1
|
Xu L, Ge G, Li D, Li J, Gong Q, Shi K, Liu F, Diao N, Cui Z, Liu Y, Leng X, Du R. Establishment of a real-time fluorescent quantitative PCR detection method and phylogenetic analysis of BoAHV-1. BMC Vet Res 2024; 20:180. [PMID: 38715028 PMCID: PMC11075196 DOI: 10.1186/s12917-024-04025-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Infectious bovine rhinotracheitis (IBR), caused by Bovine alphaherpesvirus-1 (BoAHV-1), is an acute, highly contagious disease primarily characterized by respiratory tract lesions in infected cattle. Due to its severe pathological damage and extensive transmission, it results in significant economic losses in the cattle industry. Accurate detection of BoAHV-1 is of paramount importance. In this study, we developed a real-time fluorescent quantitative PCR detection method for detecting BoAHV-1 infections. Utilizing this method, we tested clinical samples and successfully identified and isolated a strain of BoAHV-1.1 from positive samples. Subsequently, we conducted a genetic evolution analysis on the isolate strain's gC, TK, gG, gD, and gE genes. RESULTS The study developed a real-time quantitative PCR detection method using SYBR Green II, achieving a detection limit of 7.8 × 101 DNA copies/μL. Specificity and repeatability analyses demonstrated no cross-reactivity with other related pathogens, highlighting excellent repeatability. Using this method, 15 out of 86 clinical nasal swab samples from cattle were found to be positive (17.44%), which was higher than the results obtained from conventional PCR detection (13.95%, 12/86). The homology analysis and phylogenetic tree analysis of the gC, TK, gG, gD, and gE genes of the isolated strain indicate that the JL5 strain shares high homology with the BoAHV-1.1 reference strains. Amino acid sequence analysis revealed that gC, gE, and gG each had two amino acid mutations, while the TK gene had one synonymous mutation and one H to Y mutation, with no amino acid mutations observed in the gD gene. Phylogenetic tree analysis indicated that the JL5 strain belongs to the BoAHV-1.1 genotype and is closely related to American strains such as C33, C14, and C28. CONCLUSIONS The established real-time fluorescent quantitative PCR detection method exhibits good repeatability, specificity, and sensitivity. Furthermore, genetic evolution analysis of the isolated BoAHV-1 JL-5 strain indicates that it belongs to the BoAHV-1.1 subtype. These findings provide a foundation and data for the detection, prevention, and control Infectious Bovine Rhinotracheitis.
Collapse
Affiliation(s)
- Lihui Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Guiyang Ge
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Dongli Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Jianming Li
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Qinglong Gong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Kun Shi
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Fei Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Naichao Diao
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Zhenzhen Cui
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yingyu Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Xue Leng
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| | - Rui Du
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| |
Collapse
|
2
|
Yu J, Zou J, Liu X, Pan Y, Mu Y, Li S, Wang J, Xu F, Wang Y. TaqMan-probe-based multiplex real-time RT-qPCR for simultaneous detection of GoAstV, GPV, and GoCV. Poult Sci 2022; 102:102396. [PMID: 36565640 PMCID: PMC9801206 DOI: 10.1016/j.psj.2022.102396] [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: 08/02/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Goose astrovirus (GoAstV), goose parvovirus (GPV), and goose circovirus (GoCV) infections have similar symptoms, such as severe diarrhea, and cause serious economic losses to the goose industry globally. Therefore, it is necessary to develop a rapid and accurate method for the differential diagnosis of the 3 viruses. In this study, a TaqMan probe-based multiplex reverse transcription-qualitative polymerase chain reaction (RT-qPCR) method was established and optimized for simultaneous detection of the three viruses. Three pairs of specific primers and probes were designed considering the conserved sequences of ORF2, VP3, and Rep of GoAstV, GPV, and GoCV, respectively. Singleplex real-time RT-qPCR detected a minimum of 10 copies of these genes, while multiplex real-time RT-qPCR detected a minimum of 100 copies. The correlation coefficients exceeded 0.99, and the amplification efficiency was 80 to 100%. The assay had high sensitivity, specificity, and repeatability. In 85 tissue samples, GoAstV and GPV were the main pathogens and demonstrated co-infection. This assay provides a rapid, efficient, specific, and sensitive tool for the detection of GoAstV, GPV, and GoCV. This can facilitate disease management and epidemiological surveillance.
Collapse
|
3
|
Development of SYBR Green I-based polymerase chain reaction for feline bocavirus 1 detection. 3 Biotech 2021; 11:61. [PMID: 33457175 PMCID: PMC7799429 DOI: 10.1007/s13205-020-02577-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
Feline bocavirus 1 (FBoV-1) may be associated with diarrhea in cats. In this study, a SYBR Green I-based quantitative polymerase chain reaction (qPCR) assay was established to detect FBoV-1. The melting curve showed a single melting peak at 83.0 ℃. The results of sensitivity showed that the detection limit of the qPCR was 3.87 × 101 copies/μL. Of note, the detection limit of the conventional polymerase chain reaction (cPCR) was 3.87 × 103 copies/μL. The highest intra-assay and inter-assay coefficients of variation (CV%) were 0.98% and 1.42%, respectively. The positive detection rate of 128 clinical samples using the qPCR and the cPCR was 7.0% (9/128) and 4.7% (6/128), respectively. Taken together, these results indicated that the established qPCR assay has good sensitivity, high specificity, and good reproducibility. Therefore, it could provide support for the rapid and efficient clinical detection of FBoV-1.
Collapse
|
4
|
Wang Y, Fu Z, Guo X, Zhang D, Bai C, Li W, Liu G, Li Y, Jiang S. Development of SYBR Green I-based real-time reverse transcription polymerase chain reaction for the detection of feline astrovirus. J Virol Methods 2020; 288:114012. [PMID: 33157149 DOI: 10.1016/j.jviromet.2020.114012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/25/2020] [Accepted: 11/01/2020] [Indexed: 02/07/2023]
Abstract
In this study, a SYBR Green I-based real-time reverse transcription-polymerase chain reaction (RT-PCR) was developed for the clinical diagnosis of feline astroviruses (FeAstVs). Specific primers were designed based on the conserved region of the FeAstV ORF1b gene. Experiments for specificity, sensitivity, and repeatability of the assay were carried out. In addition, the assay was evaluated using clinical samples. Specificity analysis indicated that the assay showed negative results with samples of Feline Parvovirus, Feline Herpesvirus, Feline Calicivirus, Feline Bocavirus, and Feline Coronavirus, indicating good specificity of the assay. Sensitivity analysis showed that the SYBR Green I-based real-time RT-PCR method could detect as low as 3.72 × 101 copies/μL of template, which is 100-fold more sensitive compared to the conventional RT-PCR. Both intra-assay and inter-assay variability were lower than 1 %, indicating good reproducibility. Furthermore, an analysis of 150 fecal samples showed that the positive detection rate of SYBR Green I-based real-time RT-PCR was higher than that of the conventional RT-PCR, indicating the high reliability of the method. The assay is cheap and effective. Therefore, it could provide support for the detection of FeAstV in large-scale clinical testing and epidemiological investigation.
Collapse
Affiliation(s)
- 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
| | - Ziteng Fu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Xu Guo
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Da Zhang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Caixia Bai
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Wei Li
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Guangqing Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
| | - Yongdong Li
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China
| | - Shudong Jiang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.
| |
Collapse
|
5
|
Wang S, Zhao J, Lu S, Huang J, Yang X. Establishment of Logic Gates Based on Conformational Changes in a Multiple-Factor Biomolecule Interaction Process by Dual Polarization Interferometry. Anal Chem 2019; 91:6971-6975. [PMID: 31081324 DOI: 10.1021/acs.analchem.9b01319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DNA-based logic gates stimulate the development of molecular scale computers and show enormous potential in nanotechnology, biotechnology, and medicine. However, the reported detectors to date usually require one to label appropriate signal probes, resulting in not only a high cost but also potentially tedious manipulation. For the first time, we established a label-free logic gate by regarding the structure-related signal as output. Dual polarization interferometry (DPI) was employed to reveal the detailed conformational transitions occurring in the multiple-factor biomolecule interactions and then was utilized as a detection tool of logic gate. As a vital merit of this system, the dependence of the density output signal on the interaction with multiple-factor input can mimic the function of signal communication in OR, INHIBIT, and IDENTITY logic gates and the INHIBIT-OR cascade circuit. Additionally, the DPI signal with logic stringency can unambiguously distinguish conformational polymorphisms and compare structural stability. This study provides a new way for the construction of a label-free logic gate, supplements information deficiency of reaction details, and extends the application of DPI in logic operation.
Collapse
Affiliation(s)
- Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China.,University of Chinese Academy of Sciences , Beijing 100039 , China
| |
Collapse
|
6
|
Luo Q, Xu J, Huang C, Lei X, Cheng D, Liu W, Cheng A, Tang L, Fang J, Ou Y, Geng Y, Chen Z. Impacts of Duck-Origin Parvovirus Infection on Cherry Valley Ducklings From the Perspective of Gut Microbiota. Front Microbiol 2019; 10:624. [PMID: 30984145 PMCID: PMC6450226 DOI: 10.3389/fmicb.2019.00624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Duck-origin goose parvovirus (D-GPV) is the causative agent of beak atrophy and dwarfism syndrome (BADS), characterized by growth retardation, skeletal dysplasia, and persistent diarrhea. However, the pathogenic mechanism of D-GPV remains undefined. Here, we first reported the gut microbiome diversity of D-GPV infected Cherry Valley ducks. In the investigation for the influence of D-GPV infection on gut microbiota through a period of infection, we found that D-GPV infection caused gut microbiota dysbiosis by reducing the prevalence of the dominant genera and decreasing microbial diversity. Furthermore, exfoliation of the intestinal epithelium, proliferation of lymphocytes, up-regulated mRNA expression of pro-inflammatory TNF-α, IL-1β, IL-6, IL-17A, and IL-22 and down-regulated mRNA expression of anti-inflammatory IL-10 and IL-4 occurred when D-GPV targeted in cecal epithelium. In addition, the content of short chain fatty acids (SCFAs) in cecal contents was significantly reduced after D-GPV infection. Importantly, the disorder of pro-inflammatory and anti-inflammatory cytokines was associated with the decrease of SCFAs-producing bacteria and the enrichment of opportunistic pathogens. Collectively, the decrease of SCFAs and the enrichment of pathogen-containing gut communities promoted intestinal inflammatory injury. These results may provide a new insight that target the gut microbiota to understand the progression of BADS disease and to research the pathogenic mechanism of D-GPV.
Collapse
Affiliation(s)
- Qihui Luo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Laboratory of Experimental Animal Disease Model, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jing Xu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Laboratory of Experimental Animal Disease Model, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Chao Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Laboratory of Experimental Animal Disease Model, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinyu Lei
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Laboratory of Experimental Animal Disease Model, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dongjing Cheng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Laboratory of Experimental Animal Disease Model, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Wentao Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Laboratory of Experimental Animal Disease Model, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Li Tang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Laboratory of Experimental Animal Disease Model, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jing Fang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yangping Ou
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yi Geng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Laboratory of Experimental Animal Disease Model, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|