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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 DOI: 10.1177/10406387241235968] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J G Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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2
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Li Y, Shang J, Wang Y, Luo J, Jiang W, Yin X, Zhang F, Deng C, Yu X, Liu H. Establishment of two assays based on reverse transcription recombinase-aided amplification technology for rapid detection of H5 subtype avian influenza virus. Microbiol Spectr 2023; 11:e0218623. [PMID: 37811963 PMCID: PMC10715165 DOI: 10.1128/spectrum.02186-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/10/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Avian influenza virus (AIV) subtype H5 is a highly contagious zoonotic disease and a serious threat to the farming industry and public health. Traditional detection methods, including virus isolation and real-time PCR, require tertiary biological laboratories and are time-consuming and complex to perform, making it difficult to rapidly diagnose H5 subtype avian influenza viruses. In this study, we successfully developed two methods, namely, RF-RT-RAA and RT-RAA-LFD, for rapid detection of H5-AIV. The assays are characterized by their high specificity, sensitivity, and user-friendliness. Moreover, the results of the reaction can be visually assessed, which are suitable for both laboratory testing and grassroots farm screening for H5-AIV.
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Affiliation(s)
- Yang Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Jiajing Shang
- China Animal Health and Epidemiology Center, Qingdao, China
- School of Life Science and Food Engineering, Hebei University of Engineering, Hebei, China
| | - Yixin Wang
- College of Veterinary Medicine, Shandong Agricultural University, Shandong, China
| | - Juan Luo
- China Animal Health and Epidemiology Center, Qingdao, China
- School of Life Science and Food Engineering, Hebei University of Engineering, Hebei, China
| | - Wenming Jiang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xin Yin
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Fuyou Zhang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Chunran Deng
- China Animal Health and Epidemiology Center, Qingdao, China
- School of Life Science and Food Engineering, Hebei University of Engineering, Hebei, China
| | - Xiaohui Yu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - HuaLei Liu
- China Animal Health and Epidemiology Center, Qingdao, China
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3
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Li D, Zhao J, Lan W, Zhao Y, Sun X. Effect of food matrix on rapid detection of Vibrio parahaemolyticus in aquatic products based on toxR gene. World J Microbiol Biotechnol 2023; 39:188. [PMID: 37156898 DOI: 10.1007/s11274-023-03640-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Vibrio parahaemolyticus has become an important public threat to human health. Rapid and robust pathogen diagnostics are necessary for monitoring its outbreak and spreading. Herein, we report an assay for the detection of V. parahaemolyticus based on recombinase aided amplification (RAA) combined with lateral flow dipstick (LFD), namely RAA-LFD. The RAA-LFD took 20 min at 36~38 ℃, and showed excellent specificity. It detected as low as 6.4 fg/µL of V. parahaemolyticus in genomic DNA, or 7.4 CFU/g spiked food samples with 4 h of enrichment. The limit of detection in shrimp (Litopenaeus Vannamei), fish (Carassius auratus), clam (Ruditapes philippinarum) evidenced that sensitivity was considerably affected by the food matrix. The presence of food matrix reduced the sensitivity of spiked food samples by 10 ~ 100 times. In the filed samples detection, RAA-LFD method showed good coincidence with GB4789.7-2013 method and PCR method at rates of 90.6% and 94.1%, respectively. RAA-LFD has high accuracy and sensitivity for the detection of V. parahaemolyticus, which can serve as a model tool to meet the growing need for point-of-care diagnosis of V. parahaemolyticus.
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Affiliation(s)
- Darong Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Jiayi Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Weiqing Lan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, 201306, People's Republic of China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, 201306, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, 201306, People's Republic of China
| | - Xiaohong Sun
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, 201306, People's Republic of China.
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, 201306, People's Republic of China.
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Liu F, Zhang C, Duan Y, Ma J, Wang Y, Chen G. A detection method for Prorocentrum minimum by an aptamer-gold nanoparticles based colorimetric assay. J Hazard Mater 2023; 449:131043. [PMID: 36827721 DOI: 10.1016/j.jhazmat.2023.131043] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Here, to give early waring for harmful algal blooms caused by Prorocentrum minimum, we reported a simple and rapid colorimetric assay that is named aptamer-gold nanoparticles (GNPs) based colorimetric assay (AGBCA). The GNPs maintain a dispersed state and have a strong characteristic absorption peak at 520 nm. With the addition of NaCl, the stability of the solution will be destroyed and the dispersed GNPs will aggregate. Therefore, the characteristic absorption peak of the GNPs solution will change from 520 nm to 670 nm. Aptamers can be adsorbed on the surface of GNPs, effectively preventing the aggregation of GNPs. In the presence of P. minimum, aptamers will specifically bind to P. minimum, causing the dissociation of the aptamers from GNPs. Consequently, the GNPs will aggregate in the NaCl solution, corresponding to a new absorption peak at 670 nm. A linear relationship between the absorbance ratio variation (ΔA670/A520) and the P. minimum concentration was observed in the concentration range of 1 × 102 - 1 × 107 cells mL-1, with a low detection limit of 8 cells mL-1. The developed AGBCA is characterized by simplicity, strong specificity, and high sensitivity and is thus promising for the quantitative detection of P. minimum in natural samples.
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Affiliation(s)
- Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
| | - Yu Duan
- School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Jinju Ma
- School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
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Ding X, Wang H, Cui M, Cheng M, Zhao Q, Bai Y, Zhang C, Zhang C, Xu S, Li T. Development of a Real-Time Recombinase-Aided Amplification Method to Rapidly Detect Methicillin-Resistant Staphylococcus aureus. Microorganisms 2022; 10. [PMID: 36557604 DOI: 10.3390/microorganisms10122351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/03/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2022] Open
Abstract
Methicillin-resistant staphylococcus aureus (MRSA) is a major pathogen responsible for human hospital and community-onset diseases and severe invasive livestock infections. Rapid detection of MRSA is essential to control the spread of MRSA. Conventional identification methods and antibacterial susceptibility tests of MRSA are time-consuming. The commonly used qPCR assay also has the disadvantages of being complicated and expensive, restricting its application in resource-limited clinical laboratories. Here, a real-time fluorescent recombinase-assisted amplification (RAA) assay targeting the most conserved regions within the mecA gene of MRSA was developed and evaluated to detect MRSA. The detection limit of this assay was determined to be 10 copies/reaction of positive plasmids. The established RAA assay showed high specificity for MRSA detection without cross-reactivities with other clinically relevant bacteria. The diagnostic performance of real-time RAA was evaluated using 67 clinical S. aureus isolates from dairy farms, which were detected in parallel using the TaqMan probe qPCR assay. The results showed that 56 and 54 samples tested positive for MRSA by RAA and qPCR, respectively. The overall agreement between both assays was 97.01% (65/67), with a kappa value of 0.9517 (p < 0.001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9012, p < 0.0001), indicating that this RAA assay possesses similar detection performance to the qPCR assay. In conclusion, our newly established RAA assay is a time-saving and convenient diagnostic tool suitable for MRSA detection and screening.
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He A, Fang C, Ming Y, Tan H, Zhang M, Zhang R, Li J, Nie M, Li F, Hu Y, Shen X, Rong X, Ma X. Development of field-applicable endogenous internally controlled recombinase-aided amplification (EIC-RAA) assays for the detection of human papillomavirus genotypes 6 and 11 using sample releasing agent. Heliyon 2022; 8:e11323. [DOI: 10.1016/j.heliyon.2022.e11323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/25/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
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Abstract
INTRODUCTION Recombinase polymerase amplification (RPA) is a promising and emerging technology for rapidly amplifying target nucleic acid from minimally processed samples and through small portable instruments. RPA is suitable for point-of-care testing (POCT) and on-site field testing, and it is compatible with microfluidic devices. Several detection assays have been developed, but limited research has dug deeper into the chemistry of RPA to understand its kinetics and fix its shortcomings. AREAS COVERED This review provides a detailed introduction of RPA molecular mechanism, kits formats, optimization, application, pros, and cons. Moreover, this critical review discusses the nonspecificity issue of RPA, highlights its consequences, and emphasizes the need for more research to resolve it. This review discusses the reaction kinetics of RPA in relation to target length, product quantity, and sensitivity. This critical review also questions the novelty of recombinase-aided amplification (RAA). In short, this review discusses many aspects of RPA technology that have not been discussed previously and provides a deeper insight and new perspectives of the technology. EXPERT OPINION RPA is an excellent choice for pathogen detection, especially in low-resource settings. It has a potential to replace PCR for all purposes, provided its shortcomings are fixed and its reagent accessibility is improved.
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Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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Ma C, Tian Z, Yang L, Cao J. Validation of qPCR from a crude extract for the rapid detection of white spot syndrome virus. Aquac Int 2022; 30:2679-2690. [PMID: 35910332 PMCID: PMC9309450 DOI: 10.1007/s10499-022-00920-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED White spot disease (WSD) has posed a serious threat to the China and the global shrimp aquaculture. In order to diagnose white spot syndrome virus (WSSV) early and prevent the spread and outbreak of WSD, it is necessary to establish a highly sensitive WSSV diagnosis method suitable for shrimp farming sites. In this study, a pre-amplification qPCR assay from the crude extract of samples heated lysis was established, which was further compared with the universal qPCR assay to verify the shrimp samples. The limit of detection (LOD) of pre-amplification qPCR assay and universal qPCR assay was 2.80 copies and 20.57 copies per reaction at 95% CI, respectively. It had good WSSV specificity and did not show cross-detection of infectious hypodermal and hematopoietic necrosis virus (IHHNV), hepatopancreatic parvovirus (HPV), Enterocytozoon hepatopenaei (EHP), acute hepatopancreas necrosis disease (AHPND), necrotizing hepatopancreatitis bacteria (NHPB), and decapod iridescent virus 1 (DIV1). A total of 36 shrimp samples were detected as WSSV DNA positive by pre-amplification qPCR with crude extract from samples heated lysis and universal qPCR with DNA extraction. The diagnostic sensitivity and specificity were 97.22% (85.5 ~ 99.9%, 95% CI) and 100% (81.5 ~ 100%, 95% CI), respectively. The agreement Kappa value was 0.959 (0.879 ~ 1, 95% CI), and the analysis results were basically consistent. Eliminating the tedious steps of extracting DNA and using pre-amplified qPCR to detect WSSV in shrimp, it is a good choice for aquaculture farms. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10499-022-00920-9.
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Affiliation(s)
- Chao Ma
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
| | - Zhuo Tian
- Dalian Customs Technology Center, Dalian, China
| | - Lili Yang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
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Hou L, Li D, Zhang N, Zhao J, Zhao Y, Sun X. Development of an isothermal recombinase-aided amplification assay for the rapid and visualized detection of Klebsiella pneumoniae. J Sci Food Agric 2022; 102:3879-3886. [PMID: 34936095 DOI: 10.1002/jsfa.11737] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Klebsiella pneumoniae is a zoonotic opportunistic pathogen, leading to severe infections in dairy cows and humans. Efficient, on-site and accurate detection of K. pneumoniae is necessary to reduce the harm of cow mastitis and human infections. The objective of this study was to establish a recombinase-aided amplification (RAA) method combined with lateral flow dipstick (LFD) for rapid detection of K. pneumoniae. RESULTS The primer concentration, incubation temperature and incubation time of the RAA reaction were optimized. When the primer concentration was 100 nmol L-1 , the strongest band could be obtained by incubation at 37 °C for 20 min. The RAA-LFD method had high specificity to K. pneumoniae and showed no cross-reaction with other pathogens. In addition, the detection limit of RAA-LFD for K. pneumoniae was 20 fg genomic DNA and 2.5 × 102 CFU mL-1 of bacteria in pure culture, which is 100 times higher than that of polymerase chain reaction (PCR) detection. Moreover, the RAA-LFD method can detect K. pneumoniae at initial concentrations as low as 2.5 CFU per 25 mL in artificially spiked milk samples after at least incubation for 6 h. Importantly, RAA-LFD had a high agreement with a test accuracy of 96.9%, compared with the biochemical identification method. Also, the detection accuracy of RAA-LFD was higher than that of the PCR assay (95.3%). CONCLUSIONS The results demonstrated that the RAA-LFD assay is an accurate, sensitive, simple and point-of-use detection method for K. pneumoniae, which could be used as a potential application in the research laboratory and for disease diagnosis. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Laiwang Hou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Darong Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Ni Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Jiayi Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, People's Republic of China
| | - Xiaohong Sun
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, People's Republic of China
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Xiao F, Liu J, Feng X, Xie G, Zhang W, Xu H. Rapid enrichment and detection of Staphylococcus aureus in milk using polyethyleneimine functionalized magnetic nanoparticles. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107388] [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] [Indexed: 11/25/2022]
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Li JY, Chen XP, Tie YQ, Sun XL, Zhang RQ, He AN, Nie MZ, Fan GH, Li FY, Tian FY, Shen XX, Feng ZS, Ma XJ. Detection of low-load Epstein-Barr virus in blood samples by enriched recombinase aided amplification assay. AMB Express 2022; 12:71. [PMID: 35689713 PMCID: PMC9188631 DOI: 10.1186/s13568-022-01415-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/10/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
Epstein-Barr virus (EBV), a common human γ-herpesvirus, infects more than 90% of adults worldwide. The purpose of this study was to establish a novel EBV detection method by combining the recombinase aided amplification (RAA) assay with an initial enrichment step that utilizes magnetic beads coated with a recombinant human mannan-binding lectin (rhMBL, M1 protein). An M1 protein–protein A magnetic bead complex (M1 beads) was prepared and used to achieve separation and enrichment of EBV from blood. After nucleic acid extraction, DNA was amplified by RAA. Using 388 whole blood samples and 1 serum sample, we explored the specificity, sensitivity and applicability of the newly developed detection method and compared it with commercial quantitative real-time polymerase chain reaction (qPCR) following M1 bead enrichment, traditional qPCR and traditional RAA. After enrichment, the positivity rate of EBV was increased from 15.94% to 17.74% by RAA (P < 0.05) and from 7.20% to 15.17% by qPCR (P < 0.05). The viral loads after enrichment were increased by 1.13 to 23.19-fold (P < 0.05). Our data demonstrates that an RAA assay incorporating M1 bead enrichment is a promising tool for detecting low EBV viral loads in blood samples that will facilitate an early response to EBV infection. The RAA with an enrichment step that utilizes magnetic beads coated with M1 protein. A very effective method for detecting low-load virus in blood samples. The first report describing virus detection using this method.
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Affiliation(s)
- Jing-Yi Li
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xiao-Ping Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Yan-Qing Tie
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China
| | - Xiu-Li Sun
- Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,North China University of Science and Technology, No. 46 West Xinhua Road, Tangshan, 063009, Hebei, China
| | - Rui-Qing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - An-Na He
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,North China University of Science and Technology, No. 46 West Xinhua Road, Tangshan, 063009, Hebei, China
| | - Ming-Zhu Nie
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Guo-Hao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Feng-Yu Li
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Feng-Yu Tian
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
| | - Zhi-Shan Feng
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China. .,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
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Liu L, Zhao G, Li X, Xu Z, Lei H, Shen X. Development of rapid and easy detection of Salmonella in food matrics using RPA-CRISPR/Cas12a method. Lebensm Wiss Technol 2022; 162:113443. [DOI: 10.1016/j.lwt.2022.113443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Nie MZ, Zhang RQ, Zhao MC, Tan H, Hu YX, Fan GH, Li JY, He AN, Tian FY, Li FY, Zheng YH, Shen XX, Tie YQ, Ma XJ. Development of a duplex recombinase-aided amplification assay for direct detection of Mycoplasma pneumoniae and Chlamydia trachomatis in clinical samples. J Microbiol Methods 2022; 198:106504. [PMID: 35654228 DOI: 10.1016/j.mimet.2022.106504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Pneumonia caused by Mycoplasma pneumoniae is common in the elderly and children, and pneumonia caused by Chlamydia trachomatis is prevalent in newborns. This study aimed to establish a rapid, sensitive, and simple method for the direct detection of M. pneumoniae and C. trachomatis in clinical samples without DNA extraction. METHODS We established a duplex recombinase-aided amplification (RAA) assay with the RNAseP gene as an internal control for detecting the P1 gene of M. pneumoniae and the ORF8 gene of C. trachomatis, respectively. The results were obtained at 39 °C within 15-20 min. A total of 130 clinical samples suspected of M. pneumoniae or C. trachomatis infection were collected and tested by duplex RAA and PCR. DNA extracted via a commercial kit or treated with a nucleic acid-releasing agent was used and compared, respectively. Standard recombinant plasmids were used to test the sensitivity of the duplex RAA assay. In addition, other similar common pathogens were used to verify the specificity of the duplex RAA assay. RESULTS The sensitivity of the duplex RAA assay for detecting M. pneumoniae and C. trachomatis was 10 copies/μL using recombinant plasmids. Compared with PCR, the sensitivity and specificity of duplex RAA assays for M. pneumoniae and C. trachomatis was 100% using clinical DNA samples extracted using a commercial kit and a nucleic acid-releasing agent, and the Kappa value was 1. CONCLUSION The advantages of this duplex RAA assay include high sensitivity and specificity, short duration, and simple extraction steps, with potential for use in the on-site detection of M. pneumoniae and C. trachomatis in resource-limited settings.
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Affiliation(s)
- Ming-Zhu Nie
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China.
| | - Rui-Qing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China.
| | - Meng-Chuan Zhao
- Children's Hospital of Hebei Province, Shijiazhuang 050031, Hebei, China
| | - He Tan
- Hebei General Hospital, Shijiazhuang 050051, Hebei, China
| | - Ya-Xin Hu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China; North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Guo-Hao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China
| | - Jing-Yi Li
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China
| | - An-Na He
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China; North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Feng-Yu Tian
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China
| | - Feng-Yu Li
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China
| | - Ye-Huan Zheng
- Autobio Diagnostics CO., Ltd, Zhengzhou 450000, Henan, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China.
| | - Yan-Qing Tie
- Hebei General Hospital, Shijiazhuang 050051, Hebei, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing 102206, China.
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Zhao J, Li Y, Xue Q, Zhu Z, Zou M, Fang F. A novel rapid visual detection assay for Toxoplasma gondii combining recombinase-aided amplification and lateral flow dipstick coupled with CRISPR-Cas13a fluorescence (RAA-Cas13a-LFD). Parasite 2022; 29:21. [PMID: 35420541 PMCID: PMC9009239 DOI: 10.1051/parasite/2022021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/14/2021] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
Toxoplasmosis, a parasitic disease resulting from Toxoplasma gondii infection, remains prevalent worldwide, and causes great harm to immunodepressed patients, pregnant women and newborns. Although various molecular approaches to detect T. gondii infection are available, they are either costly or technically complex. This study aimed at developing a rapid visual detection assay using recombinase-aided amplification (RAA) and lateral flow dipstick (LFD) coupled with CRISPR-Cas13a fluorescence (RAA-Cas13a-LFD) to detect T. gondii. The RAA-Cas13a-LFD assay was performed in an incubator block at 37 °C within 2 h, and the amplification results were visualized and determined through LFD by the naked eye. The detection limit was 1 × 10-6 ng/μL by our developed RAA-Cas13a-LFD protocol, 100-fold higher than that by qPCR assay (1 × 10-8 ng/μL). No cross-reaction occurred either with the DNA of human blood or Ascaris lumbricoides, Digramma interrupta, Entamoeba coli, Fasciola gigantica, Plasmodium vivax, Schistosoma japonicum, Taenia solium, and Trichinella spiralis, and the positive rate by RAA-Cas13a-LFD assay was identical to that by qPCR assay (1.50% vs. 1.50%) in detecting T. gondii infection in the unknown blood samples obtained from clinical settings. Our findings demonstrate that this RAA-Cas13a-LFD assay is not only rapid, sensitive, and specific and allows direct visualization by the naked eye, but also eliminates sophisticated and costly equipment. More importantly, this technique can be applied to on-site surveillance of T. gondii.
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Affiliation(s)
- Jinhong Zhao
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China - Provincial Key Laboratory of Active Biological Macro-Molecules, Wuhu 241002, Anhui, China
| | - Yuanyuan Li
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Qiqi Xue
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Zhiwei Zhu
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Minghui Zou
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Fang Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China
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Li X, Wang C, Zhang Z, Wang C, Wang W, Zhao Z, Li J, Shang Z, Lv J, Zhang T. Fast detection of duck circovirus by real-time fluorescence-based recombinase-aided amplification. Poult Sci 2022; 101:101707. [PMID: 35108659 PMCID: PMC8814383 DOI: 10.1016/j.psj.2022.101707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/10/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/18/2022] Open
Abstract
Duck circovirus disease (DuCVD), as an immunosuppressive disease, is a threat to the poultry industry. In order to diagnose this disease quickly and accurately, a real-time fluorescence-based recombinase-aided amplification (RF-RAA) method was established to detect duck circovirus (DuCV). The results showed that the quantity of amplification products was positively correlated with the value of fluorescence signal. Obvious detection results can be observed at 41°C after 15 min reaction. This method has good specificity and has no cross reaction with Muscovy duck parvovirus (MDPV), duck enteritis virus (DEV), fowl adenovirus (FAdV), porcine circovirus (PCV), and duck hepatitis A virus (DHAV). The sensitivity test showed that the minimum concentration of template detected by RF-RAA for DuCV was 10° copies/μL, and its sensitivity was 10 times higher than that of real-time fluorescence-based quantitative PCR (RFQ-PCR) and 10,000 times higher than that of polymerase chain reaction (PCR). Fifty-two clinical samples were detected by RF-RAA and RFQ-PCR, and the coincidence rate of the two methods was 98.08%. This method has the advantages of simple operation, good specificity and high sensitivity, and can be used for laboratory detection and clinical diagnosis of DuCV.
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Affiliation(s)
- Xinyue Li
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Chunguang Wang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Zongshu Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Chao Wang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Wenjing Wang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Ziyu Zhao
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Jikai Li
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Zihan Shang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Jiancun Lv
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Tie Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China.
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Feng ZS, Li JY, Zhang JY, Li FY, Guan HX, Zhang RQ, Liu H, Guo Q, Shen XX, Kan B, Ma XJ. Development and evaluation of a sensitive recombinase aided amplification assay for rapid detection of Vibrio parahaemolyticus. J Microbiol Methods 2022; 193:106404. [PMID: 34990645 DOI: 10.1016/j.mimet.2021.106404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 11/15/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/27/2022]
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is a widely distributed pathogen in the coastal areas, which causes food poisoning and leads to gastroenteritis and sepsis. Therefore, developing a simple, sensitive, and rapid detection method for V. parahaemolyticus is a major concern globally. This study established a sensitive and rapid technique based on recombinase aided amplification (RAA) to detect V. parahaemolyticus. The RAA reaction was carried out successfully at 39 °C within 30 min. The sensitivity of the RAA assay was 101 copies/μL using the recombinant plasmid and 10-3 ng/μL using the V. parahaemolyticus strain. In addition, RAA directly detected 7 × 103 CFU/mL of simulated fecal samples and 0.1 CFU/mL after enrichment for 4 h. The sensitivity and specificity of the RAA assay using fecal and fish samples were 100% similar to that of the real-time PCR. We conclude that the RAA assay is an ideal screening method for detecting V. parahaemolyticus due to its rapidity, high accuracy, and simplicity in operation.
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Affiliation(s)
- Zhi-Shan Feng
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, Hebei, China
| | - Jing-Yi Li
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, Hebei, China; NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jing-Yun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute forCommunicable DiseaseControl and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Feng-Yu Li
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, Hebei, China; NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hong-Xia Guan
- Wuxi Center for Disease Control and Prevention, Wuxi 214023, Jiangsu, China
| | - Rui-Qing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Hong Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences and Medicine, Shandong University of Technology, Zibo255049, Shandong, China
| | - Qi Guo
- Laboratory of Virology, Beijing Key Laboratory ofEtiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing 100020, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute forCommunicable DiseaseControl and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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Chu H, Liu C, Liu J, Yang J, Li Y, Zhang X. Recent advances and challenges of biosensing in point-of-care molecular diagnosis. Sens Actuators B Chem 2021; 348:130708. [PMID: 34511726 PMCID: PMC8424413 DOI: 10.1016/j.snb.2021.130708] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/07/2023]
Abstract
Molecular diagnosis, which plays a major role in infectious disease screening with successful understanding of the human genome, has attracted more attention because of the outbreak of COVID-19 recently. Since point-of-care testing (POCT) can expand the application of molecular diagnosis with the benefit of rapid reply, low cost, and working in decentralized environments, many researchers and commercial institutions have dedicated tremendous effort and enthusiasm to POCT-based biosensing for molecular diagnosis. In this review, we firstly summarize the state-of-the-art techniques and the construction of biosensing systems for POC molecular diagnosis. Then, the application scenarios of POCT-based biosensing for molecular diagnosis were also reviewed. Finally, several challenges and perspectives of POC biosensing for molecular diagnosis are discussed. This review is expected to help researchers deepen comprehension and make progresses in POCT-based biosensing field for molecular diagnosis applications.
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Affiliation(s)
- Hongwei Chu
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Conghui Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Jinsen Liu
- Shenzhen ENCO Instrument Co., Ltd, Shenzhen 518000, China
| | - Jiao Yang
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Yingchun Li
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Xueji Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
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18
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Fan G, Zhang R, He X, Tian F, Nie M, Shen X, Ma X. RAP: A Novel Approach to the Rapid and Highly Sensitive Detection of Respiratory Viruses. Front Bioeng Biotechnol 2021; 9:766411. [PMID: 34805120 PMCID: PMC8602363 DOI: 10.3389/fbioe.2021.766411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/29/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Recombinase aided amplification (RAA) is an emerging isothermal amplification method used for detecting various pathogens. However, RAA requires a complex and long probe to ensure high sensitivity during fluorescence assay. TaqMan probe used for quantitative PCR (qPCR) is simple and universal. Herein, we developed a new approach for detecting nucleic acids of pathogens, known as RAP (Recombinase aided PCR). The method combines RAA and qPCR to ensure a rapid and highly sensitive detection using a conventional qPCR device. RAP is a two-stage amplification process performed in a single tube within 1 hour. The method involves an RAA reaction for 10 min at 39°C (first stage) followed by 15 cycles of qPCR (second stage). Using human adenovirus 3 (HADV3) and human adenovirus 7 (HADV7) plasmids, the sensitivities of RAP assays for detecting HADV3 and HADV7 were 6 and 17 copies per reaction, respectively. The limit of RAP detection was at least 16-fold lower than the corresponding qPCR, and no-cross reaction with other respiratory viruses was observed. The results of RAP analysis revealed 100% consistency with qPCR assay. This study shows that RAP assay is a rapid, specific, and highly sensitive detection method with a potential for clinical and laboratory application.
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Affiliation(s)
- Guohao Fan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaozhou He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fengyu Tian
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mingzhu Nie
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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Li H, Chen H, Liu B, Cai R, Jiang N, Yue T, Wang Z. Establishment of quantitative PCR assays for the rapid detection of Alicyclobacillus spp. that can produce guaiacol in apple juice. Int J Food Microbiol 2021; 360:109329. [PMID: 34275638 DOI: 10.1016/j.ijfoodmicro.2021.109329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/06/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022]
Abstract
Alicyclobacillus species are one of the most significant qualities and safety factors in fruit juice and beverages. The growth of some Alicyclobacillus genus can lead to sour spoilage with the off-odor of medicinal, phenolic or antiseptic, which is mainly caused by the metabolites of guaiacol, dihalophenol and dibromophenol. Especially, guaiacol is regarded as the predominant taint in Alicyclobacillus-spoiled products. In this study, quantitative PCR (qPCR) assays were proposed for the detection of A. acidoterrestris, A. acidiphilus, A. cycloheptanicus and A. herbarius that can produce guaiacol in fruit juice. The 16S rDNA sequences of these four kinds of Alicyclobacillus species were identified and the primers suitable for the qPCR assay were obtained. The sensitivity and specificity of the established methods were evaluated. The results indicated that the developed qPCR approaches were distinctive enough to detect A. acidoterrestris, A. acidiphilus, A. cycloheptanicus and A. herbarius with the sensitivity of 2.6 × 102 CFU/mL, 74 CFU/mL, 2.8 × 102 CFU/mL and 3.1 × 102 CFU/mL, respectively. The correlation coefficients of standard curves were from 0.9807 to 0.9985. Based on the pretreatment of filtration-culture, these bacteria with the initial concentration of 10-1 CFU/mL, 100 CFU/mL and 101 CFU/mL can be effectively detected in 2-20 h, which depended on the target bacteria and their initial concentration. The results displayed that the proposed procedures were effective for the rapid detection of Alicyclobacillus species that can produce guaiacol in apple juice.
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Affiliation(s)
- Hui Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Bin Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Rui Cai
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Nan Jiang
- Rushan R & D Center of SDIC Zhonglu Fruit Juice Co., Ltd, Weihai 264500, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China.
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20
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Wang X, Pecoraro L. Analysis of Soil Fungal and Bacterial Communities in Tianchi Volcano Crater, Northeast China. Life (Basel) 2021; 11:280. [PMID: 33810555 DOI: 10.3390/life11040280] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 03/16/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/26/2022] Open
Abstract
High-altitude volcanoes, typical examples of extreme environments, are considered of particular interest in biology as a possible source of novel and exclusive microorganisms. We analyzed the crater soil microbial diversity of Tianchi Volcano, northeast China, by combining molecular and morphological analyses of culturable microbes, and metabarcoding based on Illumina sequencing, in order to increase our understanding of high-altitude volcanic microbial community structure. One-hundred and seventeen fungal strains belonging to 51 species and 31 genera of Ascomycota, Basidiomycota and Mucoromycota were isolated. Penicillium, Trichoderma, Cladosporium, Didymella, Alternaria and Fusarium dominated the culturable fungal community. A considerable number of isolated microbes, including filamentous fungi, such as Aureobasidium pullulans and Epicoccum nigrum, yeasts (Leucosporidium creatinivorum), and bacteria (Chryseobacterium lactis and Rhodococcus spp.), typical of high-altitude, cold, and geothermal extreme environments, provided new insights in the ecological characterization of the investigated environment, and may represent a precious source for the isolation of new bioactive compounds. A total of 1254 fungal and 2988 bacterial operational taxonomic units were generated from metabarcoding. Data analyses suggested that the fungal community could be more sensitive to environmental and geographical change compared to the bacterial community, whose network was characterized by more complicated and closer associations.
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21
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Brunauer A, Verboket RD, Kainz DM, von Stetten F, Früh SM. Rapid Detection of Pathogens in Wound Exudate via Nucleic Acid Lateral Flow Immunoassay. Biosensors (Basel) 2021; 11:bios11030074. [PMID: 33800856 PMCID: PMC8035659 DOI: 10.3390/bios11030074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/24/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
The rapid detection of pathogens in infected wounds can significantly improve the clinical outcome. Wound exudate, which can be collected in a non-invasive way, offers an attractive sample material for the detection of pathogens at the point-of-care (POC). Here, we report the development of a nucleic acid lateral flow immunoassay for direct detection of isothermally amplified DNA combined with fast sample preparation. The streamlined protocol was evaluated using human wound exudate spiked with the opportunistic pathogen Pseudomonas aeruginosa that cause severe health issues upon wound colonization. A detection limit of 2.1 × 105 CFU per mL of wound fluid was achieved, and no cross-reaction with other pathogens was observed. Furthermore, we integrated an internal amplification control that excludes false negative results and, in combination with the flow control, ensures the validity of the test result. The paper-based approach with only three simple hands-on steps has a turn-around time of less than 30 min and covers the complete analytical process chain from sample to answer. This newly developed workflow for wound fluid diagnostics has tremendous potential for reliable pathogen POC testing and subsequent target-oriented therapy.
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Affiliation(s)
- Anna Brunauer
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - René D Verboket
- Department of Trauma-, Hand- and Reconstructive Surgery, University Hospital Frankfurt, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Daniel M Kainz
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Susanna M Früh
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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Fang W, Cai Y, Zhu L, Wang H, Lu Y. Rapid and Highly Sensitive Detection of Toxigenic Vibrio cholerae Based on Recombinase-Aided Amplification Combining with Lateral Flow Assay. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01909-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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23
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Wang J, Liu J, Song G, Cao Z, Pan J, Li X, Gao Y, Qi J, Chen Z, Fan G, Bai X, Zhang R, Wang R, Duan Q, Li L, Shen X, Ma X. Internally controlled recombinase-aided amplification (IC-RAA) assays for the detection of human papillomavirus genotypes 16 and 18 using extracted DNA and samples treated with nucleic acid releasing agent. Arch Virol 2020; 165:2241-2247. [PMID: 32681408 DOI: 10.1007/s00705-020-04722-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/25/2020] [Indexed: 10/23/2022]
Abstract
Cervical cancer is primarily caused by persistent infection with high-risk human papillomavirus (HPV), and 70% of cases are associated with HPV16 and 18 infections. The objective of this study was to establish rapid, simple, and sensitive internally controlled recombinase-aided amplification (IC-RAA) assays for the detection of HPV16 and 18. The assays were performed at 39 ℃ and were completed within 30 min. A total of 277 clinical samples of exfoliated cervical cells were tested by IC-RAA assays and commercial HPV real-time fluorescent PCR kits using extracted DNA and samples treated with nucleic acid releasing agent. The analytical sensitivity of the IC-RAA assay was found to be 10 copies/μL for the detection of HPV16 and 18 when using recombinant plasmids as targets. The optimal concentration of the internal control (IC) plasmid and 18 was 1000 copies/μL for HPV16 and 100 copies/μL for HPV18. The clinical sensitivity of the IC-RAA assays for HPV16 using extracted DNA and samples treated with nucleic acid releasing agent was 98.73% and 97.47%, respectively, with kappa values of 0.977 (P < 0.01) and 0.955 (P < 0.01), respectively, and 100% The specificity in both cases. For HPV18, the sensitivity and specificity were 100%, and the kappa value was 1 for both samples (P < 0.01). The IC-RAA assay is a promising tool for the detection of HPV16 and HPV18, especially in resource-constrained settings.
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Affiliation(s)
- Jinrong Wang
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Jianli Liu
- General Administration of Customs (Beijing) International Travel Healthcare Centre, No. 20 Heping Li North Street, Dongcheng District, Beijing, 100013, China
| | - Guowei Song
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Zhi Cao
- Beijing Chaoyang Maternal and Child Health Hospital, No. 25 Huaweili, Chaoyang District, Beijing, China
| | - Jing Pan
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Xinna Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Yuan Gao
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Juju Qi
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Ziwei Chen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Guohao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xueding Bai
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Ruiqing Zhang
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Ruihuan Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Qingxia Duan
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Lixin Li
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China. .,Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China.
| | - Xinxin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
| | - Xuejun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
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24
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Wang J, Cai K, He X, Shen X, Wang J, Liu J, Xu J, Qiu F, Lei W, Cui L, Ge Y, Wu T, Zhang Y, Yan H, Chen Y, Yu J, Ma X, Shi H, Zhang R, Li X, Gao Y, Niu P, Tan W, Wu G, Jiang Y, Xu W, Ma X. Multiple-centre clinical evaluation of an ultrafast single-tube assay for SARS-CoV-2 RNA. Clin Microbiol Infect 2020; 26:1076-1081. [PMID: 32422410 PMCID: PMC7227500 DOI: 10.1016/j.cmi.2020.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 04/21/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To evaluate the performance of an ultrafast single-tube nucleic acid isothermal amplification detection assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA using clinical samples from multiple centres. METHODS A reverse transcription recombinase-aided amplification (RT-RAA) assay for SARS-CoV-2 was conducted within 15 minutes at 39°C with portable instruments after addition of extracted RNA. The clinical performance of RT-RAA assay was evaluated using 947 clinical samples from five institutions in four regions of China; approved commercial fluorescence quantitative real-time PCR (qRT-PCR) kits were used for parallel detection. The sensitivity and specificity of RT-RAA were compared and analysed. RESULTS The RT-RAA test results of 926 samples were consistent with those of qRT-PCR (330 were positive, 596 negative); 21 results were inconsistent. The sensitivity and specificity of RT-RAA was 97.63% (330/338, 95% confidence interval (CI) 95.21 to 98.90) and 97.87% (596/609, 95% CI 96.28 to 98.81) respectively. The positive and negative predictive values were 96.21% (330/343, 95% CI 93.45 to 97.88) and 98.68% (596/604, 95% CI 97.30 to 99.38) respectively. The total coincidence rate was 97.78% (926/947, 95% CI 96.80 to 98.70), and the kappa was 0.952 (p < 0.05). CONCLUSIONS With comparable sensitivity and specificity to the commercial qRT-PCR kits, RT-RAA assay for SARS-CoV-2 exhibited the distinctive advantages of simplicity and rapidity in terms of operation and turnaround time.
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Affiliation(s)
- J Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - K Cai
- Hubei Center for Disease Control and Prevention, Wuhan 430000, China
| | - X He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - J Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Hebei Medical University, Shijiazhuang 050031, China
| | - J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - J Xu
- Hubei Center for Disease Control and Prevention, Wuhan 430000, China
| | - F Qiu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - W Lei
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - L Cui
- NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Y Ge
- NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - T Wu
- NHC Key Laboratories of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Y Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310000, China
| | - H Yan
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310000, China
| | - Y Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310000, China
| | - J Yu
- The NO.1 Affiliated hospital of Shanxi Datong University, Institute of Brain Science-Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Datong 037000, China
| | - X Ma
- The NO.1 Affiliated hospital of Shanxi Datong University, Institute of Brain Science-Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Datong 037000, China; The Fifth People's Hospital of DaTong, Datong 037000, China
| | - H Shi
- Datong City Center for Disease Control and Prevention, Datong 037000, China
| | - R Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Hebei Medical University, Shijiazhuang 050031, China
| | - X Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Hebei Medical University, Shijiazhuang 050031, China
| | - P Niu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - W Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - G Wu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y Jiang
- Hubei Center for Disease Control and Prevention, Wuhan 430000, China.
| | - W Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - X Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
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25
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Xiong Y, Luo Y, Li H, Wu W, Ruan X, Mu X. Rapid visual detection of dengue virus by combining reverse transcription recombinase-aided amplification with lateral-flow dipstick assay. Int J Infect Dis 2020; 95:406-412. [PMID: 32272263 DOI: 10.1016/j.ijid.2020.03.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 01/21/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES Dengue caused by infection with the dengue virus (DENV) is endemic in the tropical and subtropical regions of the world and of greatest public health concern. With more large outbreaks in rural areas, the purpose of this study was to develop a point-of-care test using recombinase-aided amplification and lateral-flow dipsticks for rapidly detecting DENV in low-resource settings. METHODS The primers for the recombinase-aided amplification (RAA) assay were designed based on 3' UTR of the DENV genome and screened. The RAA temperature, time and the concentration of primers were then optimized, as well as the lateral-flow dipstick assay (LFD) time. Finally, the diagnostic performance of the reverse transcription (RT)-RAA-LFD assay was evaluated using blood samples from 247 patients who were clinically suspected to be infected with DENV. RESULTS The RAA primer pair F1/R2 was the optimal combination for detecting DENV. The RT-RAA was performed in an incubator block at 37°C for 20minutes, and the amplicons were visible in the flow dipsticks from a naked eye within 3minutes. The detection limit of the developed RT-RAA-LFD assay was 10 copies/μL with high specificity for DENV. Compared with commercial reverse transcription quantitative PCR assay, the kappa value of RT-RAA-LFD in the 247 clinical samples was 0.957. CONCLUSIONS In this study, a rapid and visual point-of-care test based on RT-RAA and LFD assay was developed. It was found to be suitable for reliable detection of DENV in low-resource settings with limited laboratory capabilities and optimal storage conditions.
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Affiliation(s)
- Yufeng Xiong
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Yasha Luo
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Huan Li
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Weixiang Wu
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Xiaolin Ruan
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Xiaoping Mu
- Department of Clinical laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China.
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