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Cao X, Huang M, Wang Y, Chen Y, Yang H, Quan F. Immunogenicity Analysis of PCV3 Recombinant Capsid Protein Virus-like Particles and Their Application in Antibodies Detection. Int J Mol Sci 2023; 24:10377. [PMID: 37373524 DOI: 10.3390/ijms241210377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Porcine circovirus type 3 is a newly emerging pathogen of porcine circovirus associated disease (PCVAD). Currently, there is no commercially available vaccine, resulting in huge economic losses to the pig industry. Porcine circovirus type 3 capsid protein (Cap) can self-assemble into virus-like particles (VLPs). Therefore, the expression of the recombinant Cap protein is of great significance for the prevention, diagnosis and control of porcine circovirus type 3 associated diseases. In this study, the recombinant Cap protein was successfully expressed in Escherichia coli by deleting the nuclear localization sequence (NLS). The VLPs were observed by transmission electron microscopy. To evaluate the immunogenicity of the recombinant Cap protein, mice were immunized. As a result, the recombinant Cap protein can induce higher levels of humoral and cellular immune responses. A VLP-based ELISA method was developed for the detection of antibodies. The established ELISA method has good sensitivity, specificity, repeatability and clinical applicability. These results demonstrate the successful expression of the PCV3 recombinant Cap protein and the preparation of recombinant Cap protein VLPs, which can be used for the preparation of subunit vaccines. Meanwhile, the established I-ELISA method lays a foundation for the development of the commercial PCV3 serological antibody detection kit.
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Affiliation(s)
- Xuyang Cao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, China
| | - Min Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, China
| | - Ying Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, China
| | - Yanzhi Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, China
| | - Hanwen Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, China
| | - Fusheng Quan
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, China
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2
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Yu Z, Zhao Z, Chen L, Yan H, Cui Q, Ju X, Yong Y, Liu X, Ma X, Zhang G. Development of a droplet digital PCR assay to detect bovine alphaherpesvirus 1 in bovine semen. BMC Vet Res 2022; 18:125. [PMID: 35366879 PMCID: PMC8976375 DOI: 10.1186/s12917-022-03235-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Infectious bovine rhinotracheitis (IBR) caused by bovine alphaherpesvirus 1 (BoHV-1) is one of the most important contagious diseases in bovine. This is one of the most common infectious disease of cattle. This has led to high economic losses in the cattle farming industry. BoHV-1 can potentially be transmitted via semen during natural or artificial insemination (AI). Therefore, testing methods for the early diagnosis of BoHV-1 infection are urgently needed for international trade of ruminant semen. In this study, we developed a novel droplet digital PCR (ddPCR) assay for the detection of BoHV-1 DNA in semen samples.
Results
The ddPCR results showed that the detection limit was 4.45 copies per reaction with high reproducibility. The established method was highly specific for BoHV-1 and did not show cross-reactivity with specify the organisms (BTV, BVDV, Brucella, M . bovis). The results of clinical sample testing showed that the positivity rate of ddPCR (87.8%) was higher than that of qPCR (84.1%).
Conclusions
The ddPCR assay showed good accuracy for mixed samples and could be a new added diagnostic tool for detecting BoHV-1.
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3
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Five years of porcine circovirus 3: what have we learned about the clinical disease, immune pathogenesis, and diagnosis. Virus Res 2022; 314:198764. [DOI: 10.1016/j.virusres.2022.198764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/24/2022]
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4
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Wang W, Zhou L, Ge X, Han J, Guo X, Chen Y, Zhang Y, Yang H. Development of a VP2-based real-time fluorescent reverse transcription recombinase-aided amplification assay to rapidly detect Senecavirus A. Transbound Emerg Dis 2021; 69:2828-2839. [PMID: 34931455 DOI: 10.1111/tbed.14435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 01/28/2023]
Abstract
Senecavirus A (SVA), a newly emergent picornavirus correlated with sudden neonatal mortality and vesicular lesions in pigs, has had a considerable impact on the global pig farming industry. Timely and dependable detection of SVA is helpful in preventing the further spread of this pathogenic virus. In the current study, a real-time fluorescent reverse transcription recombinase-aided amplification (rRT-RAA) assay, which targets the most conserved region within the VP2 gene of SVA, was developed and evaluated for SVA detection. The detection limit for this assay was tested to be 1.185 50% tissue culture infective dose (TCID50 ) of SVA RNA per reaction at a 95% confidence interval, which is comparable to that of a previously published rRT-PCR assay for SVA. The testing results of the rRT-RAA assay were very reproducible and repeatable, with inter- and intra-assay coefficient of variation values less than 7.0%. In addition, the established rRT-RAA assay displayed excellent specificity for SVA detection without cross-reaction with other clinically important swine pathogenic viruses. The diagnostic performance of rRT-RAA was evaluated using 189 clinical swine samples, which were detected in parallel using the reference rRT-PCR assay. The results showed that 146 and 151 samples tested positive for SVA by rRT-RAA and rRT-PCR, respectively. The overall agreement between both assays was 97.4% (184/189) with a kappa value of 0.927 (p < .001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9192, p < .0001). Taken together, our newly established rRT-RAA assay is a powerful and time-saving diagnostic tool for SVA detection in clinical samples. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wenlong Wang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Yanhong Chen
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
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5
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Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs). Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.
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Cui X, Abd El-Aty AM, Zhang C, Xu L, Liu H, Jia H, Wang Y, Cao Z, Salvador JP, She Y, Jin F, Wang J, Jin M, Hammock BD. Enhanced Bio-Barcode Immunoassay Using Droplet Digital PCR for Multiplex Detection of Organophosphate Pesticides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11131-11141. [PMID: 34494438 DOI: 10.1021/acs.jafc.1c03216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A bio-barcode immunoassay based on droplet digital polymerase chain reaction (ddPCR) was developed to simultaneously quantify triazophos, parathion, and chlorpyrifos in apple, cucumber, cabbage, and pear. Three gold nanoparticle (AuNP) probes and magnetic nanoparticle (MNP) probes were prepared, binding through their antibodies with the three pesticides in the same tube. Three groups of primers, probes, templates, and three antibodies were designed to ensure the specificity of the method. Under the optimal conditions, the detection limits (expressed as IC10) of triazophos, parathion, and chlorpyrifos were 0.22, 0.45, and 4.49 ng mL-1, respectively. The linear ranges were 0.01-20, 0.1-100, and 0.1-500 ng mL-1, and the correlation coefficients (R2) were 0.9661, 0.9834, and 0.9612, respectively. The recoveries and relative standard deviations (RSDs) were in the ranges of 75.5-98.9 and 8.3-16.7%. This study provides the first insights into the ddPCR for the determination of organophosphate pesticides. It also laid the foundation for high-throughput detection of other small molecules.
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Affiliation(s)
- Xueyan Cui
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - A M Abd El-Aty
- State Key Laboratory of Biobased Material and Green Papermaking, College of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, P. R. China
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum 25240, Turkey
| | - Chan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Lingyuan Xu
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Haijin Liu
- Inspection and Testing Center of Agricultural and Livestock Products of Tibet, Lhasa 850000, P. R. China
| | - Huiyan Jia
- Ningbo Academy of Agricultural Sciences, Ningbo 315040, Zhengjiang, P. R. China
| | - Yuanshang Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Zhen Cao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - J-Pablo Salvador
- Nanobiotechnology for Diagnostics Group, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, C/ Jordi Girona, 18-26, 08034 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Avenida Monforte de Lemos, 3-5, Pavillion 11, Floor 0, 28029 Madrid, Spain
| | - Yongxin She
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Fen Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Maojun Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Bruce D Hammock
- Department of Entomology & Nematology and the UC Davis Comprehensive Cancer Center, University of California, Davis, Davis, California 95616, United States
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7
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Bian Z, Cai R, Jiang Z, Song S, Li Y, Chu P, Zhang K, Yang D, Gou H, Li C. Single Multiple Cross Displacement Amplification for Rapid and Real-Time Detection of Porcine Circovirus 3. Front Vet Sci 2021; 8:726723. [PMID: 34540937 PMCID: PMC8448386 DOI: 10.3389/fvets.2021.726723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/04/2021] [Indexed: 11/17/2022] Open
Abstract
Since 2016, a novel porcine circovirus, PCV3, has been infecting pigs, causing significant economic losses to the pig industry. In recent years, the infection rate of PCV3 has been increasing, and thus rapid and accurate detection methods for PCV3 are essential. In this study, we established a novel probe-based single multiple cross displacement amplification (P-S-MCDA) method for PCV3. The method was termed as P-S-MCDA. The P-S-MCDA uses seven primers to amplify the capsid gene, and the assay can be performed at 60°C for 30 min, greatly shortening the reaction time. The results of P-S-MCDA can not only be monitored in real time through fluorescence signals but also be determined by observing the fluorescence of the reaction tubes using a smartphone-based cassette. This method demonstrated good specificity and the same sensitivity as qPCR, with a minimum detection limit of 10 copies. In 139 clinical samples, the coincidence rate with qPCR was 100%. The P-S-MCDA can be widely applied in PCV3 detection in laboratories or in rural areas.
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Affiliation(s)
- Zhibiao Bian
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Rujian Cai
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Zhiyong Jiang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yan Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Pinpin Chu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Kunli Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Dongxia Yang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Chunling Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
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8
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Genetic diversity of porcine circovirus 3 strains and the first detection of two different PCV3 strains coinfecting the same host in Minas Gerais, Brazil. Arch Virol 2021; 166:1463-1468. [PMID: 33718993 DOI: 10.1007/s00705-021-05032-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/23/2021] [Indexed: 02/06/2023]
Abstract
Porcine circovirus 3 (PCV3) is a recently emerged circovirus discovered in 2016 that has drawn the attention of the swine industry worldwide. In this study, we evaluated the genetic diversity of PCV3 strains on pig farms. A total of 261 samples from sows, weaning pigs, growing pigs, and stillborn/mummified fetuses were analyzed by quantitative real-time PCR. The results revealed that at least two main lineages of PCV3 are circulating in Brazil. For the first time, it was possible to detect the presence of two different PCV3 strains in the same host.
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9
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Yu Z, Zhao Z, Chen L, Li J, Ju X. Development of a Droplet Digital PCR for Detection of Trichuriasis in Sheep. J Parasitol 2021; 106:603-610. [PMID: 32997756 DOI: 10.1645/20-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Trichuriasis is a serious threat to the economic development of animal husbandry. This research aimed to establish a droplet digital PCR (ddPCR) method to detect Trichuris spp. for the early diagnosis and prevention of trichuriasis in sheep. The real-time quantitative PCR (qPCR) and ddPCR methods were used for the detection of nematodes by targeted amplification of the ITS gene. Each means was evaluated to optimize the limit of detection and reproducibility. For a recombinant plasmid, the qPCR results showed that the detection limit was 31.7 copies per reaction. In contrast to qPCR, ddPCR was able to detect concentrations below 3.17 copies per reaction. Both assays exhibited good reproducibility. However, the ddPCR method was more stable for low-copy-number detection. This new assay was specific for Trichuris spp. and did not cross-react with other relevant gastrointestinal nematodes. A total of 98 clinical samples were tested with both assays. The results showed that the positive rate of ddPCR (80.6%) was higher than that of qPCR (72.4%). This method could be used as an efficient molecular biology tool to test for Trichuris spp. and could be a new valuable tool for the clinical diagnosis and prevention of trichuriasis.
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Affiliation(s)
- Zhichao Yu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China.,Technology Center, Hohhot Customs District, Hohhot, 010020, Inner Mongolia, China
| | - Zhiguo Zhao
- Technology Center, Hohhot Customs District, Hohhot, 010020, Inner Mongolia, China
| | - Linjun Chen
- Technology Center, Hohhot Customs District, Hohhot, 010020, Inner Mongolia, China
| | - Junyan Li
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China
| | - Xianghong Ju
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
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Rotondo JC, Oton-Gonzalez L, Mazziotta C, Lanzillotti C, Iaquinta MR, Tognon M, Martini F. Simultaneous Detection and Viral DNA Load Quantification of Different Human Papillomavirus Types in Clinical Specimens by the High Analytical Droplet Digital PCR Method. Front Microbiol 2020; 11:591452. [PMID: 33329471 PMCID: PMC7710522 DOI: 10.3389/fmicb.2020.591452] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Human papillomaviruses (HPVs) are small DNA tumor viruses that mainly infect mucosal epithelia of anogenital and upper respiratory tracts. There has been progressive demand for more analytical assays for HPV DNA quantification. A novel droplet digital PCR (ddPCR) method was developed to simultaneously detect and quantify HPV DNA from different HPV types. DdPCR was initially tested for assay sensitivity, accuracy, specificity as well as intra- and inter-run assay variation employing four recombinant plasmids containing HPV16, HPV18, HPV11, and HPV45 DNAs. The assay was extended to investigate/quantify HPV DNA in Cervical Intraepithelial Neoplasia (CIN, n = 45) specimens and human cell lines (n = 4). DdPCR and qPCR data from clinical samples were compared. The assay showed high accuracy, sensitivity and specificity, with low intra-/inter- run variations, in detecting/quantifying HPV16/18/11/45 DNAs. HPV DNA was detected in 51.1% (23/45) CIN DNA samples by ddPCR, whereas 40% (18/45) CIN tested HPV-positive by qPCR. Five CIN, tested positive by ddPCR, were found to be negative by qPCR. In CIN specimens, the mean HPV DNA loads determined by ddPCR were 3.81 copy/cell (range 0.002–51.02 copy/cell), whereas 8.04 copy/cell (range 0.003–78.73 copy/cell) by qPCR. DdPCR and qPCR concordantly detected HPV DNA in SiHa, CaSki and Hela cells, whereas HaCaT tested HPV-negative. The correlation between HPV DNA loads simultaneously detected by ddPCR/qPCR in CINs/cell lines was good (R2 = 0.9706, p < 0.0001). Our data indicate that ddPCR is a valuable technique in quantifying HPV DNA load in CIN specimens and human cell lines, thereby improving clinical applications, such as patient management after primary diagnosis of HPV-related lesions with HPV-type specific assays.
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Affiliation(s)
- John Charles Rotondo
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Lucia Oton-Gonzalez
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Mazziotta
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Carmen Lanzillotti
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Maria Rosa Iaquinta
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Mauro Tognon
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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11
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Stevenson A, Wakeham K, Pan J, Kavanagh K, Millan D, Bell S, McLellan D, Graham SV, Cuschieri K. Droplet digital PCR quantification suggests that higher viral load correlates with improved survival in HPV-positive oropharyngeal tumours. J Clin Virol 2020; 129:104505. [PMID: 32604039 DOI: 10.1016/j.jcv.2020.104505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 01/29/2023]
Abstract
BACKGROUND Although HPV-positive oropharyngeal cancer (OPC) patients have improved prognosis compared to HPV negative patients; there remains an HPV-positive group who have poor outcomes. Biomarkers to stratify discrete patient outcomes are thus desirable. Our objective was to analyse viral load (VL) by droplet digital PCR (ddPCR), in HPV-positive patients with OPC on whom clinical outcome data were available. METHODS In a cohort of patients that had previously tested HPV positive via conventional PCR, VL was determined using ddPCR assays for HPV16 L1 and E6 genes. VL was classed as "medium/high" if more than 5.57 copies or 8.68 copies of the HPV 16 L1 or E6 gene were detected respectively. Effect of VL on overall survival and hazard of death & disease progression was performed with adjustments made for sex, age, deprivation, smoking, alcohol consumption and stage. RESULTS L1 VL ranged from 0.0014-304 gene copies per cell with a mean of 30.9; comparatively E6 VL ranged from 0.0012-356 copies per cell with a mean of 37.9. Univariate analysis showed those with a medium/high VL had a lower hazard of death; this was significant for L1 (p = 0.02) but not for E6 (p = 0.67). The ratio of E6 to L1 deviated from n = 1 in most samples but had no influence on clinical outcomes. CONCLUSIONS HPV viral load may be informative for the further stratification of clinical outcomes in HPV positive OPC patients.
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Affiliation(s)
- A Stevenson
- Centre for Virus Research, Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - J Pan
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - K Kavanagh
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - D Millan
- Department of Pathology, The Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - S Bell
- Department of Pathology, The Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - D McLellan
- Department of Pathology, The Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - S V Graham
- Centre for Virus Research, Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - K Cuschieri
- Scottish HPV Reference Laboratory, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, UK.
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12
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Li Y, Yu Z, Jiao S, Liu Y, Ni H, Wang Y. Development of a recombinase-aided amplification assay for rapid and sensitive detection of porcine circovirus 3. J Virol Methods 2020; 282:113904. [PMID: 32470487 DOI: 10.1016/j.jviromet.2020.113904] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023]
Abstract
Porcine circovirus type 3 (PCV3) is a novel member of the genus Circovirus, first detected in the United States in 2016, with subsequent reports in many countries. PCV3 infections have caused serious economic losses in the pig industry. Alternative rapid and sensitive assays for PCV3 detection are needed for clinical diagnosis, especially in laboratories not equipped with more sophisticated equipment. Here, a real-time recombinase-aided amplification assay (RAA) was developed for PCV3 detection. Specific primers and probes targeting the conserved region of the capsid gene of PCV3 were designed. The assay was performed at 39 °C for 30 min using specialized equipment. Furthermore, 36 clinical samples were used to evaluate the RAA. The analytical sensitivity of the RAA for PCV3 was 38 copies per reaction at 95% probability level, using a probit regression model. There was no cross-reactivity with other DNA viruses belonging to the Circoviridae and Parvoviridae families. The detection rate agreed with that obtained by an established real-time PCR assay with a kappa value of 1.0. Our results demonstrated that this new RAA could be used for the rapid, accurate, and sensitive detection of PCV3.
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Affiliation(s)
- Yongdong Li
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Zhaorong Yu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Suli Jiao
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Yuhui Liu
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Hongxia Ni
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Yong Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.
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13
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Goecke NB, Hjulsager CK, Krog JS, Skovgaard K, Larsen LE. Development of a high-throughput real-time PCR system for detection of enzootic pathogens in pigs. J Vet Diagn Invest 2019; 32:51-64. [PMID: 31752620 DOI: 10.1177/1040638719890863] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Respiratory and intestinal diseases in pigs can have significant negative influence on productivity and animal welfare. A wide range of real-time PCR (rtPCR) assays are used in our laboratory (National Veterinary Institute, Technical University of Denmark) for pathogen detection, and PCR analyses are performed on traditional rtPCR platforms in which a limited number of samples can be analyzed per day given limitations in equipment and personnel. To mitigate these restrictions, rtPCR assays have been optimized for the high-throughput rtPCR BioMark platform (Fluidigm). Using this platform, we developed a high-throughput detection system that can be used for simultaneous examination of 48 samples with detection specificity for 18 selected respiratory and enteric viral and bacterial pathogens of high importance to Danish pig production. The rtPCR assays were validated and optimized to run under the same reaction conditions using a BioMark 48.48 dynamic array (DA) integrated fluidic circuit chip, and the sensitivity and specificity were assessed by testing known positive samples. Performance of the 48.48DA was similar to traditional rtPCR analysis, and the specificity of the 48.48DA was high. Application of the high-throughput platform has resulted in a significant reduction in cost and working hours and has provided production herds with a new innovative service with the potential to facilitate the optimal choice of disease control strategies such as vaccination and treatment.
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Affiliation(s)
- Nicole B Goecke
- Division for Diagnostics & Scientific Advice, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark (Goecke, Hjulsager, Krog, Skovgaard, Larsen)
| | - Charlotte K Hjulsager
- Division for Diagnostics & Scientific Advice, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark (Goecke, Hjulsager, Krog, Skovgaard, Larsen)
| | - Jesper S Krog
- Division for Diagnostics & Scientific Advice, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark (Goecke, Hjulsager, Krog, Skovgaard, Larsen)
| | - Kerstin Skovgaard
- Division for Diagnostics & Scientific Advice, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark (Goecke, Hjulsager, Krog, Skovgaard, Larsen)
| | - Lars E Larsen
- Division for Diagnostics & Scientific Advice, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark (Goecke, Hjulsager, Krog, Skovgaard, Larsen)
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14
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Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
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15
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Ouyang T, Niu G, Liu X, Zhang X, Zhang Y, Ren L. Recent progress on porcine circovirus type 3. INFECTION GENETICS AND EVOLUTION 2019; 73:227-233. [PMID: 31096019 DOI: 10.1016/j.meegid.2019.05.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/05/2019] [Accepted: 05/12/2019] [Indexed: 02/01/2023]
Abstract
Porcine circovirus 3 (PCV3) is a newly identified virus that belongs to the genus Circovirus in the family Circoviridae. Since the first identification of PCV3 in domestic swine in 2016 in the USA, exciting progress on PCV3 has emphasized the importance of the virus. The aim of this review is to present recent advances in the molecular characteristics, epidemiology, and pathogenesis of PCV3. The virus spreads widely throughout almost all tissues of pig and wild boar in various countries, with a gradual increase of the infection. PCV3 is a pathogen associated with porcine dermatitis and nephropathy syndrome (PDNS)-like clinical signs, reproductive failure, and cardiac and multiorgan inflammation. Furthermore, PCV3 has been detected in other animals and ticks, suggesting that PCV3 possesses cross-species transmission abilities and has an unexpectedly broad distribution and circulation in the wild, where these animals may serve as potential reservoirs for PCV3 and pose a threat to the swine industry or even to humans. Moreover, several detection methods, which can specifically detect PCV3 or differentiate PCV3 from the other viruses, are also reviewed. The present review provides updated knowledge on PCV3-related research. Identification of the prevailing strain of PCV3 and its reservoirs is essential for researchers to understand PCV3 infections and PCV3-related diseases.
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Affiliation(s)
- Ting Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Guyu Niu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Xiaohua Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Xinwei Zhang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Ying Zhang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun 130062, China.
| | - Linzhu Ren
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun 130062, China.
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16
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Zhao Y, Han HY, Fan L, Tian RB, Cui JT, Li JY, Chen HY, Yang MF, Zheng LL. Development of a TB green II-based duplex real-time fluorescence quantitative PCR assay for the simultaneous detection of porcine circovirus 2 and 3. Mol Cell Probes 2019; 45:31-36. [PMID: 30980890 DOI: 10.1016/j.mcp.2019.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/28/2019] [Accepted: 04/07/2019] [Indexed: 11/30/2022]
Abstract
Porcine circovirus 3 (PCV3), as a newly emerged circovirus, is widely distributed in pig populations worldwide. Co-infection of PCV2 and PCV3 has been reported frequently in clinical samples. In the present study, a TB Green II-based duplex real-time polymerase chain reaction (qPCR) was developed to rapidly and differentially detect PCV2 and PCV3. The assay specifically detected PCV2 and PCV3, with no fluorescence signals being detected for other non-targeted pig pathogens. The duplex qPCR showed a high degree of linearity (R2 > 0.998), and its limits of detection were 10 and 78 copies/μL for PCV2 and PCV3, respectively. The duplex qPCR could detect and differentiate PCV2 (melting peaks at 85.5 °C) and PCV3 (melting peaks at 82.5 °C), and showed high repeatability and reproducibility, with intra- and inter-assay coefficients of variation of less than 2.0%. Fifty-six tissue samples from 18 pig farms were used to evaluate the duplex qPCR method. The results revealed infection rates of 66.07% (37/56) and 39.28% (22/56) for PCV2 and PCV3, respectively. The PCV2 + PCV3 co-infection rate was 39.28% (22/56). The developed method could be used as an efficient molecular biology tool for epidemiological investigations of PCV2 and PCV3.
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Affiliation(s)
- Yu Zhao
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Hao-Ying Han
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Lin Fan
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Run-Bo Tian
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Jian-Tao Cui
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Jing-Yi Li
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
| | - Hong-Ying Chen
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China.
| | - Ming-Fan Yang
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China.
| | - Lan-Lan Zheng
- Zhengzhou Key Laboratory for Pig Disease Prevention and Control, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, Henan Province, People's Republic of China
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