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Sui N, Zhang R, Jiang Y, Yu H, Xu G, Wang J, Zhu Y, Xie Z, Hu J, Jiang S. Long Noncoding RNA Expression Rofiles Elucidate the Potential Roles of lncRNA- XR_003496198 in Duck Hepatitis A Virus Type 1 Infection. Front Cell Infect Microbiol 2022; 12:858537. [PMID: 35531338 PMCID: PMC9074814 DOI: 10.3389/fcimb.2022.858537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Duck hepatitis A virus type 1 (DHAV-1) is a highly lethal virus that severely affects the duck industry worldwide. Long noncoding RNAs (lncRNAs) exert crucial roles in pathogen attacks. Here, we conducted deep transcriptome analysis to investigate the dynamic changes of host lncRNAs profiles in DHAV-1-infected duck embryo fibroblasts. We identified 16,589 lncRNAs in total and characterized their genomic features. Moreover, 772 and 616 differentially expressed lncRNAs (DELs) were screened at 12 and 24 h post-infection. Additionally, we predicted the DELs' cis- and trans-target genes and constructed lncRNA-target genes regulatory networks. Functional annotation analyses indicated that the putative target genes of DELs participated in diverse vital biological processed, including immune responses, cellular metabolism, and autophagy. For example, we confirmed the dysregulation of pattern recognition receptors (TLR3, RIG-I, MDA5, LGP2, cGAS), signal transducers (STAT1), transcription factors (IRF7), immune response mediators (IL6, IL10, TRIM25, TRIM35, TRIM60, IFITM1, IFITM3, IFITM5), and autophagy-related genes (ULK1, ULK2, EIF4EBP2) using RT-qPCR. Finally, we confirmed that one DHAV-1 induced lncRNA-XR_003496198 is likely to inhibit DHAV-1 replication in DEFs. Our study comprehensively analyzed the lncRNA profiles upon DHAV-1 infection and screened the target genes involved in the innate immune response and autophagy signaling pathway, thereby revealing the essential roles of duck lncRNAs and broadening our understanding of host-virus interactions.
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Affiliation(s)
- Nana Sui
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Ruihua Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Yue Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Honglei Yu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Guige Xu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Jingyu Wang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Yanli Zhu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Zhijing Xie
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Jiaqing Hu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
- Shandong GreenBlue Biotechnology Co. Ltd., Taian, China
| | - Shijin Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
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Li Y, Cui Y, Liu H, Wang J, Li Y, Wang Y. Establishment of duplex SYBR Green I-based real-time PCR assay for simultaneous detection of duck hepatitis a virus-1 and duck astrovirus-3. Avian Dis 2021; 65:281-286. [PMID: 33496724 DOI: 10.1637/aviandiseases-d-20-00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/25/2021] [Indexed: 11/05/2022]
Abstract
Duck viral hepatitis (DVH) mainly affects ducklings under 1 month of age, causes liver necrosis, enlargement, and hemorrhage, and is highly lethal, seriously jeopardizing the duck industry. The prevalence of serotypes DHAV-1 and DAstV-3 is increasing, and co-infection is common. Moreover, the similar clinical characteristics of the DHAV-1 and DAstV-3 infections and high frequency of co-infection make diagnosis difficult. In this study, to establish a method for the rapid simultaneous detection of DHAV-1 and DAstV-3 , two pairs of specific primers were designed according to their conserved gene regions. A SYBR Green I-based real-time PCR assay was successfully established that can quickly and differentially detect the two viruses. Moreover, the assay is highly specific and does not show cross-reaction with other common viruses. The detection limit of the method is 7.34 × 10 1 copies/μL and 3.78 × 10 1 copies/μL for DHAV-1 and DAstV-3, respectively, indicating high sensitivity. A total of 34 clinical samples were tested using the established method; the positive rates for DHAV-1 and DAstV-3 was 14.71% and 8.82%, respectively, and that for co-infection was 2.94% (1/34), which was better than that obtained with conventional PCR. In summary, the SYBR Green I-based real-time PCR assay established in this study has high specificity, good sensitivity and accuracy, high feasibility, and is rapid. Thus, it can be a powerful tool for the co-infection detection of DHAV-1 and DAstV-3 and for future epidemiological studies.
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Affiliation(s)
| | | | | | | | | | - Yong Wang
- Anhui Agricultural University 130 Changjiang West Road CHINA Hefei 230036 +86 551 65786328
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Yu L, Li H, Zhao X, Wang X, Wei X, Lin W, Li P, Cui L, Yuan J. Rapid visual detection of binary toxin producing Clostridium difficile by loop-mediated isothermal amplification. Exp Ther Med 2017; 14:4781-4788. [PMID: 29201180 PMCID: PMC5704324 DOI: 10.3892/etm.2017.5178] [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: 03/08/2017] [Accepted: 07/27/2017] [Indexed: 01/05/2023] Open
Abstract
The binary toxin Clostridium difficile transferase (CDT) is frequently observed in C. difficile strains and is associated with an increased severity of C. difficile infection. CDT-producing C. difficile infections cause higher fatality rates than infections with CDT negative isolates. Thus, the rapid and accurate identification of a CDT positive C. difficile infection is critical for effective treatment. The present study demonstrates how loop-mediated isothermal amplification (LAMP) can be used to detect CDT-producing C. difficile based on visual observation. This is a low complexity, rapid molecular method that has the potential to be used within a point of care setting. The specificity and sensitivity of the primers in the LAMP reactions for CDT detection were determined using two different methods, a real-time turbidity monitor and visual detection after the addition of calcein to the reaction tube. The results revealed that target DNA was amplified and visualized by these two detection methods within 60 min at a temperature of 60°C. The sensitivity of the LAMP assay was identified to be 10-fold greater than that of polymerase chain reaction analysis. When 25 alternative bacterial strains lacking CDT were tested, the results of the amplification were negative, confirming the specificity of the primers. In conclusion, the visual LAMP method established in the present study may be a rapid, reliable and cost-effective tool for detecting CDT-producing C. difficile strains at the point of care.
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Affiliation(s)
- Lan Yu
- Department of Gastroenterology, Navy General Hospital, Beijing 100048, P.R. China
| | - Huan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Xiangna Zhao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Xiao Wei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Weishi Lin
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Puyuan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Lihong Cui
- Department of Gastroenterology, Navy General Hospital, Beijing 100048, P.R. China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, P.R. China
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Zhao X, He X, Li H, Zhao J, Huang S, Liu W, Wei X, Ding Y, Wang Z, Zou D, Wang X, Dong D, Yang Z, Yan X, Huang L, Du S, Yuan J. Detection of Streptococcus pyogenes using rapid visual molecular assay. FEMS Microbiol Lett 2015; 362:fnv148. [PMID: 26319025 DOI: 10.1093/femsle/fnv148] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2015] [Indexed: 11/14/2022] Open
Abstract
Streptococcus pyogenes is an increasingly important pathogen in many parts of the world. Rapid and accurate detection of S. pyogenes aids in the control of the infection. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed and validated for the specific detection of S. pyogenes. The assay incorporates two methods: a chromogenic analysis using a calcein/Mn(2+) complex and real-time turbidity monitoring to assess the reaction. Both methods detected the target DNA within 60 min under 64°C isothermal conditions. The assay used specifically designed primers to target spy1258, and correctly identified 111 strains of S. pyogenes and 32 non-S. pyogenes strains, including other species of the genus Streptococcus. Tests using reference strains showed that the LAMP assay was highly specific. The sensitivity of the assay, with a detection limit of 1.49 pg DNA, was 10-fold greater than that of PCR. The LAMP assay established in this study is simple, fast and sensitive, and does not rely upon any special equipment; thus, it could be employed in clinical diagnosis.
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Affiliation(s)
- Xiangna Zhao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiaoming He
- College of Food Science and Engineering, Northwest A & F University, Yangling 712100, China
| | - Huan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Jiangtao Zhao
- Emergency Center, the Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Simo Huang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiao Wei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yiwei Ding
- Clinical Laboratory, Navy general hospital, Beijing 100048, China
| | - Zhaoyan Wang
- Department of Pediatrics, Navy general hospital, Beijing 100048, China
| | - Dayang Zou
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Derong Dong
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Zhan Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiabei Yan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Liuyu Huang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Shuangkui Du
- College of Food Science and Engineering, Northwest A & F University, Yangling 712100, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
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Loop-mediated isothermal amplification for diagnosis of 18 World Organization for Animal Health (OIE) notifiable viral diseases of ruminants, swine and poultry. Anim Health Res Rev 2015; 16:89-106. [PMID: 25900363 DOI: 10.1017/s1466252315000018] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a simple, powerful state-of-the-art gene amplification technique used for the rapid diagnosis and early detection of microbial diseases. Many LAMP assays have been developed and validated for important epizootic diseases of livestock. We review the LAMP assays that have been developed for the detection of 18 viruses deemed notifiable of ruminants, swine and poultry by the World Organization for Animal Health (OIE). LAMP provides a fast (the assay often takes less than an hour), low cost, highly sensitive, highly specific and less laborious alternative to detect infectious disease agents. The LAMP procedure can be completed under isothermal conditions so thermocyclers are not needed. The ease of use of the LAMP assay allows adaptability to field conditions and works well in developing countries with resource-limited laboratories. However, this technology is still underutilized in the field of veterinary diagnostics despite its huge capabilities.
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Liu W, Xu Y, Dong D, Li H, Zhao X, Li L, Zhang Y, Wei X, Wang X, Huang S, Zeng M, Huang L, Zhang S, Yuan J. Survey and Rapid Detection of Bordetella pertussis in Clinical Samples Targeting the BP485 in China. Front Public Health 2015; 3:39. [PMID: 25798436 PMCID: PMC4350411 DOI: 10.3389/fpubh.2015.00039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/11/2015] [Indexed: 11/22/2022] Open
Abstract
Bordetella pertussis is an important human respiratory pathogen. Here, we describe a loop-mediated isothermal amplification (LAMP) method for the rapid detection of B. pertussis in clinical samples based on a visual test. The LAMP assay detected the BP485 target sequence within 60 min with a detection limit of 1.3 pg/μl, a 10-fold increase in sensitivity compared with conventional PCR. All 31 non-pertussis respiratory pathogens tested were negative for LAMP detection, indicating the high specificity of the primers for B. pertussis. To evaluate the application of the LAMP assay to clinical diagnosis, of 105 sputum and nasopharyngeal samples collected from the patients with suspected respiratory infections in China, a total of 12 B. pertussis isolates were identified from 33 positive samples detected by LAMP-based surveillance targeting BP485. Strikingly, a 4.5 months old baby and her mother were found to be infected with B. pertussis at the same time. All isolates belonged to different B. pertussis multilocus sequence typing groups with different alleles of the virulence-related genes including four alleles of ptxA, six of prn, four of tcfA, two of fim2, and three of fim3. The diversity of B. pertussis carrying toxin genes in clinical strains indicates a rapid and continuing evolution of B. pertussis. This combined with its high prevalence will make it difficult to control. In conclusion, we have developed a visual detection LAMP assay, which could be a useful tool for rapid B. pertussis detection, especially in situations where resources are poor and in point-of-care tests.
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Affiliation(s)
- Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Yinghua Xu
- National Institutes for Food and Drug Control , Beijing , China
| | - Derong Dong
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Huan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Xiangna Zhao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Lili Li
- National Institutes for Food and Drug Control , Beijing , China
| | - Ying Zhang
- National Institutes for Food and Drug Control , Beijing , China
| | - Xiao Wei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Simo Huang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Ming Zeng
- National Institutes for Food and Drug Control , Beijing , China
| | - Liuyu Huang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
| | - Shumin Zhang
- National Institutes for Food and Drug Control , Beijing , China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences , Beijing , China
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Woźniakowski G, Samorek-Salamonowicz E. First survey of the occurrence of duck enteritis virus (DEV) in free-ranging Polish water birds. Arch Virol 2013; 159:1439-44. [DOI: 10.1007/s00705-013-1936-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/27/2013] [Indexed: 11/28/2022]
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Genetic characterization of Duck Hepatitis A Viruses isolated in China. Virus Res 2013; 178:211-6. [DOI: 10.1016/j.virusres.2013.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 11/19/2022]
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Li C, Chen Z, Meng C, Liu G. Rapid detection of duck hepatitis A virus genotype C using reverse transcription loop-mediated isothermal amplification. J Virol Methods 2013; 196:193-8. [PMID: 24291148 DOI: 10.1016/j.jviromet.2013.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 11/13/2013] [Accepted: 11/19/2013] [Indexed: 01/20/2023]
Abstract
A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was used and optimized to develop a rapid and sensitive detection system for duck hepatitis A virus genotype C (DHAV-C) RNA. A set of four specific primers was designed against highly conserved sequences located within the 3D gene from DHAV (strain GX1201). Under optimal reaction conditions, the sensitivity of DHAV-C-specific RT-LAMP was 100-fold higher than that of reverse transcriptase-polymerase chain reaction (RT-PCR), with a detection limit of 0.3pg (6.59×10(4) copies) per reaction. No cross-reactivity was observed from the samples of other duck viruses, which is in good accordance with RT-PCR. Furthermore, a positive reaction can be visually inspected by observing turbidity or color change after the addition of SYBR green I dye. The DHAV-C-specific RT-LAMP assay was applied to the samples and compared with RT-PCR. The positive-sample ratios were 26.7% (12 of 45) by RT-LAMP and 20% (9 of 45) by RT-PCR. Therefore, the newly developed RT-LAMP assay is a rapid, specific, sensitive, and cost-effective method of DHAV-C detection. This assay has potential applications in both clinical diagnosis and field surveillance of DHAV-C infection.
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Affiliation(s)
- Chuanfeng Li
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Zongyan Chen
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Chunchun Meng
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Guangqing Liu
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
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