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Xu J, Wang Y, Zhang Y, Wang S, Su N, Chang X, Ren W, Zou Y, Liu S, Li L, Li J, Bao J, Wang Z. Establishment of a RAA-CRISPR Cas12a based diagnostic method for peste des petits ruminants virus N gene and M gene. J Virol Methods 2024; 329:114971. [PMID: 38876255 DOI: 10.1016/j.jviromet.2024.114971] [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: 03/03/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024]
Abstract
Peste des petis ruminants (PPR) is an acute, highly contagious fatal disease affecting both domestic and wild small ruminants, caused by Morbillivirus caprinae (also known as peste des petis ruminants virus (PPRV)). Herein, a rapid method based on recombinase aided amplification-clustered regularly interspaced short palindromic repeats-Cas12a (RAA-CRISPR Cas12a) to detect PPRV was developed. CRISPR RNAs and RAA primers for PPRV-N (nucleocapsid) and PPRV-M (matrix) fragments were designed. The reaction system was constructed following screening and optimization. Detection could be completed within in 50minutes at 37°C. Detection of gradient dilutions of plasmids carrying of PPRV N and M gene fragments indicated a minimum limit of detection of 10 copies/μL. There were no cross-reactions with related viruses and all tested lineages of PPRV were detected successfully. The method also showed good repeatability. The detection of clinical samples (previously detected using reverse transcription polymerase chain reaction (RT-PCR)) indicated good consistency between the RAA-CRISPR Cas12a method and RT-PCR. Thus, the RAA-CRISPR Cas12a method for rapid PPRV diagnosis has strong specificity, high sensitivity, and stable repeatability. Moreover, the results can be observed visually under blue or UV light or using lateral flow strips without complex instruments.
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Affiliation(s)
- Jiao Xu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yingli Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | | | - Shujuan Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Na Su
- Qingdao Agricultural University, Qingdao, China
| | - Xing Chang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Weijie Ren
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Yanli Zou
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Shan Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Lin Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Jinming Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Jingyue Bao
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao, China.
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ZHANG S, WANG C, MENG K, LIU J. Recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) designed for rapid detection of canine distemper virus. J Vet Med Sci 2024; 86:584-591. [PMID: 38462524 PMCID: PMC11144539 DOI: 10.1292/jvms.23-0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/18/2024] [Indexed: 03/12/2024] Open
Abstract
In the present study, recombinase polymerase amplification (RPA) was combined with the colloidal gold lateral flow dipstick (LFD) method to establish a new, stable, and efficient assay for the detection of canine distemper virus (CDV). We designed a set of specific primers labeled with biotin and a specific probe labeled with dSpacer and C3 spacer, according to the conserved region in the N-terminal gene sequence of CDV. The reaction conditions and systems were then optimized, and the sensitivity and specificity were analyzed for potential clinical application. The results showed that the RPA-LFD assay for CDV detection was successfully established. We also found that the temperature in a closed fist (35°C) is optimal for the RPA reaction. The optimal ratio of primer to probe was 2:1. The minimum detection limit of the RPA-LFD assay was 1 × 101 the median tissue culture infective dose (TCID50)/mL. Using this assay with samples from experimentally infected dogs, CDV was detected in nasal secretions, eye secretions, and blood on the fourth day post infection. In summary, this novel RPA-LFD assay for CDV detection is simple to use, and preliminary findings indicate its high specificity and sensitivity.
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Affiliation(s)
- Shanshan ZHANG
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chengyu WANG
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Keyin MENG
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jun LIU
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
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Eini O, Pfitzer R, Varrelmann M. Rapid and specific detection of Pentastiridius leporinus by recombinase polymerase amplification assay. BULLETIN OF ENTOMOLOGICAL RESEARCH 2024:1-8. [PMID: 38708571 DOI: 10.1017/s0007485324000099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Pentastiridius leporinus (Hemiptera: Cixiidae) is the main vector of an emerging and fast spreading sugar beet disease, the syndrome 'basses richesses' (SBR), in different European countries. The disease is caused by the γ-3-proteobacterium 'Candidatus Arsenophonus phytopathogenicus' and the phytoplasma 'Candidatus Phytoplasma solani' which are exclusively transmitted by planthoppers and can lead to a significant loss of sugar content and yield. Monitoring of this insect vector is important for disease management. However, the morphological identification is time consuming and challenging as two additional cixiid species Reptalus quinquecostatus and Hyalesthes obsoletus with a very close morphology have been reported in sugar beet fields. Further, identification of females and nymphs of P. leporinus at species level based on taxonomic key is not possible. In this study, an isothermal nucleic acid amplification based on recombinase polymerase amplification (RPA) was developed to specifically detect P. leporinus. In addition, real-time RPA was developed to detect both adults (male and female) and nymph stages using pure or crude nucleic acid extracts. The sensitivity of the real-time RPA for detection of P. leporinus was comparable to real-time PCR, but a shorter time (< 7 min) was required. This is a first report for real-time RPA application for P. leporinus detection using crude nucleic acid templates which can be applied for fast and specific detection of this vector in the field.
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Affiliation(s)
- Omid Eini
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - René Pfitzer
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
- Agricultural Entomology, Department of Crop Sciences, Faculty of Agricultural Sciences, University of Göttingen, Grisebachstrasse 6, 37077 Göttingen, Germany
| | - Mark Varrelmann
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
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Muritala I, Bemji MN, Ozoje MO, Ajayi OL, Oluwayinka EB, Sonibare AO, James IJ, Ibeagha-Awemu EM. Comparative study of HA and HNB staining RT-LAMP assays for peste des petits ruminants virus detection in West African Dwarf goats. Trop Anim Health Prod 2023; 55:356. [PMID: 37821730 DOI: 10.1007/s11250-023-03747-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Peste des petits ruminants (PPR) cause severe economic losses to many countries of the world where the disease is endemic. It has been targeted for global eradication by 2030 following the successful eradication of rinderpest in 2011. The proposed eradication program would benefit from efficient and relatively reliable diagnostic tools for early PPR virus (PPRV) detection. A total of 33 eight to 12 months old West African Dwarf (WAD) goats were used. Nineteen goats infected by commingling with two PPR virus-positive animals formed the infected group (PPRV-infected goats) while 14 non-infected goats formed the control group (CTG). The suitability of hydroxyl naphthol blue (HNB) staining of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and haemagglutination (HA) assays was compared for their sensitivity to detect the PPRV in PPRV-infected goats and non-infected CTG. PPR disease severity in WAD goats at different days post infection (dpi) was evaluated by clinical scoring and haemagglutination titre (HAT). HNB staining RT-LAMP reaction and HA showed sensitivities of 100% and 73.68%, respectively, for PPRV detection. Expression of PPR clinical signs began from 3 dpi, attained peak at 5 dpi, thereafter showed irregular patterns till 24 dpi. Evaluation of HAT in PPRV-infected goats at 12 dpi ranged from 2 to 64 haemagglutination units (HAU), while CTG goats had 0 HAU. In conclusion, HA could be a good tool for rapid diagnosis of PPRV in a developing country setting. However, HNB staining RT-LAMP assay demonstrated high sensitivity for accurate diagnoses of PPRV and as an important diagnostic tool when precise phenotyping is desired.
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Affiliation(s)
- Ismaila Muritala
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Martha N Bemji
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria.
| | - Michael O Ozoje
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Olusola L Ajayi
- Department of Pathology, College of Veterinary Medicine, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Eniope B Oluwayinka
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Adekayode O Sonibare
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Ikechukwu J James
- Department of Animal Physiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
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Zhang QB, Zhu P, Zhang S, Rong YJ, Huang ZA, Sun LW, Cai T. Hypervirulent Klebsiella pneumoniae detection methods: a minireview. Arch Microbiol 2023; 205:326. [PMID: 37672079 DOI: 10.1007/s00203-023-03665-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/07/2023]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp), characterized by high virulence and epidemic potential, has become a global public health challenge. Therefore, improving the identification of hvKp and enabling earlier and faster detection in the community to support subsequent effective treatment and prevention of hvKp are an urgent issue. To address these issues, a number of assays have emerged, such as String test, Galleria mellonella infection test, PCR, isothermal exponential amplification, and so on. In this paper, we have collected articles on the detection methods of hvKp and conducted a retrospective review based on two aspects: traditional detection technology and biomarker-based detection technology. We summarize the advantages and limitations of these detection methods and discuss the challenges as well as future directions, hoping to provide new insights and references for the rapid detection of hvKp in the future. The aim of this study is to focus on the research papers related to Hypervirulent Klebsiella pneumoniae involving the period from 2012 to 2022. We conducted searches using the keywords "Hypervirulent Klebsiella pneumoniae, biomarkers, detection techniques" on ScienceDirect and Google Scholar. Additionally, we also searched on PubMed, using MeSH terms associated with the keywords (such as Klebsiella pneumoniae, Klebsiella Infections, Virulence, Biomarkers, diagnosis, etc.).
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Affiliation(s)
- Qi-Bin Zhang
- The Affiliated People's Hospital of Ningbo University, Ningbo, China
| | - Peng Zhu
- Ningbo No. 2 Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Shun Zhang
- Ningbo No. 2 Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Yan-Jing Rong
- Ningbo No. 2 Hospital, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Zuo-An Huang
- Ningbo No. 2 Hospital, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | | | - Ting Cai
- Ningbo No. 2 Hospital, Ningbo, China.
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China.
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Recombinase-Aided Amplification Assay for Rapid Detection of Hypervirulent Klebsiella pneumoniae (hvKp) and Characterization of the hvKp Pathotype. Microbiol Spectr 2023:e0398422. [PMID: 36912637 PMCID: PMC10100362 DOI: 10.1128/spectrum.03984-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) is a major human pathogen associated with liver abscess, pneumonia, meningitis, and endophthalmitis. It is challenging to differentiate hvKp from classical Klebsiella pneumoniae (cKp) using conventional methods, necessitating the development of a rapid, sensitive, and convenient assay for hvKp detection. In this study, we constructed a recombinase-aided amplification (RAA) method targeting hvKp genes peg344 and rmpA, and also analyzed the pathogenic characteristics of hvKp. We optimized the reaction temperature and system, and evaluated its sensitivity, specificity, and clinical application. The primer and probe sets peg344-set1 and rmpA-set2 delivered significant fluorescent signals at 39°C with the shortest gene amplification times (sensitivity: 20 copies/reaction). This RAA assay showed no cross-reactivity with 15 other common pathogenic bacteria. Its applicability was confirmed by the evaluation of 208 clinical specimens, of which 45 were confirmed to be hvKp. The sensitivity and specificity of the RAA assay were both 100% compared with real-time PCR as the reference standard. To verify the assay, we also assessed the diversity of molecular characteristics among the hvKp isolates and identified serotype K1 and sequence type ST23 as the dominant clone. Virulence factors iroN and iutA were highly associated with virulence level. In conclusion, our novel RAA assay is a powerful tool for early diagnosis and epidemiological surveillance of hvKp. IMPORTANCEKlebsiella pneumoniae is the most common opportunistic bacterial species and a major threat to public health. Since the 1990s, hvKp has received increasing attention from public health officials and infectious disease specialists. Hypervirulent strains differ from classical strains in terms of phenotypic features and clinical outcomes. It is hard to identify hvKp from cKp using the conventional methods including colony morphology analysis, serum killing assays, mouse lethality assays, string tests, and real-time PCR. In this study, we established a rapid, sensitive and convenient recombinase-aided amplification assay for hvKp detection targeting virulence genes peg344 and rmpA. Our RAA assay provides an important tool for the rapid diagnosis of infectious diseases caused by hvKp, particularly in primary laboratories.
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Asa TA, Kumar P, Lee J, Seo YJ. Multiple ligation–Assisted recombinase polymerase amplification for highly sensitive and selective colorimetric detection of SARS-CoV-2. Talanta 2023; 252:123835. [PMID: 35985194 PMCID: PMC9375730 DOI: 10.1016/j.talanta.2022.123835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/29/2022] [Accepted: 08/07/2022] [Indexed: 11/19/2022]
Abstract
In this paper we present a new method for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), targeting a specific region “N gene.” Under isothermal reaction conditions, we integrated ligation (Lig; high selectivity) and recombinase polymerase amplification (RPA; high sensitivity) processes, obtaining a robust method of detection. For point-of-care testing, we incorporated our laboratory-produced pyrophosphate ion (PPi)–sensing probe (PK-probe) for colorimetric analysis of the reaction. The total detection system was efficient and effective at diagnosing this RNA virus–mediated disease rapidly (30 min). In a full-genome SARS-CoV-2 study, our PK-probe/Lig-RPA system functioned with a limit of detection of 1160 copies/ml, with a single-mismatch level of selectively, and it was highly selective even in the presence of bacterial genomes commonly found in the human mouth and nose. This robust, straightforward, selective, efficient, and ultrasensitive colorimetric detection method, with potential for point-of-care analysis, should also be effective in detecting a diverse range of other RNA-based diseases.
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Affiliation(s)
- Tasnima Alam Asa
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Pradeep Kumar
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Jaehyeon Lee
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, 54896, South Korea
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea.
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Zheng X, Li Y, Yuan M, Shen Y, Chen S, Duan G. Rapid detection of HPV16/18 based on a CRISPR-Cas13a/Cas12a dual-channel system. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:5065-5075. [PMID: 36449008 DOI: 10.1039/d2ay01536f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
PURPOSE cervical cancer is the leading cause of cancer deaths in women in the developing world, with high-risk HPV16 and HPV18 accounting for approximately 70% of all cervical cancers. Early detection of HPV, especially high-risk HPV types, is essential to prevent disease progression. METHODS in this study, we established a highly sensitive and specific nucleic acid assay based on a CRISPR-Cas13a/Cas12a dual-channel system combined with multiplex RAA for rapid detection and typing of HPV16/18, which provides a new idea for cervical cancer screening. To meet the application of field testing, we designed a portable fluorescence imaging assay that can judge the test results directly with the naked eye or through cell phone imaging. RESULTS the lower limit of detection for both HPV16 and HPV18 based on the CRISPR-Cas12a/Cas13a dual-channel assay was 100 copies per μL. The dual-channel assay was validated with 55 clinical samples, showing 97.06% sensitivity, 100% specificity, 100% positive predictive value, and 96.55% negative predictive value. The results of the portable fluorescence imaging assay were fully comparable to those of the real-time fluorescent RAA-based CRISPR-Cas12a/Cas13a dual-channel assay. CONCLUSIONS this developed portable dual gene assay platform may provide new technical support for cervical cancer screening in resource-limited settings.
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Affiliation(s)
- Xue Zheng
- College of Public Health, Zhengzhou University, Zhengzhou, 450000, China.
| | - Yuankun Li
- Obstetrics and Gynecology Department, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China.
| | - Mingzhu Yuan
- College of Public Health, Zhengzhou University, Zhengzhou, 450000, China.
| | - Yue Shen
- College of Public Health, Zhengzhou University, Zhengzhou, 450000, China.
| | - Shuaiyin Chen
- College of Public Health, Zhengzhou University, Zhengzhou, 450000, China.
| | - Guangcai Duan
- College of Public Health, Zhengzhou University, Zhengzhou, 450000, China.
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Yang L, Wang L, Lv M, Sun Y, Cao J. Clinical Validation of DNA Extraction-Free qPCR, Visual LAMP, and Fluorescent LAMP Assays for the Rapid Detection of African Swine Fever Virus. Life (Basel) 2022; 12:1067. [PMID: 35888155 PMCID: PMC9320077 DOI: 10.3390/life12071067] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023] Open
Abstract
The global pig industry and food safety are seriously threatened by outbreaks of African swine fever (ASF). To permit early diagnosis of African swine fever virus (ASFV), prevent its spread, and limit its outbreaks, a highly sensitive diagnostic method that can be performed at pig farms is required. Herein, we established DNA extraction-free real-time PCR (qPCR), visual loop-mediated isothermal amplification (LAMP), and fluorescent LAMP assays, which were compared with the results of World Organization for Animal Health (OIE) qPCR to assess ASFV-infected clinical samples. Based on plasmid DNA, the limit of detection for the three assays and OIE qPCR were 5.8 copies/μL. All four assays had good ASFV specificity and showed no cross-reactivity with other tested viruses. These assays were used to diagnose 100 clinical samples. The assays showed good diagnostic consistency, with kappa values of 1.0, 0.84, and 0.88, respectively. Compared with OIE qPCR, the diagnostic specificity/sensitivity of DNA extraction-free qPCR, visual LAMP, and fluorescent LAMP assays were 100%/100%, 100%/87.1%, and 100%/90.32%, respectively. The assays eliminated the need for DNA extraction and are more suitable for ASF diagnosis by inexperienced farmers in low-resource environments, making them a good choice for on-site monitoring of pig farms.
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Affiliation(s)
- Lili Yang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China; (L.Y.); (M.L.)
| | - Lin Wang
- Beijing Animal Disease Prevention and Control Center, Beijing 102629, China;
| | - Meihui Lv
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China; (L.Y.); (M.L.)
| | - Yu Sun
- China Animal Disease Prevention and Control Center, Beijing 102206, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China; (L.Y.); (M.L.)
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Research Progress on Emerging Viral Pathogens of Small Ruminants in China during the Last Decade. Viruses 2022; 14:v14061288. [PMID: 35746759 PMCID: PMC9228844 DOI: 10.3390/v14061288] [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: 05/18/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 11/26/2022] Open
Abstract
China is the country with the largest number of domestic small ruminants in the world. Recently, the intensive and large-scale sheep/goat raising industry has developed rapidly, especially in nonpastoral regions. Frequent trading, allocation, and transportation result in the introduction and prevalence of new pathogens. Several new viral pathogens (peste des petits ruminants virus, caprine parainfluenza virus type 3, border disease virus, enzootic nasal tumor virus, caprine herpesvirus 1, enterovirus) have been circulating and identified in China, which has attracted extensive attention from both farmers and researchers. During the last decade, studies examining the etiology, epidemiology, pathogenesis, diagnostic methods, and vaccines for these emerging viruses have been conducted. In this review, we focus on the latest findings and research progress related to these newly identified viral pathogens in China, discuss the current situation and problems, and propose research directions and prevention strategies for different diseases in the future. Our aim is to provide comprehensive and valuable information for the prevention and control of these emerging viruses and highlight the importance of surveillance of emerging or re-emerging viruses.
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11
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Petrucci S, Costa C, Broyles D, Kaur A, Dikici E, Daunert S, Deo SK. Monitoring Pathogenic Viable E. coli O157:H7 in Food Matrices Based on the Detection of RNA Using Isothermal Amplification and a Paper-Based Platform. Anal Chem 2021; 94:2485-2492. [PMID: 34968033 DOI: 10.1021/acs.analchem.1c04305] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In recent years, the number of product recalls and contamination incidents involving pathogenic bacteria has significantly increased, and the ensuing infections continue to be an ongoing problem for public health and agriculture. Due to the widespread impact of these pathogens, there is a critical need for rapid, on-site assays that can provide rapid results. In this work, we demonstrate the development of a rapid and simple test based on the combination of reverse transcription with recombinase polymerase amplification followed by lateral flow strip detection of viable Escherichia coli O157:H7 cells by detecting the RNA of the pathogen. The optimized method can be performed for approximately 2 h with a detection limit of 10 CFU/mL of E. coli O157:H7 in buffer, spinach, and ground beef samples. Our assay is sensitive, detecting only E. coli O157:H7 and not nonpathogenic E. coli or other similar pathogens. This strategy was able to distinguish viable from nonviable bacteria and more significantly was able to detect viable but nonculturable bacteria, which is a major issue when using culture-based methods for monitoring pathogenic bacteria. An important advantage of this test is that it can provide timely identification and removal of contaminated consumables prior to distribution without an extensive sample preparation.
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Affiliation(s)
- Sabrina Petrucci
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
| | - Connor Costa
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
| | - David Broyles
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
| | - Avinash Kaur
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States.,Clinical and Translational Science Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
| | - Sapna K Deo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States.,Dr. John T. MacDonald Foundation Biomedical Nanotechnology Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
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Wang Y, Wang Q, Bergmann SM, Li Y, Li B, Lv Y, Yin J, Yang G, Qv Y, Wang Y, Zeng W. Development and comparative evaluation of real-time PCR and real-time RPA assays for detection of tilapia lake virus. Mol Cell Probes 2021; 60:101776. [PMID: 34740779 DOI: 10.1016/j.mcp.2021.101776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/04/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022]
Abstract
Tilapia lake virus (TiLV) is a newly emerged pathogen responsible for high mortality and economic losses in the global tilapia industry. Early and accurate diagnosis is an important priority for TiLV disease control. In order to evaluate the methodology in the molecular diagnosis of TiLV, we compared newly developed quantitative real-time PCR (qPCR) and real-time recombinase polymerase amplification (real-time RPA) assays regarding their sensitivities, specificities and detection effect on clinical samples. Real-time RPA amplified the target pathogen in less than 30 min at 39 °C with a detection limit of 620 copies, while qPCR required about 60 min with a detection limit of 62 copies. Both assays were specific for TiLV and there were no cross-reactions observed with other common fish pathogens. The assays were validated using 35 tissue samples from clinically infected and 60 from artificially infected animals. The sensitivities for the real-time RPA and qPCR assays were 93.33 and 100%, respectively, and the specificity was 100% for both. Both methods have their advantages and can play their roles in different situations. The qPCR is more suitable for quantitative analysis and accurate detection of TiLV in a diagnostic laboratory, whereas real-time RPA is more suitable for the diagnosis of clinical diseases and preliminary screening for TiLV infection in poorly equipped laboratories as well as in fish farms.
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Affiliation(s)
- Yahui Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China; College of Fisheries, Tianjin Agriculture University, Tianjin, China
| | - Qing Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Yingying Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China
| | - Bo Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Yuefeng Lv
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China; College of Fisheries, Tianjin Agriculture University, Tianjin, China
| | - Jiyuan Yin
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China
| | - Guang Yang
- College of Fisheries, Tianjin Agriculture University, Tianjin, China
| | - Yang Qv
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Yingying Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China.
| | - Weiwei Zeng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China.
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13
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Gao S, Xu G, Zeng Z, Lv J, Huang L, Wang H, Wang X. Transboundary spread of peste des petits ruminants virus in western China: A prediction model. PLoS One 2021; 16:e0257898. [PMID: 34555121 PMCID: PMC8459964 DOI: 10.1371/journal.pone.0257898] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/13/2021] [Indexed: 11/23/2022] Open
Abstract
In pan Pamir Plateau countries, Peste des petits ruminants (PPR) has brought huge losses to the livestock industry and threaten the endangered wildlife. In unknown regions, revealing PPRV transmission among countries is the premise of effective prevention and control, therefore calls for quantified monitoring on disease communication among countries. In this paper, a MaxEnt model was built for the first time to predict the PPR risk within the research area. The least cost path (LCP) for PPR transboundary communication were calculated and referred to as the maximum available paths (MAP). The results show that there are many places with high-risk in the research area, and the domestic risk in China is lower than that in foreign countries and is mainly determined by human activities. Five LCPs representing corridors among Kazakhstan, Tajikistan, Pakistan, India and China were obtained. This study proves for the first time that there is the possibility of cross-border transmission of diseases by wild and domestic animals. In the future, it will play an important role in monitoring the PPR epidemic and blocking-up its cross-border transmission.
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Affiliation(s)
- Shan Gao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang province, P. R. China
- Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, Heilongjiang province, The People’s Republic of China
| | - GuoYong Xu
- The Second Geomatics Cartography Institute of National Administration of Ministry of Natural Resources, Harbin, Heilongjiang province, P. R. China
| | - Zan Zeng
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang province, P. R. China
- Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, Heilongjiang province, The People’s Republic of China
| | - JiaNing Lv
- Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, Heilongjiang province, The People’s Republic of China
| | - LiYa Huang
- Changbai Mountain Academy of Sciences, Antu, Jilin province, P. R. China
| | - HaoNing Wang
- School of Geography and Tourism, Harbin University, Harbin, Heilongjiang province, The People’s Republic of China
| | - XiaoLong Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang province, P. R. China
- Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, Heilongjiang province, The People’s Republic of China
- * E-mail:
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14
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Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Depner K, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Sihvonen LH, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Gubbins S, Libeau G, Broglia A, Aznar I, Van der Stede Y. Assessment of the control measures of the category A diseases of Animal Health Law: peste des petits ruminants. EFSA J 2021; 19:e06708. [PMID: 34354766 PMCID: PMC8323035 DOI: 10.2903/j.efsa.2021.6708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
EFSA received a mandate from the European Commission to assess the effectiveness of some of the control measures against diseases included in the Category A list according to Regulation (EU) 2016/429 on transmissible animal diseases ('Animal Health Law'). This opinion belongs to a series of opinions where these control measures will be assessed, with this opinion covering the assessment of control measures for peste des petits ruminants (PPR). In this opinion, EFSA and the AHAW Panel of experts review the effectiveness of: (i) clinical and laboratory sampling procedures, (ii) monitoring period and (iii) the minimum radii of the protection and surveillance zones, and the minimum length of time the measures should be applied in these zones. The general methodology used for this series of opinions has been published elsewhere; nonetheless, the transmission kernels used for the assessment of the minimum radii of the protection and surveillance zones are shown. Several scenarios for which these control measures had to be assessed were designed and agreed prior to the start of the assessment. The monitoring period of 21 days was assessed as effective, except for the first affected establishments detected, where 33 days is recommended. It was concluded that beyond the protection (3 km) and the surveillance zones (10 km) only 9.6% (95% CI: 3.1-25.8%) and 2.3% (95% CI: 1-5.5%) of the infections from an affected establishment may occur, respectively. This may be considered sufficient to contain the disease spread (95% probability of containing transmission corresponds to 5.3 km). Recommendations provided for each of the scenarios assessed aim to support the European Commission in the drafting of further pieces of legislation, as well as for plausible ad-hoc requests in relation to PPR.
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Wang X, Xu LL, Zuo XY, Lin JW, Jin Z, Shen R, Du D, Tang YZ. Rapid detection of the New Delhi metallo-β-lactamase (NDM) gene by recombinase polymerase amplification. INFECTION GENETICS AND EVOLUTION 2020; 87:104678. [PMID: 33321225 DOI: 10.1016/j.meegid.2020.104678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/27/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022]
Abstract
New Delhi metallo-β-lactamase (NDM) is a series of enzyme conferring resistance to β-lactam antibiotics including the carbapenems. The blaNDM gene has been reported in a variety of Gram-negative bacilli, especially in the Enterobacteriaceae and Acinetobacter spp., which is deeply disconcerting for public health worldwide. In this study, recombinase polymerase amplification assays using a basic detection (Basic-RPA) and a real-time fluorescent detection (Exo-RPA) were established for detecting blaNDM gene. The RPA reactions were performed at 39 °C and finished within 20 min. Using different copy numbers of pMD18T-NDM plasmid DNA as templates, we identified the detection limit of Basic-RPA assay (1.85 × 103 copies/μL), conventional PCR assay (1.85 × 104 copies/μL), Exo-RPA assay (1.85 × 102 copies/μL) and real-time PCR assay (1.85 × 102 copies/μL). Both Basic-RPA and Exo-RPA assays were highly specific for detecting blaNDM, as there were no cross-reactions with the strains without blaNDM gene. Examination of 62 clinical samples by RPA assays and PCR assays showed the same results, suggesting that RPA assays are reliable in clinical diagnosis. The amplification time of RPA is much shorter than that of other molecular techniques, it is easy to implement and has the potential for clinical application.
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Affiliation(s)
- Xiao Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ling-Ling Xu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiang-Yi Zuo
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jia-Wen Lin
- Cancer Research Center, Department of Stomatology, School of medicine, Xiamen University, Xiamen, Fujian, China
| | - Zhen Jin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Rong Shen
- Cancer Research Center, Department of Stomatology, School of medicine, Xiamen University, Xiamen, Fujian, China
| | - Dan Du
- Cancer Research Center, Department of Stomatology, School of medicine, Xiamen University, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Reproductive Health Research, School of medicine, Xiamen University, Xiamen, Fujian, China.
| | - You-Zhi Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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16
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Development of a reverse transcription recombinase polymerase based isothermal amplification coupled with lateral flow immunochromatographic assay (CTV-RT-RPA-LFICA) for rapid detection of Citrus tristeza virus. Sci Rep 2020; 10:20593. [PMID: 33244066 PMCID: PMC7693335 DOI: 10.1038/s41598-020-77692-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 10/26/2020] [Indexed: 01/27/2023] Open
Abstract
Tristeza is a highly destructive disease of citrus caused by the phloem-limited, flexuous filamentous Citrus tristeza virus (CTV) in the genus Closterovirus and the family Closteroviridae. It has been a major constraint for higher productivity and has destroyed millions of citrus trees globally. CTV is graft transmissible and spread through use of virus infected nursery plants. Therefore, virus detection by using specific and reliable diagnostic tools is very important to mitigate disease outbreaks. Currently, the standard molecular techniques for CTV detection include RT-PCR and RT-qPCR. These diagnostic methods are highly sensitive but time consuming, labor intensive and require sophisticated expensive instruments, thus not suitable for point-of-care use. In the present study, we report the development of a rapid, sensitive, robust, reliable, and highly specific reverse transcription-RPA technique coupled with a lateral flow immunochromatographic assay (CTV-RT-RPA-LFICA). RT-RPA technique was standardized to amplify the coat protein gene of CTV (CTV-p25) and detect double labeled amplicons on a sandwich immunoassay by designing specific labeled primer pair and probe combinations. The optimally performing primer set (CTRPA-F1/CTRPA-R9-Btn) and the corresponding TwistAmp nfo probe (CTRPA-Probe) was optimized for temperature and reaction time using purified cDNA and viral RNA as template. The sensitivity of the developed assay was compared with other detection techniques using in vitro-transcribed RNA. The efficacy and specificity of the assay was evaluated using CTV positive controls, healthy samples, field grown citrus plants of unknown status, and other virus and bacterial pathogens that infect citrus plants. The RT-RPA-LFICA was able to detect ≤ 141 fg of RNA when cDNA used as a template. The assay detected ≤ 0.23 ng/µl of CTV RNA when directly used as template without cross-reactivity with other citrus pathogens. Best results were achieved at the isothermal temperature of 40 °C within 15-20 min. The study demonstrated that RT-RPA-LFICA has potential to become an improved detection technique for end users in bud-wood certification and quarantine programs and a promising platform for rapid point-of-care diagnostics for citrus farmers and small nurseries in low resource settings.
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"FastCheck FLI PPR-like"-A Molecular Tool for the Fast Genome Detection of PPRV and Differential Diagnostic Pathogens. Viruses 2020; 12:v12111227. [PMID: 33138260 PMCID: PMC7694148 DOI: 10.3390/v12111227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/16/2020] [Accepted: 10/28/2020] [Indexed: 11/17/2022] Open
Abstract
To assist the global eradication of peste des petits ruminants virus (PPRV), a molecular test for the rapid and reliable detection of PPRV was developed which additionally enables the detection of pathogens relevant for differential diagnostics. For this purpose, the necessary time frame of a magnetic bead-based nucleic acid extraction protocol was markedly shortened to 7 min and 13 s. The optimized extraction was run on a BioSprint 15 platform. Furthermore, a high-speed multi-well RT-qPCR for the genome detection of PPRV and additional important pathogens such as Foot-and-mouth disease virus, Parapoxvirus ovis, Goatpox virus, and Mycoplasma capricolum subsp. capripneumoniae was established and combined with suitable internal control assays. The here-described qPCR is based on a lyophilized master mix and takes only around 30 to 40 min. Several qPCR cyclers were evaluated regarding their suitability for fast-cycling approaches and for their diagnostic performance in a high-speed RT-qPCR. The final evaluation was conducted on the BioRad CFX96 and also on a portable Liberty16 qPCR cycler. The new molecular test designated as "FastCheckFLI PPR-like", which is based on rapid nucleic acid extraction and high-speed RT-qPCR, delivered reliable results in less than one hour, allowing its use also in a pen-side scenario.
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18
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Verchot J, Herath V, Urrutia CD, Gayral M, Lyle K, Shires MK, Ong K, Byrne D. Development of a Reverse Genetic System for Studying Rose Rosette Virus in Whole Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1209-1221. [PMID: 32815767 DOI: 10.1094/mpmi-04-20-0094-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rose rosette virus (RRV) is a negative-sense RNA virus with a seven-segmented genome that is enclosed by a double membrane. We constructed an unconventional minireplicon system encoding the antigenomic (ag)RNA1 (encoding the viral RNA-dependent RNA polymerase [RdRp]), agRNA3 (encoding the nucleocapsid protein [N]), and a modified agRNA5 containing the coding sequence for the iLOV protein in place of the P5 open reading frame (R5-iLOV). iLOV expression from the R5-iLOV template was amplified by activities of the RdRp and N proteins in Nicotiana benthamiana leaves. A mutation was introduced into the RdRp catalytic domain and iLOV expression was eliminated, indicating RNA1-encoded polymerase activity drives iLOV expression from the R5-iLOV template. Fluorescence from the replicon was highest at 3 days postinoculation (dpi) and declined at 7 and 13 dpi. Addition of the tomato bushy stunt virus (TBSV) P19 silencing-suppressor protein prolonged expression until 7 dpi. A full-length infectious clone system was constructed of seven binary plasmids encoding each of the seven genome segments. Agro-delivery of constructs encoding RRV RNAs 1 through 4 or RNAs 1 through 7 to N. benthamiana plants produced systemic infection. Finally, agro-delivery of the full-length RRV infectious clone including all segments produced systemic infection within 60 dpi. This advance opens new opportunities for studying RRV infection biology.
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Affiliation(s)
- Jeanmarie Verchot
- Texas A&M Agrilife Center in Dallas, 17360 Coit Rd, Dallas, TX, U.S.A
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, U.S.A
| | - Venura Herath
- Texas A&M Agrilife Center in Dallas, 17360 Coit Rd, Dallas, TX, U.S.A
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, U.S.A
- Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, 20400, Sri Lanka
| | - Cesar D Urrutia
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, U.S.A
| | - Mathieu Gayral
- Texas A&M Agrilife Center in Dallas, 17360 Coit Rd, Dallas, TX, U.S.A
| | - Kelsey Lyle
- Department of Biological Sciences, The University of Texas at Dallas, Dallas, TX, U.S.A
| | - Madalyn K Shires
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, U.S.A
| | - Kevin Ong
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, U.S.A
| | - David Byrne
- Department of Horticulture Sciences, Texas A&M University, College Station, TX, U.S.A
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19
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Fan X, Li L, Zhao Y, Liu Y, Liu C, Wang Q, Dong Y, Wang S, Chi T, Song F, Sun C, Wang Y, Ha D, Zhao Y, Bao J, Wu X, Wang Z. Clinical Validation of Two Recombinase-Based Isothermal Amplification Assays (RPA/RAA) for the Rapid Detection of African Swine Fever Virus. Front Microbiol 2020; 11:1696. [PMID: 32793160 PMCID: PMC7385304 DOI: 10.3389/fmicb.2020.01696] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
African swine fever (ASF), caused by African swine fever virus (ASFV), is a devastating infectious disease of domestic pigs and wild boars, and has tremendous negative socioeconomic impact on the swine industry and food security worldwide. It is characterized as a notifiable disease by World Organisation for Animal Health (OIE). No effective vaccine or treatment against ASF has so far been available. Early detection and rapid diagnosis are of potential significance to control the spread of ASF. Recombinase-based isothermal amplification assay, recombinase polymerase amplification (RPA) developed by TwistDx (Cambridge, United Kingdom) or recombinase-aided amplification (RAA) by Qitian (Wuxi, China), is becoming a molecular tool for the rapid, specific, and cost-effective identification of multiple pathogens. In this study, we aim to investigate if RPA/RAA can be a potential candidate for on-site, rapid and primary detection of ASFV. A panel of 152 clinical samples previously well-characterized by OIE-recommended qPCR was enrolled in this study, including 20 weak positive (Ct value ≥ 30) samples. This panel was consisted of different types, such as EDTA-blood, spleen, lung, lymph node, kidney, tonsil, liver, brain. We evaluated two recombinase-based isothermal amplification assays, RPA or RAA, by targeting the ASFV B646L gene (p72), and validated the clinical performance in comparison with OIE real-time PCR. Our result showed that the analytical sensitivity of RPA and RAA was as 93.4 and 53.6 copies per reaction, respectively at 95% probability in 16 min, at 39°C. They were universally specific for all 24 genotypes of ASFV and no cross reaction to other pathogens including Classical swine fever virus (CSV), Foot-and-mouth disease virus (FMDV), Pseudorabies virus, Porcine circovirus 2 (PCV2), Porcine Reproductive and respiratory syndrome virus (PPRSV). The results on detection of various kinds of clinical samples indicated an excellent diagnostic agreement between RPA, RAA and OIE real-time PCR method, with the kappa value of 0.960 and 0.973, respectively. Compared to real-time PCR, the specificity of both RPA and RAA was 100% (94.40% ∼ 100%, 95% CI), while the sensitivity was 96.59% (90.36% ∼ 99.29%, 95% CI) and 97.73% (92.03% ∼ 99.72%, 95% CI), respectively. Our data demonstrate that the developed recombinase-based amplification assay (RPA/RAA), promisingly equipped with field-deployable instruments, offers a sensitive and specific platform for the rapid and reliable detection of ASFV, especially in the resource-limited settings for the purpose of screening and surveillance of ASF.
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Affiliation(s)
- Xiaoxu Fan
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Lin Li
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yonggang Zhao
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yutian Liu
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Chunju Liu
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Qinghua Wang
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yaqin Dong
- Livestock Disease Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao, China
| | - Shujuan Wang
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Tianying Chi
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Fangfang Song
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Chengyou Sun
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yingli Wang
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Dengchuriya Ha
- Vocational and Technical College, Inner Mongolia Agricultural University, Hohhot, China
| | - Yang Zhao
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China.,College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Jingyue Bao
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiaodong Wu
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Zhiliang Wang
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
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Halecker S, Joseph S, Mohammed R, Wernery U, Mettenleiter TC, Beer M, Hoffmann B. Comparative evaluation of different antigen detection methods for the detection of peste des petits ruminants virus. Transbound Emerg Dis 2020; 67:2881-2891. [PMID: 32502324 DOI: 10.1111/tbed.13660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/15/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Peste des petits ruminants (PPR) is a fatal disease of small ruminants which has spread rapidly to previously PPR-free countries in recent decades, causing enormous economic losses in the affected regions. Here, two newly emerged PPR virus (PPRV) isolates from India and from the Middle East were tested in an animal trial to analyse their pathogenesis, and to evaluate serological and molecular detection methods. Animals infected with the two different PPRV isolates showed marked differences in clinical manifestation and scoring. The PPRV isolate from India was less virulent than the virus from the Middle East. Commercially available rapid detection methods for PPRV antigen (two Lateral Flow Devices (LFDs) and one antigen ELISA) were evaluated in comparison with a nucleic acid detection method. For this purpose, ocular and nasal swabs were used. Due to the easy non-invasive sampling, faecal samples were also analysed. For all rapid antigen detection methods, a high specificity of 100% was observed independent of the sample matrix and dilution buffers used. Both antigen ELISA and LFD tests showed highest sensitivities for nasal swabs. Here, the detection rate of the antigen ELISA, the LFD-PESTE-TEST and the LFD-ID Rapid-Test was 78%, 75% and 78%, respectively. Ocular swabs were less suitable for antigen detection of PPRV. These results reflect the increased viral load in nasal swabs of PPRV infected goats compared to ocular swabs. The faecal samples were the least suitable for antigen detection. In conclusion, nasal swab samples are the first choice for the antigen and genome detection of PPRV. Nevertheless, based on the excellent diagnostic specificity of the rapid tests, positive results generated with other sample matrices are solid. In contrast, negative test results can be caused on the reduced analytical sensitivity of the rapid antigen tests and must be treated with caution.
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Affiliation(s)
- Sabrina Halecker
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Sunitha Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Rubeena Mohammed
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | | | - Martin Beer
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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21
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Gao S, Wang J, Li D, Li Y, Lou C, Zha E, Yue X, Tiezhong Z. Development and evaluation of a time-saving RT-qRPA method for the detection of genotype 4 HEV presence in raw pork liver. Int J Food Microbiol 2020; 322:108587. [PMID: 32203767 DOI: 10.1016/j.ijfoodmicro.2020.108587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
Hepatitis E virus (HEV) is a zoonotic pathogen spreading worldwide. Pig was known as its first and main animal reservoir. In China, pork consumption is very large and the risk of potential HEV contamination should not be underestimated. The present study aims to develop a quantitative real-time reverse transcription combining recombinase polymerase amplification assay (RT-qRPA) for the rapid detection of HEV RNA presence in raw pork liver on the Jinzhou markets in China. Methods: the specific primers and probes for RT-qRPA assay were designed targeting the ORF2/3 conserved region in genotype 4 swine HEV isolate (accession no. DQ279091.2) according to the TwistDx manual instructions. The specificity, sensitivity and reproducibility evaluations of the RT-qRPA method were subsequently conducted in assessing agreement with the standard RT-qPCR method. Results: the qRPA method step exhibited the obvious time-saving advantage which worked under the isothermal condition at 39 °C within about 30 min to complete the run while the compared standard qPCR method in the same cycle took almost 60 min to do. Both methods could exclusively detect the HEV genome equivalents from the quantified HEV-VLPs spiked samples. And both methods shared the same limit of detection (LOD) that was estimated at 1.25 × 103 genome equivalents copies/g spiked sample by the probit analysis. The recovery rate of HEV-VLPs reached a range of 9.56-14.65% by the RT-qRPA method which was higher than that of 1.34-2.34% by the standard RT-qPCR method. The detected HEV RNA positive rate in the field was 1.8% (1 out of 55) by both methods under Cohen's kappa statistic accessing with perfect agreement (κ = 1.00, p < 0.0005). The viral load in positive sample detected by the RT-qRPA method was estimated at 2.2125 × 105 genome copies/g pork liver sample. Conclusions, the present reported RT-qRPA method mainly targeting genotype 4 HEV is a rapid and reliable method. Its time-saving quality offers a promising for the development of a portable tool used in the routine monitoring of HEV contamination in the field.
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Affiliation(s)
- Shenyang Gao
- College of Animal Husbandry & Veterinary Medicine, Jinzhou Medical University, No. 5-48 Renmin Street, Jinzhou 121001, China.
| | - Jiaying Wang
- College of Animal Husbandry & Veterinary Medicine, Jinzhou Medical University, No. 5-48 Renmin Street, Jinzhou 121001, China
| | - Dandan Li
- Animal Quarantine Lab, Inspection & Quarantine Technology Center of Hainan Entry-Exit Inspection & Quarantine Bureau, Haikou 570000, China
| | - Yang Li
- College of Animal Husbandry & Veterinary Medicine, Jinzhou Medical University, No. 5-48 Renmin Street, Jinzhou 121001, China
| | - Cheng Lou
- College of Animal Husbandry & Veterinary Medicine, Jinzhou Medical University, No. 5-48 Renmin Street, Jinzhou 121001, China
| | - Enhui Zha
- College of Food Science, Jinzhou Medical University, No. 5-48 Renmin Street, Jinzhou 121001, China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, No.120 Dongling Road, Shenyang 110866, China
| | - Zhou Tiezhong
- College of Animal Husbandry & Veterinary Medicine, Jinzhou Medical University, No. 5-48 Renmin Street, Jinzhou 121001, China
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22
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Cong F, Zeng F, Wu M, Wang J, Huang B, Wang Y, Wang Q, Zhang S, Ma L, Guo P, Zeng W. Development of a real-time reverse transcription recombinase polymerase amplification assay for rapid detection of spring viremia of carp virus. Mol Cell Probes 2019; 50:101494. [PMID: 31863825 DOI: 10.1016/j.mcp.2019.101494] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/26/2022]
Abstract
Spring viremia of carp virus (SVCV) is a significant pathogenic agent that can cause large-scale outbreaks of spring viremia of carp (SVC) in many types of fish and bring huge economic losses to the aquaculture industry. A simple and convenient detection method is imperative for SVCV diagnosis. In this study, the real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed and validated. Primers and probe targeting the conserved region of M gene were designed and applied to the real-time RT-RPA assay that performed at 39 °C for 20 min. The specificity analysis showed that no cross-reaction with other pathogenic viruses of fish was found, indicating appropriate specificity of the assay. In vitro transcribed RNA standards were used to estimate the sensitivity of the assay and the detection limit was 102copies/reaction. To further evaluate the assay, 65 clinical samples were tested using both real-time RT-RPA assay and real-time RT-PCR method. The same detection results were observed, suggesting the potential application of real-time RT-RPA assay in clinical sample detection. This is the first report on RPA assay for SVCV detection and this new developed assay would be useful in both laboratory and in the field for diagnosis of SVCV.
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Affiliation(s)
- Feng Cong
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Fanwen Zeng
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China; College of Animal Science, South China Agricultural University, Guangzhou, 510640, China.
| | - Miaoli Wu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Jingjing Wang
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Diseases, Nanjing, 210000, China.
| | - Bihong Huang
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Yingying Wang
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Qing Wang
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Shouquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, 510640, China.
| | - Lei Ma
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Pengju Guo
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Weiwei Zeng
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
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