antebrachial skin) are sufficient to detect and identify the relative quantity of SQPV DNA in both squirrel species, while rectal swabs and blood cell pellets can be used to reliably indicate SADV infection. These assays are sensitive and specific with an endogenous internal control providing confidence in negative results and allowing comparison across laboratories. Using such assays should prove advantageous in wildlife studies with limited resources while allowing the maximum data yield.
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Affiliation(s)
- Timothy D. Dale
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
| | | | - David Jones
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Kieran Pounder
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
| | - David J. Everest
- Animal and Plant Health Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB UK
| | - Michael E. Begon
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
| | - Julian Chantrey
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
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Kaur G, Chandra M, Dwivedi P, Narang D. Multiplex real-time PCR for identification of canine parvovirus antigenic types. J Virol Methods 2016; 233:1-5. [DOI: 10.1016/j.jviromet.2016.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/20/2016] [Accepted: 02/20/2016] [Indexed: 11/29/2022]
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