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Ochwo S, Perez AM, Pérez Aguirreburualde MS. Beyond accuracy: leveraging ASSURED criteria for field evaluation of point-of-care tests for food animal diseases. Front Vet Sci 2023; 10:1239111. [PMID: 37720479 PMCID: PMC10500061 DOI: 10.3389/fvets.2023.1239111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
The growing availability of point-of-care tests (POCTs) for food-animal diseases offers opportunities for timely diagnosis, facilitating the efficient implementation of control measures. However, field assessment of new POCTs are yet to be standardized. This paper discusses the opportunity of expanding the current approach for the evaluation and validation of POCTs in food animal disease diagnosis, highlighting the limitations of traditional practice that primarily relies on estimating diagnostic accuracy (sensitivity and specificity). Here, the use of a protocol referred to as FIT-REASSURED, a modified framework combining the ASSURED and REASSURED criteria, is proposed to comprehensively assess POCTs. FIT-REASSURED encompasses key criteria such as fitness for purpose, real-time connectivity, ease of specimen collection, affordability, sensitivity, specificity, user-friendliness, rapidity and robustness, equipment-free operation, and deliverability. By incorporating these attributes, FIT-REASSURED provides a customizable approach to assess the accuracy, affordability, and utility of POCTs. Through collaborative efforts among stakeholders, the implementation of a standardized scorecard based on these FIT-REASSURED criteria can improve the reliability and practicality of POCTs in food-animal health.
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Affiliation(s)
- Sylvester Ochwo
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
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Cavalera S, Colitti B, De Mia GM, Feliziani F, Giudici SD, Angioi PP, D'Errico F, Scalas D, Scollo A, Serra T, Chiarello M, Testa V, Di Nardo F, Baggiani C, Oggiano A, Rosati S, Anfossi L. Development of molecular and antigenic-based rapid tests for the identification of African swine fever virus in different tissues. Talanta 2023; 258:124443. [PMID: 36933298 DOI: 10.1016/j.talanta.2023.124443] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
African swine fever (ASF) is a severe haemorrhagic infectious disease affecting suids, thus representing a great economic concern. Considering the importance of the early diagnosis, rapid point of care testing (POCT) for ASF is highly demanded. In this work, we developed two strategies for the rapid onsite diagnosis of ASF, based on Lateral Flow Immunoassay (LFIA) and Recombinase Polymerase Amplification (RPA) techniques. The LFIA was a sandwich-type immunoassay exploiting a monoclonal antibody directed towards the p30 protein of the virus (Mab). The Mab was anchored onto the LFIA membrane to capture the ASFV and was also labelled with gold nanoparticles for staining the antibody-p30 complex. However, the use of the same antibody for capturing and as detector ligand showed a significant competitive effect for antigen binding, so required an experimental design to minimize reciprocal interference and maximize the response. The RPA assay, employing primers to the capsid protein p72 gene and an exonuclease III probe, was performed at 39 °C. The limit of detection of the method was assessed using a plasmid encoding the target gene and resulted in 5 copy/μL. The new LFIA and RPA were applied for ASFV detection in the animal tissues usually analysed by conventional assays (i.e., real-time PCR), such as kidney, spleen, and lymph nodes. A simple and universal virus extraction protocol was applied for sample preparation, followed by DNA extraction and purification for the RPA. The LFIA only required the addition of 3% H2O2 to limit matrix interference and prevent false positive results. The two rapid methods (25 min and 15 min were needed to complete the analysis for RPA and LFIA, respectively) showed high diagnostic specificity (100%) and sensitivity (93% and 87% for LFIA and RPA, respectively) for samples with high viral load (Ct < 27). False negative results were observed for samples with low viral load (Ct > 28) and/or also containing specific antibodies to ASFV, which decreased antigen availability and were indicative of a chronic, poorly transmissible infection. The simple and rapid sample preparation and the diagnostic performance of the LFIA suggested its large practical applicability for POC diagnosis of ASF.
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Affiliation(s)
- Simone Cavalera
- Department of Chemistry, University of Turin, Turin, TO, Italy.
| | - Barbara Colitti
- Department of Veterinary Sciences, University of Turin, Turin, TO, Italy.
| | - Gian Mario De Mia
- National Reference Laboratory for Asfivirus and Pestivirus Istituto Zooprofilattico Sperimentale Dell'Umbria e Delle Marche (IZSUM), Perugia, PG, Italy
| | - Francesco Feliziani
- National Reference Laboratory for Asfivirus and Pestivirus Istituto Zooprofilattico Sperimentale Dell'Umbria e Delle Marche (IZSUM), Perugia, PG, Italy
| | - Silvia Dei Giudici
- Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, SS, Italy
| | - Pier Paolo Angioi
- Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, SS, Italy
| | - Federica D'Errico
- National Reference Laboratory for Asfivirus and Pestivirus Istituto Zooprofilattico Sperimentale Dell'Umbria e Delle Marche (IZSUM), Perugia, PG, Italy
| | - Daniela Scalas
- Department of Veterinary Sciences, University of Turin, Turin, TO, Italy
| | - Annalisa Scollo
- Department of Veterinary Sciences, University of Turin, Turin, TO, Italy
| | - Thea Serra
- Department of Chemistry, University of Turin, Turin, TO, Italy
| | | | - Valentina Testa
- Department of Chemistry, University of Turin, Turin, TO, Italy
| | - Fabio Di Nardo
- Department of Chemistry, University of Turin, Turin, TO, Italy
| | | | - Annalisa Oggiano
- Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, SS, Italy
| | - Sergio Rosati
- Department of Veterinary Sciences, University of Turin, Turin, TO, Italy
| | - Laura Anfossi
- Department of Chemistry, University of Turin, Turin, TO, Italy
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Elnagar A, Blome S, Beer M, Hoffmann B. Point-of-Care Testing for Sensitive Detection of the African Swine Fever Virus Genome. Viruses 2022; 14:v14122827. [PMID: 36560831 PMCID: PMC9781289 DOI: 10.3390/v14122827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
African swine fever (ASF) is a contagious viral hemorrhagic disease that affects domestic pigs and wild boar. The disease is notifiable to the World Organization of Animal Health (WOAH), and causes significant deaths and economic losses. There is currently no fully licensed vaccine available. As a result, early identification of the causative agent, ASF virus (ASFV), is crucial for the implementation of control measures. PCR and real-time PCR are the WOAH-recommended standard methods for the direct detection of ASFV. However, under special field conditions or in simple or remote field laboratories, there may be no sophisticated equipment or even stable electricity available. Under these circumstances, point-of-care systems can be put in place. Along these lines, a previously published, rapid, reliable, and electricity-free extraction method (TripleE) was used to isolate viral nucleic acid from diagnostic specimens. With this tool, nucleic acid extraction from up to eight diagnostic samples can be realized in one run in less than 10 min. In addition, the possibility of completely omitting viral DNA extraction was analyzed with so-called direct real-time PCR protocols using ASFV original samples diluted to 1:40 in RNase-free water. Furthermore, three real-time PCR cyclers, developed for use under field conditions (IndiField, Liberty16 and UF-300 GenecheckerTM), were comparatively applied for the sensitive high-speed detection of ASFV genomes, with overall PCR run times between 20 and 54 min. Depending on the viral DNA extraction/releasing method used and the point-of-care cycler applied, a total time for detection of 30 to 60 min for up to eight samples was feasible. As expected, the limitations in analytical sensitivity were positively correlated to the analysis time. These limitations are acceptable for ASFV diagnostics due to the expected high ASFV genome loads in diseased animals or carcasses.
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Ata EB, Li Z, Shi C, Yang G, Yang W, Wang C. African swine fever virus: A raised global upsurge and a continuous threaten to pig husbandry. Microb Pathog 2022. [DOI: 10.1016/j.micpath.2022.105561] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/01/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022]
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Wu Y, Yang Y, Ru Y, Qin X, Li M, Zhang Z, Zhang R, Li Y, Zhang Z, Li Y. The Development of a Real-Time Recombinase-Aid Amplification Assay for Rapid Detection of African Swine Fever Virus. Front Microbiol 2022; 13:846770. [PMID: 35369479 PMCID: PMC8969597 DOI: 10.3389/fmicb.2022.846770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
African swine fever (ASF), caused by the African swine fever virus (ASFV), is an acute, deadly, infectious disease of domestic pigs and wild boars and has a tremendous negative socioeconomic impact on the swine industry. ASF is a notifiable disease to the World Organization for Animal Health (OIE). Currently, no effective vaccine or treatment against ASF is available. Early detection and rapid diagnosis are potentially significant to control ASF spread with the emerging ASFV mutant strains and non-classical symptoms. In this study, we developed a real-time recombinase-aid amplification (RAA) assay to detect the ASFV genome rapidly. Thirty samples were detected using commercial lysis buffer for DNA extraction and equipped with a portable testing instrument. The results showed that the sensitivity of RAA was 103 copies per reaction at 95% probability in 9 min at 39°C. The method was universally specific for three strains of ASFV, and there was no cross-reaction with other pathogens, including foot-and-mouth disease virus (FMDV), classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus 2 (PCV2), pseudorabies virus (PRV), and porcine parvovirus (PPV). The coefficient of variation (C.V) of repetitive experiments was 0%, and the coincidence rate was 100% compared to the real-time qPCR. 123 field samples were detected by the real-time RAA assay, and the results showed that the clinical coincidence rate of the real-time RAA assay was 98% compared to the real-time qPCR assay. The advantages of this method were as follows: the extraction of DNA can be performed on site, the DNA template is directly used, a small battery-powered instrument is easily available, and the on-site diagnostic process is finished within an hour. These suggest that this assay could be used to detect different genotypes of ASFV and play a vital role in the control of ASF.
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Affiliation(s)
- Yongshu Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yang Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yi Ru
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaodong Qin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Miaomiao Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhixiong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Rui Zhang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Yijing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zhidong Zhang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Yanmin Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
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Ceruti A, Kobialka RM, Ssekitoleko J, Okuni JB, Blome S, Abd El Wahed A, Truyen U. Rapid Extraction and Detection of African Swine Fever Virus DNA Based on Isothermal Recombinase Polymerase Amplification Assay. Viruses 2021; 13:v13091731. [PMID: 34578312 PMCID: PMC8472937 DOI: 10.3390/v13091731] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
African swine fever virus (ASFV) is the causative agent of a deadly disease in pigs and is spread rapidly across borders. Samples collected from suspected cases must be sent to the reference laboratory for diagnosis using polymerase chain reaction (PCR). In this study, we aimed to develop a simple DNA isolation step and real-time recombinase polymerase amplification (RPA) assay for rapid detection of ASFV. RPA assay based on the p72 encoding B646L gene of ASFV was established. The assays limit of detection and cross-reactivity were investigated. Diagnostic performance was examined using 73 blood and serum samples. Two extraction approaches were tested: silica-column-based extraction method and simple non-purification DNA isolation (lysis buffer and heating, 70 °C for 20 min). All results were compared with well-established real-time PCR. In a field deployment during a disease outbreak event in Uganda, 20 whole blood samples were tested. The assay’s analytical sensitivity was 3.5 DNA copies of molecular standard per µL as determined by probit analysis on eight independent assay runs. The ASFV RPA assay only detected ASFV genotypes. Compared to real-time PCR, RPA diagnostic sensitivity and specificity were 100%. Using the heating/lysis buffer extraction procedure, ASFV-RPA revealed better tolerance to inhibitors than real-time PCR (97% and 38% positivity rate, respectively). In Uganda, infected animals were identified before the appearance of fever. The ASFV-RPA assay is shown to be as sensitive and specific as real-time PCR. Moreover, the combination of the simple extraction protocol allows its use at the point of need to improve control measures.
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Affiliation(s)
- Arianna Ceruti
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (A.C.); (R.M.K.); (U.T.)
| | - Rea Maja Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (A.C.); (R.M.K.); (U.T.)
| | - Judah Ssekitoleko
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala P.O. Box 7062, Uganda; (J.S.); (J.B.O.)
- National Agricultural Research Organisation, Entebbe P.O. Box 295, Uganda
| | - Julius Boniface Okuni
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala P.O. Box 7062, Uganda; (J.S.); (J.B.O.)
| | - Sandra Blome
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, 17493 Greifswald, Germany;
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (A.C.); (R.M.K.); (U.T.)
- Correspondence:
| | - Uwe Truyen
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (A.C.); (R.M.K.); (U.T.)
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Li Z, Wei J, Di D, Wang X, Li C, Li B, Qiu Y, Liu K, Gu F, Tong M, Wang S, Wu X, Ma Z. Rapid and accurate detection of African swine fever virus by DNA endonuclease-targeted CRISPR trans reporter assay. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1413-1419. [PMID: 33201182 DOI: 10.1093/abbs/gmaa135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
The first case of African swine fever (ASF) outbreak in China was reported in a suburban pig farm in Shenyang in 2018. Since then, the rapid spread and extension of ASF has become the most serious threat for the swine industry. Therefore, rapid and accurate detection of African swine fever virus (ASFV) is essential to provide effective strategies to control the disease. In this study, we developed a rapid and accurate ASFV-detection method based on the DNA endonuclease-targeted CRISPR trans reporter (DETECTR) assay. By combining recombinase polymerase amplification with CRISPR-Cas12a proteins, the DETECTR assay demonstrated a minimum detection limit of eight copies with no cross reactivity with other swine viruses. Clinical blood samples were detected by DETECTR assay and showed 100% (30/30) agreement with real-time polymerase chain reaction assay. The rapid and accurate detection of ASFV may facilitate timely eradication measures and strict sanitary procedures to control and prevent the spread of ASF.
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Affiliation(s)
- Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Di Di
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Xin Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Chenxi Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Feng Gu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture, Shanghai 200241, China
| | - Minglong Tong
- Yixing Customs, General Administration of Customs of the People’s Republic of China, Yixing 214206, China
| | - Shuiming Wang
- Yixing Customs, General Administration of Customs of the People’s Republic of China, Yixing 214206, China
| | - Xiaodong Wu
- National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao 266032, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
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Lamb HJ, Hayes BJ, Nguyen LT, Ross EM. The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock. Genes (Basel) 2020; 11:E1478. [PMID: 33317066 PMCID: PMC7763041 DOI: 10.3390/genes11121478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Oxford Nanopore Technologies' MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: 'crush-side genotyping' for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.
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Affiliation(s)
- Harrison J. Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4067, Australia; (B.J.H.); (L.T.N.); (E.M.R.)
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Chaudhari J, Vu HLX. Porcine Reproductive and Respiratory Syndrome Virus Reverse Genetics and the Major Applications. Viruses 2020; 12:E1245. [PMID: 33142752 DOI: 10.3390/v12111245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/15/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a positive sense, single-stranded RNA virus that is known to infect only pigs. The virus emerged in the late 1980s and became endemic in most swine producing countries, causing substantial economic losses to the swine industry. The first reverse genetics system for PRRSV was reported in 1998. Since then, several infectious cDNA clones for PRRSV have been constructed. The availability of these infectious cDNA clones has facilitated the genetic modifications of the viral genome at precise locations. Common approaches to manipulate the viral genome include site-directed mutagenesis, deletion of viral genes or gene fragments, insertion of foreign genes, and swapping genes between PRRSV strains or between PRRSV and other members of the Arteriviridae family. In this review, we describe the approaches to construct an infectious cDNA for PRRSV and the ten major applications of these infectious clones to study virus biology and virus–host interaction, and to design a new generation of vaccines with improved levels of safety and efficacy.
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Daigle J, Onyilagha C, Truong T, Le VP, Nga BTT, Nguyen TL, Clavijo A, Ambagala A. Rapid and highly sensitive portable detection of African swine fever virus. Transbound Emerg Dis 2020; 68:952-959. [PMID: 32762007 DOI: 10.1111/tbed.13770] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/30/2020] [Accepted: 08/01/2020] [Indexed: 01/03/2023]
Abstract
African swine fever (ASF) continues to spread across Asia, devastating pig populations. The disease is nearly 100% fatal in pigs, and currently, there is no effective vaccine available. Therefore, early detection of ASF is critical for effective disease control. The testing process usually requires samples to be shipped to a central laboratory, which may take many hours of travel or shipping time, delaying the results needed for a rapid response. The ability to confirm ASFV-infected animals on-site or in a regional laboratory that has limited technical capacity and/or infrastructure should eliminate these issues. This study describes the successful transfer of a highly sensitive and specific laboratory-validated real-time PCR assay to a portable pen-side thermocycler, which can be operated in the field for rapid detection of ASFV following a quick manual nucleic acid extraction from a wide array of clinical samples including aggregate samples such as oral fluids. The performance of the portable assay was comparable to the laboratory-based assay. The true portability of the assay was evaluated in seven ASF-suspected farms in Vietnam by testing eighty-nine freshly collected whole blood samples on-site. The results obtained on-site were in agreement with the laboratory data obtained the following day. Availability of this field-deployable molecular assay would eliminate the need to ship samples to a central laboratory, when rapid laboratory results are required, ultimately improving the response time.
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Affiliation(s)
- Jade Daigle
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Chukwunonso Onyilagha
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Thang Truong
- Canadian Science Centre for Human and Animal Health - National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Van Phan Le
- College of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Trau Quy- Gia Lam- Hanoi, Vietnam
| | - Bui Thi To Nga
- College of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Trau Quy- Gia Lam- Hanoi, Vietnam
| | - Thi Lan Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Trau Quy- Gia Lam- Hanoi, Vietnam
| | - Alfonso Clavijo
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada.,USDA, Agricultural Research Service, Manhattan, KS, USA
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada.,Department of Comparative Biology, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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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: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Abstract
African swine fever virus (ASFV) is the sole member of the family Asfarviridae, and the only known DNA arbovirus. Since its identification in Kenya in 1921, ASFV has remained endemic in Africa, maintained in a sylvatic cycle between Ornithodoros soft ticks and warthogs (Phacochoerus africanus) which do not develop clinical disease with ASFV infection. However, ASFV causes a devastating and economically significant disease of domestic (Sus scrofa domesticus) and feral (Sus scrofa ferus) swine. There is no ASFV vaccine available, and current control measures consist of strict animal quarantine and culling procedures. The virus is highly stable and easily spreads by infected swine, contaminated pork products and fomites, or via transmission by the Ornithodoros vector. Competent Ornithodoros argasid soft tick vectors are known to exist not only in Africa, but also in parts of Europe and the Americas. Once ASFV is established in the argasid soft tick vector, eradication can be difficult due to the long lifespan of Ornithodoros ticks and their proclivity to inhabit the burrows of warthogs or pens and shelters of domestic pigs. Establishment of endemic ASFV infections in wild boar populations further complicates the control of ASF. Between the late 1950s and early 1980s, ASFV emerged in Europe, Russia and South America, but was mostly eradicated by the mid-1990s. In 2007, a highly virulent genotype II ASFV strain emerged in the Caucasus region and subsequently spread into the Russian Federation and Europe, where it has continued to circulate and spread. Most recently, ASFV emerged in China and has now spread to several neighboring countries in Southeast Asia. The high morbidity and mortality associated with ASFV, the lack of an efficacious vaccine, and the complex makeup of the ASFV virion and genome as well as its lifecycle, make this pathogen a serious threat to the global swine industry and national economies. Topics covered by this review include factors important for ASFV infection, replication, maintenance, and transmission, with attention to the role of the argasid tick vector and the sylvatic transmission cycle, current and future control strategies for ASF, and knowledge gaps regarding the virus itself, its vector and host species.
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Affiliation(s)
- Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Daniel W. Madden
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - William C. Wilson
- Arthropod Borne Animal Diseases Research Unit, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS, United States
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
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13
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Cappai S, Loi F, Rolesu S, Coccollone A, Laddomada A, Sgarangella F, Masala S, Bitti G, Floris V, Desini P. Evaluation of the cost-effectiveness of ASF detection with or without the use of on-field tests in different scenarios, in Sardinia. J Vet Sci 2020; 21:e14. [PMID: 31940693 PMCID: PMC7113566 DOI: 10.4142/jvs.2020.21.e14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/14/2019] [Accepted: 11/21/2019] [Indexed: 11/20/2022] Open
Abstract
African swine fever (ASF) is a highly contagious disease of domestic pigs and wild boars (WBs). Without a vaccine, early antibody and antigen detection and rapid diagnosis are crucial for the effective prevention of the disease and the employment of control measures. In Sardinia, where 3 different suid populations coexisted closely for a long time, the disease persists since 1978. The recent ASF eradication plan involves more stringent measures to combat free-ranging pigs and any kind of illegality in the pig industry. However, critical issues such as the low level of hunter cooperation with veterinary services and the time required for ASF detection in the WBs killed during the hunting season still remain. Considering the need to deliver true ASF negative carcasses as early as possible, this study focuses on the evaluation and validation of a duplex pen-side test that simultaneously detects antibodies and antigens specific to ASF virus, to improve molecular diagnosis under field conditions. The main goal was to establish the specificity of the two pen-side tests performed simultaneously and to determine their ability to detect the true ASF negative carcasses among the hunted WBs. Blood and organ samples of the WBs hunted during the 2018/2019 hunting seasons were obtained. A total of 160 animals were tested using the pen-side kit test; samples were collected for virological and serological analyses. A specificity of 98% was observed considering the official laboratory tests as gold standards. The new diagnostic techniques could facilitate faster and cost-effective control of the disease.
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Affiliation(s)
- Stefano Cappai
- Osservatorio Epidemiologico Veterinario Regionale della Sardegna, via XX Settembre, 09125 Cagliari, Italy
- Istituto Zooprofilattico Sperimentale della sardegna "G.Pegreffi", Via Duca degli Abruzzi 8, 07100 Sassari, Italy.
| | - Federica Loi
- Osservatorio Epidemiologico Veterinario Regionale della Sardegna, via XX Settembre, 09125 Cagliari, Italy
- Istituto Zooprofilattico Sperimentale della sardegna "G.Pegreffi", Via Duca degli Abruzzi 8, 07100 Sassari, Italy
| | - Sandro Rolesu
- Osservatorio Epidemiologico Veterinario Regionale della Sardegna, via XX Settembre, 09125 Cagliari, Italy
- Istituto Zooprofilattico Sperimentale della sardegna "G.Pegreffi", Via Duca degli Abruzzi 8, 07100 Sassari, Italy
| | - Annamaria Coccollone
- Osservatorio Epidemiologico Veterinario Regionale della Sardegna, via XX Settembre, 09125 Cagliari, Italy
- Istituto Zooprofilattico Sperimentale della sardegna "G.Pegreffi", Via Duca degli Abruzzi 8, 07100 Sassari, Italy
| | - Alberto Laddomada
- Istituto Zooprofilattico Sperimentale della sardegna "G.Pegreffi", Via Duca degli Abruzzi 8, 07100 Sassari, Italy
| | | | - Sergio Masala
- ATS Sardegna, ASSL Sassari, Servizio di Sanità Animale, 07100 Sassari, Italy
| | - Giuseppe Bitti
- ATS Sardegna, ASSL Sassari, Servizio di Sanità Animale, 07100 Sassari, Italy
| | - Vincenzo Floris
- ATS Sardegna, ASSL Sassari, Servizio di Sanità Animale, 07100 Sassari, Italy
| | - Pietro Desini
- ATS Sardegna, ASSL Sassari, Servizio di Sanità Animale, 07100 Sassari, Italy
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14
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Li Y, Huang B, Shen C, Cai C, Wang Y, Edwards J, Zhang G, Robertson ID. Pig trade networks through live pig markets in Guangdong Province, China. Transbound Emerg Dis 2020; 67:1315-1329. [PMID: 31903722 PMCID: PMC7228257 DOI: 10.1111/tbed.13472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 12/27/2019] [Accepted: 12/27/2019] [Indexed: 11/28/2022]
Abstract
This study used social network analysis to investigate the indirect contact network between counties through the movement of live pigs through four wholesale live pig markets in Guangdong Province, China. All 14,118 trade records for January and June 2016 were collected from the markets and the patterns of pig trade in these markets analysed. Maps were developed to show the movement pathways. Evaluating the network between source counties was the primary objective of this study. A 1‐mode network was developed. Characteristics of the trading network were explored, and the degree, betweenness and closeness were calculated for each source county. Models were developed to compare the impacts of different disease control strategies on the potential magnitude of an epidemic spreading through this network. The results show that pigs from 151 counties were delivered to the four wholesale live pig markets in January and/or June 2016. More batches (truckloads of pigs sourced from one or more piggeries) were traded in these markets in January (8,001) than in June 2016 (6,117). The pigs were predominantly sourced from counties inside Guangdong Province (90%), along with counties in Hunan, Guangxi, Jiangxi, Fujian and Henan provinces. The major source counties (46 in total) contributed 94% of the total batches during the two‐month study period. Pigs were sourced from piggeries located 10 to 1,417 km from the markets. The distribution of the nodes' degrees in both January and June indicates a free‐scale network property, and the network in January had a higher clustering coefficient (0.54 vs. 0.39) and a shorter average pathway length (1.91 vs. 2.06) than that in June. The most connected counties of the network were in the central, northern and western regions of Guangdong Province. Compared with randomly removing counties from the network, eliminating counties with higher betweenness, degree or closeness resulted in a greater reduction of the magnitude of a potential epidemic. The findings of this study can be used to inform targeted control interventions for disease spread through this live pig market trade network in south China.
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Affiliation(s)
- Yin Li
- School of Veterinary Medicine, Murdoch University, Perth, WA, Australia.,China Animal Health and Epidemiology Center, Qingdao, China
| | - Baoxu Huang
- School of Veterinary Medicine, Murdoch University, Perth, WA, Australia.,China Animal Health and Epidemiology Center, Qingdao, China
| | - Chaojian Shen
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Chang Cai
- Research and Innovation Office, Murdoch University, Murdoch, WA, Australia.,China Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Youming Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - John Edwards
- School of Veterinary Medicine, Murdoch University, Perth, WA, Australia.,China Animal Health and Epidemiology Center, Qingdao, China
| | - Guihong Zhang
- South China Agriculture University, Guangzhou, China
| | - Ian D Robertson
- School of Veterinary Medicine, Murdoch University, Perth, WA, Australia.,China-Australia Joint Research and Training Centre for Veterinary Epidemiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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15
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Miao F, Zhang J, Li N, Chen T, Wang L, Zhang F, Mi L, Zhang J, Wang S, Wang Y, Zhou X, Zhang Y, Li M, Zhang S, Hu R. Rapid and Sensitive Recombinase Polymerase Amplification Combined With Lateral Flow Strip for Detecting African Swine Fever Virus. Front Microbiol 2019; 10:1004. [PMID: 31156571 PMCID: PMC6530510 DOI: 10.3389/fmicb.2019.01004] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/18/2019] [Indexed: 01/23/2023] Open
Abstract
African swine fever virus (ASFV), the etiological agent of African swine fever (ASF), a hemorrhagic fever of domestic pigs, has devastating consequences for the pig farming industry. More than 1,000,000 pigs have been slaughtered since 3 August 2018 in China. However, vaccines or drugs for ASF have yet to be developed. As such, a rapid test that can accurately detect ASFV on-site is important to the timely implementation of control measures. In this study, we developed a rapid test that combines recombinase polymerase amplification (RPA) of the ASFV p72 gene with lateral flow detection (LFD). Results showed that the sensitivity of recombinase polymerase amplification with lateral flow dipstick (RPA-LFD) for ASFV was 150 copies per reaction within 10 min at 38°C. The assay was highly specific to ASFV and had no cross-reactions with other porcine viruses, including classical swine fever virus (CSFV). A total of 145 field samples were examined using our method, and the agreement of the positive rate between RPA-LFD (10/145) and real-time PCR (10/145) was 100%. Overall, RPA-LFD provides a novel alternative for the simple, sensitive, and specific identification of ASFV and showed potential for on-site ASFV detection.
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Affiliation(s)
- Faming Miao
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Jingyuan Zhang
- College of Life Science, Ningxia University, Yinchuan, China.,Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Nan Li
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Teng Chen
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Lidong Wang
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Fei Zhang
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Lijuan Mi
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Jinxia Zhang
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Shuchao Wang
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Ying Wang
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Xintao Zhou
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Yanyan Zhang
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Min Li
- College of Life Science, Ningxia University, Yinchuan, China
| | - Shoufeng Zhang
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
| | - Rongliang Hu
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, China
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