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Chang MM, Natoli ME, Wilkinson AF, Tubman VN, Airewele GE, Richards-Kortum RR. A multiplexed, allele-specific recombinase polymerase amplification assay with lateral flow readout for sickle cell disease detection. LAB ON A CHIP 2024; 24:4115-4127. [PMID: 39051493 PMCID: PMC11334763 DOI: 10.1039/d4lc00281d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/17/2024] [Indexed: 07/27/2024]
Abstract
Isothermal nucleic acid amplification tests have the potential to improve disease diagnosis at the point of care, but it remains challenging to develop multiplexed tests that can detect ≥3 targets or to detect point mutations that may cause disease. These capabilities are critical to enabling informed clinical decision-making for many applications, such as sickle cell disease (SCD). To address this, we describe the development of a multiplexed allele-specific recombinase polymerase amplification (RPA) assay with lateral flow readout. We first characterize the specificity of RPA using primer design strategies employed in PCR to achieve point mutation detection, and demonstrate the utility of these strategies in achieving selective isothermal amplification and detection of genomic DNA encoding for the healthy βA globin allele, or genomic DNA containing point mutations encoding for pathologic βS and βC globin alleles, which are responsible for most sickle cell disorders. We then optimize reaction conditions to achieve multiplexed amplification and identification of the three alleles in a single reaction. Finally, we perform a small pilot study with 20 extracted genomic DNA samples from SCD patients and healthy volunteers - of the 13 samples with valid results, the assay demonstrated 100% sensitivity and 100% specificity for detecting pathologic alleles, and an overall accuracy of 92.3% for genotype prediction. This multiplexed assay is rapid, minimally instrumented, and when combined with point-of-care sample preparation, could enable DNA-based diagnosis of SCD in low-resource settings. The strategies reported here could be applied to other challenges, such as detection of mutations that confer drug resistance.
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Affiliation(s)
- Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Mary E Natoli
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | | | - Venée N Tubman
- Texas Children's Cancer and Hematology Centers, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Gladstone E Airewele
- Texas Children's Cancer and Hematology Centers, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
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Xu Q, Zhang Y, Sadigh Y, Tang N, Chai J, Cheng Z, Gao Y, Qin A, Shen Z, Yao Y, Nair V. Specific and Sensitive Visual Proviral DNA Detection of Major Pathogenic Avian Leukosis Virus Subgroups Using CRISPR-Associated Nuclease Cas13a. Viruses 2024; 16:1168. [PMID: 39066330 PMCID: PMC11281634 DOI: 10.3390/v16071168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Avian leukosis viruses (ALVs) include a group of avian retroviruses primarily associated with neoplastic diseases in poultry, commonly referred to as avian leukosis. Belonging to different subgroups based on their envelope properties, ALV subgroups A, B, and J (ALV-A, ALV-B, and ALV-J) are the most widespread in poultry populations. Early identification and removal of virus-shedding birds from infected flocks are essential for the ALVs' eradication. Therefore, the development of rapid, accurate, simple-to-use, and cost effective on-site diagnostic methods for the detection of ALV subgroups is very important. Cas13a, an RNA-guided RNA endonuclease that cleaves target single-stranded RNA, also exhibits non-specific endonuclease activity on any bystander RNA in close proximity. The distinct trans-cleavage activity of Cas13 has been exploited in the molecular diagnosis of multiple pathogens including several viruses. Here, we describe the development and application of a highly sensitive Cas13a-based molecular test for the specific detection of proviral DNA of ALV-A, B, and J subgroups. Prokaryotically expressed LwaCas13a, purified through ion exchange and size-exclusion chromatography, was combined with recombinase polymerase amplification (RPA) and T7 transcription to establish the SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) molecular detection system for the detection of proviral DNA of ALV-A/B/J subgroups. This novel method that needs less sample input with a short turnaround time is based on isothermal detection at 37 °C with a color-based lateral flow readout. The detection limit of the assay for ALV-A/B/J subgroups was 50 copies with no cross reactivity with ALV-C/D/E subgroups and other avian oncogenic viruses such as reticuloendotheliosis virus (REV) and Marek's disease virus (MDV). The development and evaluation of a highly sensitive and specific visual method of detection of ALV-A/B/J nucleic acids using CRISPR-Cas13a described here will help in ALV detection in eradication programs.
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Affiliation(s)
- Qingqing Xu
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Guildford, Surrey GU24 ONF, UK; (Q.X.); (Y.Z.); (Y.S.)
- UK-China Centre of Excellence for Research on Avian Diseases, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou 256600, China; (N.T.); (Z.S.)
- Sino-UK Laboratory for Poultry Disease Research, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou 256600, China
| | - Yaoyao Zhang
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Guildford, Surrey GU24 ONF, UK; (Q.X.); (Y.Z.); (Y.S.)
| | - Yashar Sadigh
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Guildford, Surrey GU24 ONF, UK; (Q.X.); (Y.Z.); (Y.S.)
| | - Na Tang
- UK-China Centre of Excellence for Research on Avian Diseases, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou 256600, China; (N.T.); (Z.S.)
- Sino-UK Laboratory for Poultry Disease Research, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou 256600, China
| | - Jiaqian Chai
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China; (J.C.); (Z.C.)
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China; (J.C.); (Z.C.)
| | - Yulong Gao
- State Key Laboratory of Veterinary Biotechnology, Division of Avian Infectious Diseases, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150008, China;
| | - Aijian Qin
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, Yangzhou 225109, China;
| | - Zhiqiang Shen
- UK-China Centre of Excellence for Research on Avian Diseases, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou 256600, China; (N.T.); (Z.S.)
- Sino-UK Laboratory for Poultry Disease Research, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou 256600, China
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Guildford, Surrey GU24 ONF, UK; (Q.X.); (Y.Z.); (Y.S.)
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Guildford, Surrey GU24 ONF, UK; (Q.X.); (Y.Z.); (Y.S.)
- The Jenner Institute Laboratories, University of Oxford, Oxford OX3 7DQ, UK
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
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3
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Wang Y, Zheng T, Li X, Wu P. Integrating Recombinase Polymerase Amplification and Photosensitization Colorimetric Detection in One Tube for Fast Screening of C. sakazakii in Formula Milk Powder. Anal Chem 2024; 96:5727-5733. [PMID: 38546834 DOI: 10.1021/acs.analchem.4c01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Cronobacter sakazakii (C. sakazakii) is a widely existing opportunistic pathogen and thus threatens people with low immunity, especially infants. To prevent the outbreak, a rapid and accurate on-site testing method is required. The current standard culture-based method is time-consuming (3-4 days), while the nucleic acid amplification (PCR)-based detection is mostly carried out in central laboratories. Herein, isothermal recombinase polymerase amplification (RPA) coupled with a photosensitization colorimetric assay (PCA) was adopted for the on-site detection of C. sakazakii in powdered infant formulas (PIFs). The lowest visual detection concentration of C. sakazakii is 800 cfu/mL and 2 cfu/g after 8 h bacteria pre-enrichment. Furthermore, to avoid typical cap opening-resulted aerosol pollution, the PCA reagents were lyophilized onto the cap of the RPA tube (containing lyophilized RPA reagents). After amplification, the tube was subjected to simple shaking to mix the PCA reagents with the amplification products for light-driven color development. Such a one-tube assay offered a lowest concentration of 1000 copies of genomic DNA of C. sakazakii within 1 h. After 8 h of bacterial enrichment, the lowest detecting concentration could be pushed down to 5 cfu/g bacteria in PIF. To facilitate on-site monitoring, a portable, battery-powered PCA device was designed to mount the typical RPA 8-tube strip, and a color analysis cellphone APP was further employed for facile readout.
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Affiliation(s)
- Yanying Wang
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Ting Zheng
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xianming Li
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Peng Wu
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
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Bachmann I, Behrmann O, Klingenberg-Ernst M, Rupnik M, Hufert FT, Dame G, Weidmann M. Rapid Isothermal Detection of Pathogenic Clostridioides difficile Using Recombinase Polymerase Amplification. Anal Chem 2024; 96:3267-3275. [PMID: 38358754 DOI: 10.1021/acs.analchem.3c02985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Nosocomial-associated diarrhea due to Clostridioides difficile infection (CDI) is diagnosed after sample precultivation by the detection of the toxins in enzyme immunoassays or via toxin gene nucleic acid amplification. Rapid and direct diagnosis is important for targeted treatment to prevent severe cases and recurrence. We developed two singleplex and a one-pot duplex fluorescent 15 min isothermal recombinase polymerase amplification (RPA) assays targeting the toxin genes A and B (tcdA and tcdB). Furthermore, we adapted the singleplex RPA to a 3D-printed microreactor device. Analytical sensitivity was determined using a DNA standard and DNA extracts of 20 C. difficile strains with different toxinotypes. Nineteen clostridial and gastrointestinal bacteria strains were used to determine analytical specificity. Adaptation of singleplex assays to duplex assays in a 50 μL volume required optimized primer and probe concentrations. A volume reduction by one-fourth (12.4 μL) was established for the 3D-printed microreactor. Mixing of RPA was confirmed as essential for optimal analytical sensitivity. Detection limits (LOD) ranging from 119 to 1411 DNA molecules detected were similar in the duplex tube format and in the singleplex 3D-printed microreactor format. The duplex RPA allows the simultaneous detection of both toxins important for the timely and reliable diagnosis of CDI. The 3D-printed reaction chamber can be developed into a microfluidic lab-on-a-chip system use at the point of care.
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Affiliation(s)
- Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
| | - Ole Behrmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
| | | | - Maja Rupnik
- Center for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food, Prvomajska ulica 1, 2000 Maribor, Slovenia
- Faculty of Medicine, Maribor, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Department of Virology, University Medical Center, Kreuzbergring 57, 37075 Göttingen, Germany
- Brandenburg University of Technology Cottbus - Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany
- Department of Virology, University Medical Center, Kreuzbergring 57, 37075 Göttingen, Germany
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Lian Y, Zhang M, Zhu Y, Wu M, Huang B, Xiao L, Shi K, Li P, Cong F, Wang H. The establishment of a recombinase polymerase amplification technique for the detection of mouse poxvirus. BMC Vet Res 2023; 19:256. [PMID: 38053140 DOI: 10.1186/s12917-023-03703-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 08/23/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Ectromelia virus (ECTV) is the causative agent of mousepox in mice. In the past century, ECTV was a serious threat to laboratory mouse colonies worldwide. Recombinase polymerase amplification (RPA), which is widely used in virus detection, is an isothermal amplification method. RESULTS In this study, a probe-based RPA detection method was established for rapid and sensitive detection of ECTV.Primers were designed for the highly conserved region of the crmD gene, the main core protein of recessive poxvirus, and standard plasmids were constructed. The lowest detection limit of the ECTV RT- RPA assay was 100 copies of DNA mol-ecules per reaction. In addition, the method showed high specificity and did not cross-react with other common mouse viruses.Therefore, the practicability of the RPA method in the field was confirmed by the detection of 135 clinical samples. The real-time RPA assay was very similar to the ECTV real-time PCR assay, with 100% agreement. CONCLUSIONS In conclusion, this RPA assay offers a novel alternative for the simple, sensitive, and specific identification of ECTV, especially in low-resource settings.
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Affiliation(s)
- Yuexiao Lian
- Guangdong laboratory animals monitoring instituteand Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510663, China
| | - Mengdi Zhang
- Guangdong laboratory animals monitoring instituteand Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510663, China
| | - Yujun Zhu
- Guangdong laboratory animals monitoring instituteand Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510663, China
| | - Miaoli Wu
- Guangdong laboratory animals monitoring instituteand Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510663, China
| | - Bihong Huang
- Guangdong laboratory animals monitoring instituteand Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510663, China
| | - Li Xiao
- Guangdong laboratory animals monitoring instituteand Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510663, China
| | - Kehang Shi
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Peide Li
- Wenzhou Engineering Research Center of Pet, Department of Animal Science, Wenzhou Vocational College of Science & Technology, Wenzhou, 325006, China.
| | - Feng Cong
- Guangdong laboratory animals monitoring instituteand Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510663, China.
| | - Huanan Wang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, 310058, China.
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Kumar S, Singh H, Feder-Kubis J, Nguyen DD. Recent advances in nanobiosensors for sustainable healthcare applications: A systematic literature review. ENVIRONMENTAL RESEARCH 2023; 238:117177. [PMID: 37751831 DOI: 10.1016/j.envres.2023.117177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 09/28/2023]
Abstract
The need for novel healthcare treatments and drugs has increased due to the expanding human population, detection of newer diseases, and looming pandemics. The development of nanotechnology offers a platform for cutting-edge in vivo non-invasive monitoring and point-of-care-testing (POCT) for rehabilitative disease detection and management. The advancement and uses of nanobiosensors are currently becoming more common in a variety of scientific fields, such as environmental monitoring, food safety, biomedical, clinical, and sustainable healthcare sciences, since the advent of nanotechnology. The identification and detection of biological patterns connected to any type of disease (communicable or not) have been made possible in recent years by several sensing techniques utilizing nanotechnology concerning biosensors and nanobiosensors. In this work, 2218 articles are drawn and screened from six digital databases out of which 17 were shortlisted for this review by using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) technique. As a result, this study uses a systematic methodology to review some recently developed extremely sensitive nanobiosensors, along with their biomedical, point-of-care diagnostics (POCD), or healthcare applications and their capabilities, particularly for the prediction of some fatal diseases based on a few of the most recent publications. The potential of nanobiosensors for medicinal, therapeutic, or other sustainable healthcare applications, notably for ailments diagnostics, is also recognized as a way forward in the manifestation of future trends.
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Affiliation(s)
- Sunil Kumar
- Department of Electronics and Communication Engineering, Chandigarh University, Mohali, Punjab, India
| | - Harbinder Singh
- Department of Electronics and Communication Engineering, Chandigarh University, Mohali, Punjab, India.
| | - Joanna Feder-Kubis
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - D Duc Nguyen
- Department of Civil & Energy System Engineering, Kyonggi University, Suwon 16227, South Korea
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Wu X, Chen S, Zhang Z, Zhang Y, Li P, Chen X, Liu M, Lu Q, Li Z, Wei Z, Xu P. Development of Recombinase Polymerase Amplification Combined with Lateral Flow Strips for Rapid Detection of Cowpea Mild Mottle Virus. THE PLANT PATHOLOGY JOURNAL 2023; 39:486-493. [PMID: 37817494 PMCID: PMC10580057 DOI: 10.5423/ppj.oa.02.2023.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 10/12/2023]
Abstract
Cowpea mild mottle virus (CPMMV) is a global plant virus that poses a threat to the production and quality of legume crops. Early and accurate diagnosis is essential for effective managing CPMMV outbreaks. With the advancement in isothermal recombinase polymerase amplification and lateral flow strips technologies, more rapid and sensitive methods have become available for detecting this pathogen. In this study, we have developed a reverse transcription recombinase polymerase amplification combined with lateral flow strips (RT-RPA-LFS) method for the detection of CPMMV, specifically targeting the CPMMV coat protein (CP) gene. The RT-RPA-LFS assay only requires 20 min at 40°C and demonstrates high specificity. Its detection limit was 10 copies/μl, which is approximately up to 100 times more sensitive than RT-PCR on agarose gel electrophoresis. The developed RT-RPA-LFS method offers a rapid, convenient, and sensitive approach for field detection of CPMMV, which contribute to controlling the spread of the virus.
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Affiliation(s)
- Xinyang Wu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou 310018, China
| | - Shuting Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zixin Zhang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yihan Zhang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Pingmei Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xinyi Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Miaomiao Liu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Qian Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongyi Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou 310018, China
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Liu Y, Xiang J, Gao Y, Wang J, Liu L, Li R, Wang J. Rapid detection of Cryptosporidium spp. in diarrheic cattle feces by isothermal recombinase polymerase amplification assays. Heliyon 2023; 9:e20794. [PMID: 37860527 PMCID: PMC10582492 DOI: 10.1016/j.heliyon.2023.e20794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 09/10/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
As a zoonotic parasite, Cryptosporidium spp. could cause severe diarrhea mainly in calves and children globally. Monitoring and prevention of Cryptosporidium spp.'s prevalence is of great significance in both economy and public health aspects. In this study, specific primers and probes were designed within the conserved region of 18S rRNA gene for Cryptosporidium spp. and recombinase polymerase amplification assays based on the fluorescence monitoring (real-time RPA) as well as combined with a lateral flow strip (LFS RPA) were developed. Both of the two RPA assays allowed the exponential amplification of the target fragment within 20 min. After incubation on a metal bath at 42 °C, the LFS RPA results were displayed on the lateral flow strip within 5 min while real-time RPA allowed the real-time observation of the results in Genie III at 39 °C. The RPA assays showed high specificity for Cryptosporidium spp. without any cross-reaction with other tested pathogens causing diarrhea in cattle. With the recombinant plasmid DNA containing the 18S rRNA gene of Cryptosporidium spp. serving as a template, the limit of detection for real-time RPA and LFS RPA assays were 14.6 and 12.7 copies/reaction, respectively. Moreover, the RPA assays were validated by testing diarrheic cattle fecal samples and compared with a real-time PCR. The positive ratio of Cryptosporidium spp. was 24.04 % (44/183) and 26.23 % (48/183) in both RPA assays and real-time PCR assay, respectively, and the kappa coefficient value was 0.942. The diagnostic specificity and diagnostic sensitivity of both RPA assays were 100 % and 91.67 %, respectively. Forty-one of 48 positive samples were successfully sequenced and four Cryptosporidium species were detected, including C. parvum (n = 20), C. andersoni (n = 17), C. bovis (n = 3) and C. ryanae (n = 1). The developed RPA assays are easy to operate and faster to obtain the detection results, and they are suiting for the point-of-care detection and facilitating the prevention and control of Cryptosporidium spp. infections.
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Affiliation(s)
- Yuelin Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jialin Xiang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Yaxin Gao
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jinfeng Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Libing Liu
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Ruiwen Li
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jianchang Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
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9
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Ji T, Zhang J, Gao Y, Zhao C, Gao X. A rapid and visual detection of Staphylococcus haemolyticus in clinical specimens with RPA-LFS. Anal Chim Acta 2023; 1273:341534. [PMID: 37423664 DOI: 10.1016/j.aca.2023.341534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/29/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023]
Abstract
Staphylococcus haemolyticus (S. haemolyticus), which is highly prevent in the hospital environment, is an etiological factor for nosocomial infections. Point-of-care rapid testing (POCT) of S. haemolyticus is not possible with the currently used detection methods. Recombinase polymerase amplification (RPA) is a novel isothermal amplification technology with high sensitivity and specificity. The combination of RPA and lateral flow strips (LFS) can achieve rapid pathogen detection, enabling POCT. This study developed an RPA-LFS methodology using a specific probe/primer pair to identify S. haemolyticus. A basic RPA reaction was performed to screen the specific primer from 6 primer pairs targeting mvaA gene. The optimal primer pair was selected based on agarose gel electrophoresis, and the probe was designed. To eliminate false-positive results caused by the byproducts, base mismatches were introduced in the primer/probe pair. The improved primer/probe pair could specifically identify the target sequence. To explore the optimal reaction conditions, the effects of reaction temperature and duration of the RPA-LFS method were systematically investigated. The improved system enabled optimal amplification at 37 °C for 8 min, and the results were visualized within 1 min. The S. haemolyticus detection sensitivity of the RPA-LFS method, whose performance was unaffected by contamination with other genomes, was 0.147 CFU/reaction. Furthermore, we analyzed 95 random clinical samples with RPA-LFS, quantitative polymerase chain reaction (qPCR), and traditional bacterial-culture assays and found that the RPA-LFS had 100% and 98.73% compliance rates with the qPCR and traditional culture method, respectively, which confirms its clinical applicability. In this study, we designed an improved RPA-LFS assay based on the specific probe/primer pair for the detection of S. haemolyticus via rapid POCT, free from the limitations of the precision instruments, helping to make diagnoses and treatment decisions as soon as possible.
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Affiliation(s)
- Tuo Ji
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China; Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China
| | - Junlong Zhang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China; Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China
| | - Yuzhi Gao
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China; Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China
| | - Cheng Zhao
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China; Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China.
| | - Xuzhu Gao
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China; Department of Central Laboratory, The Second People's Hospital of Lianyungang City (Cancer Hospital of Lianyungang), Lianyungang, China; Department of Central Laboratory, Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China.
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10
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Li M, Li T, Hao X, Liu Y, Lan H, Zhou C. Preliminary investigation of hepatitis E virus detection by a recombinase polymerase amplification assay combined with a lateral flow strip. J Vet Diagn Invest 2023; 35:395-398. [PMID: 37029661 PMCID: PMC10331385 DOI: 10.1177/10406387231167119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
Abstract
Hepatitis E virus (HEV) is a zoonotic pathogen that is a significant public health problem. Detecting HEV relies mainly on conventional PCR, which is time-consuming and requires sophisticated instruments and trained staff. We aimed to establish a reverse-transcription (RT)-recombinase polymerase amplification (RPA) assay (RT-RPA) combined with a lateral flow strip (LFS; RT-RPA-LFS) to rapidly detect HEV RNA in human and rabbit samples. With the optimal reaction conditions (37°C for 30 min), our assay detected as few as 1.0 × 102 copies/mL of HEV and showed no cross-reactivity with other hepatitis viruses. We tested 28 human samples (4 fecal and 24 serum samples) and 360 rabbit samples (180 fecal and 180 serum samples) with our RT-RPA-LFS assay and compared our assay to an RT-qPCR method. There was no significant difference (p > 0.05) in the test results between the 2 assays. Our RT-RPA-LFS assay detected both HEV3 and HEV4 genotypes. Our rapid, sensitive, and specific RT-RPA-LFS assay for the detection of HEV may provide a useful detection tool for limited-resource areas.
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Affiliation(s)
- Manyu Li
- Division I of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Tingting Li
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaotian Hao
- Division I of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | | | - Haiyun Lan
- Division I of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Cheng Zhou
- Division I of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
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11
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Mao G, Luo X, Ye S, Wang X, He J, Kong J, Dai J, Yin W, Ma Y. Fluorescence and Colorimetric Analysis of African Swine Fever Virus Based on the RPA-Assisted CRISPR/Cas12a Strategy. Anal Chem 2023; 95:8063-8069. [PMID: 37167072 DOI: 10.1021/acs.analchem.3c01033] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It is well-established that different detection modes are necessary for corresponding applications, which can effectively reduce matrix interference and improve the detection accuracy. Here, we reported a magnetic separation method based on recombinase polymerase amplification (RPA)-assisted clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a for dual-mode analysis of African swine fever virus (ASFV) genes, including colorimetry and fluorescence. The ASFV gene was selected as the initial RPA template to generate the amplicon. The RPA amplicon was then recognized by CRISPR-associated RNA (crRNA), activating the trans-cleavage activity of Cas12a and leading to the nonspecific cleavage of ssDNA as well as a significant release of alkaline phosphatase (ALP) in the ALP-ssDNA modified magnetic bead. The released ALP can catalyze para-nitrophenyl phosphate to generate para-nitrophenol, resulting in substantial changes in absorbance and fluorescence, both of which can be used for detection with the naked eye. This strategy allows the sensitive detection of ASFV DNA, with a 20 copies/mL detection limit; no cross-reactivity with other viruses was observed. A good linear relationship was obtained in serum. In addition, this sensor displayed 100% specificity and sensitivity for clinical sample analysis. This method integrates the high sensitivity of fluorescence with easy readout of colorimetry and enables a simple, low-cost, and highly sensitive dual-mode detection of viral nucleic acid, thereby providing a broad prospect for the practical application in the diagnosis of virus infection.
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Affiliation(s)
- Guobin Mao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Silu Ye
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xun Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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12
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Pan J, Zeng M, Zhao M, Huang L. Research Progress on the detection methods of porcine reproductive and respiratory syndrome virus. Front Microbiol 2023; 14:1097905. [PMID: 36970703 PMCID: PMC10033578 DOI: 10.3389/fmicb.2023.1097905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) causes clinical syndromes typified as reproductive disorders in sows and respiratory diseases in piglets. PRRSV remains one of the most prevalent pathogens affecting the pig industry, because of its complex infection profile and highly heterogeneous genetic and recombination characteristics. Therefore, a rapid and effective PRRSV detection method is important for the prevention and control of PRRS. With extensive in-depth research on PRRSV detection methods, many detection methods have been improved and promoted. Laboratory methods include techniques based on virus isolation (VI), enzyme-linked immunosorbent assays (ELISA), indirect immunofluorescence assays (IFA), immunoperoxidase monolayer assays (IPMA), polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), digital PCR (dPCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), clustered regularly interspaced short palindromic repeats (CRISPR), metagenomic next-generation sequencing (mNGS), and other methods. This study reviews the latest research on improving the main PRRSV detection methods and discusses their advantages and disadvantages.
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Affiliation(s)
- Jinghua Pan
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Mengyi Zeng
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Mengmeng Zhao
- School of Life Science and Engineering, Foshan University, Foshan, China
- Veterinary Teaching Hospital, Foshan University, Foshan, China
- *Correspondence: Mengmeng Zhao,
| | - Liangzong Huang
- School of Life Science and Engineering, Foshan University, Foshan, China
- Veterinary Teaching Hospital, Foshan University, Foshan, China
- Liangzong Huang,
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13
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A Rapid and Sensitive Detection of HIV-1 with a One-Pot Two-Stage Reverse Transcription Recombinase Aided Real-Time PCR Assay. Trop Med Infect Dis 2023; 8:tropicalmed8020105. [PMID: 36828521 PMCID: PMC9960739 DOI: 10.3390/tropicalmed8020105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) attacks the immune system, making people susceptible to various diseases, thus increasing their risk of death. Comprehensive detection of major HIV-1 strains circulating in China is vital for effective HIV-1 infection prevention and treatment. HIV-1 nucleic acid detection is considered effective for HIV-1 diagnosis since traditional immunological testing may fail to detect HIV-1 infection during the window period. This work demonstrates a one-pot two-stage amplification assay (RT-RAP), a combination of reverse transcription recombinase (RT- RAA), and quantitative real-time polymerase chain reaction (qRT-PCR). The turn-around time of the assay is only 50 min and can be performed with commonly available laboratory equipment, the qPCR devices. The RT-RAP assay could detect approximately 5 and 14 copies/reaction of HIV-1 DNA and RNA using recombinant plasmids and standard reference strains, respectively. Additionally, we found that the clinical performance of RT-RAP (detected 169 samples out of 170 specimens) was consistent with that of qRT-PCR. The sensitivity and specificity of RT-RAP were 100.00% (99/99) and 98.59% (70/71), respectively, while its positive and negative predictive values were 99.00% (99/100) and 100.00% (70/70), respectively. The total coincidence rate of the RT-RAP was 99.41% (169/170), with a kappa value of 0.988 (p < 0.05). We demonstrated that RT-RAP could rapidly detect the common HIV-1 subtypes commonly circulating in China with comparable sensitivity and specificity to qRT-PCR.
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14
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Tao J, Liu D, Xiong J, Dou L, Zhai W, Zhang R, Wang Y, Shen J, Wen K. Rapid On-Site Detection of Extensively Drug-Resistant Genes in Enterobacteriaceae via Enhanced Recombinase Polymerase Amplification and Lateral Flow Biosensor. Microbiol Spectr 2022; 10:e0334422. [PMID: 36445091 PMCID: PMC9769758 DOI: 10.1128/spectrum.03344-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
The widespread emergence of transferable extensively drug-resistant (XDR) genes, including blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance, in Enterobacteriaceae poses a major threat to public health. Thus, rapid on-site detection of these XDR genes is urgently needed. We developed a cascade system with a unitary polyethylene glycol (PEG) 200-enhanced recombinase polymerase amplification (RPA) as the core, combined with a modified Chelex-100 lysis method and a horseradish peroxidase (HRP)-catalyzed lateral flow immunoassay (LFIA) biosensor, to accurately detect these genes in Enterobacteriaceae. The conventional Chelex-100 lysis method was modified to allow in situ extraction of bacterial DNA in 20 min without requiring bulky high-speed centrifuges. Using PEG 200 increased the amplification efficiency of the RPA by 13%, and the HRP-catalyzed LFIA biosensor intensified the colorimetric signal of the test line. Following optimization, the sensitivity of the cascade system was <10 copies/μL with satisfactory specificity, allowing for highly sensitive detection of these XDR genes in Enterobacteriaceae. The complete detection procedure can be completed in less than 1 h without using large-scale instruments. This assay is conducive to rapid on-site visual detection of these XDR genes in Enterobacteriaceae in practical applications, thus providing better technical support for clinical surveillance of these genes and better treatment of XDR pathogens. IMPORTANCE Carbapenem, colistin, and tigecycline are considered the last resorts for treating severe bacterial infections caused by extensively drug-resistant (XDR) pathogens. A major threat to public health is the emergence and prevalence of transferable XDR genes in Enterobacteriaceae, such as blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance. Therefore, it is imperative to develop rapid on-site methods to detect these XDR genes. In this study, we constructed a cascade system for detecting these genes based on PEG 200-enhanced recombinase polymerase amplification combined with a modified Chelex-100 lysis method and HRP-catalyzed lateral flow immunoassay. The current method is capable of detecting the above-mentioned XDR genes in situ with satisfactory specificity and sensitivity, which could provide technical support for the surveillance of these genes and provide medication recommendations for the treatment of relevant clinical infections.
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Affiliation(s)
- Jin Tao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Dejun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jincheng Xiong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Leina Dou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Weishuai Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rong Zhang
- Clinical Microbiology Laboratory, 2nd Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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15
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Tharakan S, Faqah O, Asghar W, Ilyas A. Microfluidic Devices for HIV Diagnosis and Monitoring at Point-of-Care (POC) Settings. BIOSENSORS 2022; 12:949. [PMID: 36354458 PMCID: PMC9687700 DOI: 10.3390/bios12110949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Human immunodeficiency virus (HIV) is a global epidemic; however, many individuals are able to obtain treatment and manage their condition. Progression to acquired immunodeficiency syndrome (AIDS) occurs during late-stage HIV infection, which compromises the immune system, making it susceptible to infections. While there is no cure, antiretroviral therapy can be used provided that detection occurs, preferably during the early phase. However, the detection of HIV is expensive and resource-intensive when tested with conventional methods, such as flow cytometry, polymerase chain reaction (PCR), or enzyme-linked immunosorbent assays (ELISA). Improving disease detection in resource-constrained areas requires equipment that is affordable, portable, and can deliver rapid results. Microfluidic devices have transformed many benchtop techniques to on-chip detection for portable and rapid point-of-care (POC) testing. These devices are cost-effective, sensitive, and rapid and can be used in areas lacking resources. Moreover, their functionality can rival their benchtop counterparts, making them efficient for disease detection. In this review, we discuss the limitations of currently used conventional HIV diagnostic assays and provide an overview of potential microfluidic technologies that can improve HIV testing in POC settings.
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Affiliation(s)
- Shebin Tharakan
- Bio-Nanotechnology and Biomaterials (BNB) Lab, New York Institute of Technology, Old Westbury, NY 11568, USA
- Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Omair Faqah
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Waseem Asghar
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Azhar Ilyas
- Bio-Nanotechnology and Biomaterials (BNB) Lab, New York Institute of Technology, Old Westbury, NY 11568, USA
- Department of Electrical and Computer Engineering, New York Institute of Technology, Old Westbury, NY 11568, USA
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16
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Characterizing the Impact of Primer-Template Mismatches on Recombinase Polymerase Amplification. J Mol Diagn 2022; 24:1207-1216. [PMID: 36116701 DOI: 10.1016/j.jmoldx.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/18/2022] [Accepted: 08/16/2022] [Indexed: 01/13/2023] Open
Abstract
Recombinase polymerase amplification (RPA) is an isothermal amplification assay that has been ubiquitously utilized in the detection of infectious agents. Like any nucleic acid amplification technology, primer-template complementarity is critical to RPA reaction success. Mismatches arising in the primer-template complex are known to impact reaction kinetics, invalidate downstream analysis, such as nucleic acid quantification, and result in false negatives if used in a diagnostic capacity. Although the impact of specific primer-template mismatches has been well characterized for techniques such as PCR, characterization remains limited for RPA. Through our study, we systematically characterize the impact of mismatches on the RPA reaction, when located in the 3'-anchor region of the primer-template complex. Our investigation identified that the nucleotides involved, as well as position of each mismatch, influence the size of the impact, with terminal cytosine-thymine and guanine-adenine mismatches being the most detrimental. The presence of some mismatch combinations, such as a penultimate cytosine-cytosine and a terminal cytosine-adenine mismatch pairing, led to complete RPA reaction inhibition. Through the successful characterization of 315 mismatch combinations, researchers can optimize their RPA assay accordingly and seek to implement RPA technology for rapid, in-field genotyping.
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17
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Chia CT, Bender AT, Lillis L, Sullivan BP, Martin CD, Burke W, Landis C, Boyle DS, Posner JD. Rapid detection of hepatitis C virus using recombinase polymerase amplification. PLoS One 2022; 17:e0276582. [PMID: 36282844 PMCID: PMC9595512 DOI: 10.1371/journal.pone.0276582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Over 71 million people are infected with hepatitis C virus (HCV) worldwide, and approximately 400,000 global deaths result from complications of untreated chronic HCV. Pan-genomic direct-acting antivirals (DAAs) have recently become widely available and feature high cure rates in less than 12 weeks of treatment. The rollout of DAAs is reliant on diagnostic tests for HCV RNA to identify eligible patients with viremic HCV infections. Current PCR-based HCV RNA assays are restricted to well-resourced central laboratories, and there remains a prevailing clinical need for expanded access to decentralized HCV RNA testing to provide rapid chronic HCV diagnosis and linkage to DAAs in outpatient clinics. This paper reports a rapid, highly accurate, and minimally instrumented assay for HCV RNA detection using reverse transcription recombinase polymerase amplification (RT-RPA). The assay detects all HCV genotypes with a limit of detection of 25 copies per reaction for genotype 1, the most prevalent in the United States and worldwide. The clinical sensitivity and specificity of the RT-RPA assay were both 100% when evaluated using 78 diverse clinical serum specimens. The accuracy, short runtime, and low heating demands of RT-RPA may enable implementation in a point-of-care HCV test to expand global access to effective treatment via rapid chronic HCV diagnosis.
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Affiliation(s)
- Catherine T. Chia
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Andrew T. Bender
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | | | - Benjamin P. Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Coleman D. Martin
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Wynn Burke
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Charles Landis
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
| | | | - Jonathan D. Posner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
- Family Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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18
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Alsalameh S, Alnajjar K, Makhzoum T, Al Eman N, Shakir I, Mir TA, Alkattan K, Chinnappan R, Yaqinuddin A. Advances in Biosensing Technologies for Diagnosis of COVID-19. BIOSENSORS 2022; 12:898. [PMID: 36291035 PMCID: PMC9599206 DOI: 10.3390/bios12100898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
The COVID-19 pandemic has severely impacted normal human life worldwide. Due to its rapid community spread and high mortality statistics, the development of prompt diagnostic tests for a massive number of samples is essential. Currently used traditional methods are often expensive, time-consuming, laboratory-based, and unable to handle a large number of specimens in resource-limited settings. Because of its high contagiousness, efficient identification of SARS-CoV-2 carriers is crucial. As the advantages of adopting biosensors for efficient diagnosis of COVID-19 increase, this narrative review summarizes the recent advances and the respective reasons to consider applying biosensors. Biosensors are the most sensitive, specific, rapid, user-friendly tools having the potential to deliver point-of-care diagnostics beyond traditional standards. This review provides a brief introduction to conventional methods used for COVID-19 diagnosis and summarizes their advantages and disadvantages. It also discusses the pathogenesis of COVID-19, potential diagnostic biomarkers, and rapid diagnosis using biosensor technology. The current advancements in biosensing technologies, from academic research to commercial achievements, have been emphasized in recent publications. We covered a wide range of topics, including biomarker detection, viral genomes, viral proteins, immune responses to infection, and other potential proinflammatory biomolecules. Major challenges and prospects for future application in point-of-care settings are also highlighted.
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Affiliation(s)
| | - Khalid Alnajjar
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Tariq Makhzoum
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Noor Al Eman
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ismail Shakir
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Tanveer Ahmad Mir
- Laboratory of Tissue/Organ Bioengineering and BioMEMS, Organ Transplant Centre of Excellence, Transplant Research and Innovation Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Raja Chinnappan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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19
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Wang K, Wang J, Zhou C, Sun X, Liu L, Xu X, Wang J. Rapid and direct detection of hepatitis E virus in raw pork livers by recombinase polymerase amplification assays. Front Cell Infect Microbiol 2022; 12:958990. [PMID: 36132988 PMCID: PMC9483107 DOI: 10.3389/fcimb.2022.958990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Hepatitis E virus (HEV) is a zoonotic pathogen that causes global hepatitis E. Outbreaks of hepatitis E are directly linked to the consumption of pork liver products. Herein reverse transcription recombinase polymerase amplification assays targeting the ORF2 gene were developed for the rapid detection of HEV by integrating the fluorescence detection platform (qRT-RPA) and the visible lateral flow biosensor by naked eyes (LFB RT-RPA). The qRT-RPA assay effectively detected HEV RNA with a limit of detection (LOD) of 154 copies/μl (95%CI: 126–333 copies/µl) in Genie III at 41°C for 20 min. Besides this, the LFB RT-RPA detected the HEV RNA with a LOD of 24 copies/μl (95%CI: 20–57 copies/µl) in an incubator block at 41°C for 20 min. The developed RT-RPA assays also showed good specificity for HEV, with no cross-reactions with any of the other important swine pathogens examined in this work. The performance of the developed RT-RPA assays was validated on 14 HEV RNA-positive and 66 HEV RNA-negative raw pork liver samples identified by a previously described qRT-PCR. Consequently, 11 and 12 samples were HEV RNA-positive as detected by the qRT-RPA and the LFB RT-RPA, respectively. Compared to qRT-PCR, the qRT-RPA and LFB RT- RPA assays revealed a coincidence rate of 96.3 and 97.5% as well as a Kappa value of 0.858 and 0.908, respectively. These results ascertain that the developed RT-RPA assays are effective diagnostic tools for the point-of-care detection of HEV in resource-limited settings.
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Affiliation(s)
- Kairui Wang
- School of Public Health, Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, China
| | - Jinfeng Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Cang Zhou
- School of Public Health, Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, China
| | - Xiaoxia Sun
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Libing Liu
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Xiangdong Xu
- School of Public Health, Hebei Medical University, Shijiazhuang, China
- Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, China
- *Correspondence: Xiangdong Xu, ; Jianchang Wang,
| | - Jianchang Wang
- School of Public Health, Hebei Medical University, Shijiazhuang, China
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
- *Correspondence: Xiangdong Xu, ; Jianchang Wang,
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20
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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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21
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Zeng J, Wang W, Zhou L, Ge X, Han J, Guo X, Chen Y, Zhang Y, Yang H. A nucleic acid detection assay combining reverse transcription recombinase-aided amplification with a lateral flow dipstick for the rapid visual detection of porcine deltacoronavirus. Virulence 2022; 13:1471-1485. [PMID: 36005235 PMCID: PMC9450908 DOI: 10.1080/21505594.2022.2116157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen causing severe diarrhoea, dehydration, and death in nursing piglets and enormous economic losses for the global swine industry. Furthermore, it can infect multiple animal species including humans. Therefore, a rapid, definitive diagnostic assay is required for the effective control of this zoonotic pathogen. To identify PDCoV, we developed a nucleic acid detection assay combining reverse transcription recombinase-aided amplification (RT-RAA) with a lateral flow dipstick (LFD) targeting the highly conserved genomic region in the ORF1b gene. The RT-RAA-LFD assay exhibited good PDCoV detection reproducibility and repeatability and could be completed within 11 min. Ten minutes at 40 °C was required for nucleic acid amplification and 1 min at room temperature was needed for the visual LFD readout. The assay specifically detected PDCoV and did not cross-react with any other major swine pathogens. The 95% limit of detection (LOD) was 3.97 median tissue culture infectious dose PDCoV RNA per reaction. This performance was comparable to that of a reference TaqMan-based real-time RT-PCR (trRT-PCR) assay for PDCoV. Of 149 swine small intestine, rectal swab, and serum samples, 71 and 75 tested positive for PDCoV according to RT-RAA-LFD and trRT-PCR, respectively. The diagnostic coincidence rate for both assays was 97.32% (145/149) and the kappa value was 0.946 (p < 0.001). Overall, the RT-RAA-LFD assay is a user-friendly diagnostic tool that can rapidly and visually detect PDCoV.
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Affiliation(s)
- Jianyu Zeng
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
| | - Wenlong Wang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
| | - Yanhong Chen
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing,P.R. China
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22
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Duan L, Yang X, Zhan W, Tang Y, Wei M, Chen K, Liu P, Xie J, Zhang C, Zhao H, Luo M. Development of a rapid and accurate CRISPR/Cas13-based diagnostic test for GII.4 norovirus infection. Front Microbiol 2022; 13:912315. [PMID: 36090107 PMCID: PMC9449452 DOI: 10.3389/fmicb.2022.912315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Genogroup II genotype 4 (GII.4) norovirus causes acute gastroenteritis in children, and its infection is more severe than that of other genotypes. Early and precise detection and treatment are critical for controlling its spread and reducing the severity of infection. In this study, a rapid and efficient isothermal assay for the GII.4 norovirus detection (GII.4-CRISPR detection) was developed based on the CRISPR/Cas13a system. The assay can be applied without expensive instrumentation, and the results can be read via both fluorescence and lateral flow strip (LFS). The analytical sensitivity of this assay was 5 copies/reaction, and there was no cross-reaction with other genotypes of norovirus or other clinically common pathogens. There was a coincidence rate of 100% between our assay and commercial quantitative polymerase chain reaction. GII.4-CRISPR detection improves upon the shortcomings of some previously established molecular methods of detection, particularly with regard to accessibility. It provides an alternative tool for outbreak control and early diagnosis of GII.4 norovirus infection.
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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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24
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Qu G, Li Y, Zhao Z, Miao L, Wei F, Tang N, Xu Q, Nair V, Yao Y, Shen Z. Establishment and Application of a Real-Time Recombinase Polymerase Amplification Assay for the Detection of Avian Leukosis Virus Subgroup J. Front Vet Sci 2022; 9:847194. [PMID: 35873679 PMCID: PMC9301284 DOI: 10.3389/fvets.2022.847194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Avian leukosis caused by avian leukosis virus (ALV), belonging to the genus Alpharetrovirus of the family Retroviridae, is associated with benign and malignant tumors in hemopoietic cells in poultry. Although several methods have been developed for ALV detection, most of them are not suitable for rapid on-site testing due to instrument limitations, professional operators, or the low sensitivity of the method. Herein, we described the real-time recombinase polymerase amplification (RPA) assay for rapid detection of ALV subgroup J (ALV-J). The major viral structural glycoprotein gp85, highly specific for the subgroup, was used as the molecular target for the real-time RPA assay. The results were obtained at 38°C within 20 min, with the detection sensitivity of 10 copies/μl of standard plasmid pMD18-T-gp85 as the template per reaction. Real-time RPA was capable of ALV-J-specific detection without cross-reaction with other non-targeted avian pathogens. Of the 62 clinical samples tested, the ALV-positive rates of real-time RPA, PCR, and real-time PCR were 66.13% (41/62), 59.68% (37/62), and 67.74% (42/62), respectively. The diagnostic agreement between real-time RPA and real-time PCR was 98.39% (61/62), and the kappa value was 0.9636. The developed real-time ALV-J assay seems promising for rapid and sensitive detection of ALV-J in diagnostic laboratories. It is suitable for on-site detection, especially in a poor resource environment, thus facilitating the prevention and control of ALV-J.
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Affiliation(s)
- Guanggang Qu
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- *Correspondence: Guanggang Qu
| | - Yun Li
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Zhongwei Zhao
- Shandong Lvdu Biotechnology Co., Ltd, Binzhou, China
| | - Lizhong Miao
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Feng Wei
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Na Tang
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Qingqing Xu
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Guildford, United Kingdom
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Guildford, United Kingdom
- Yongxiu Yao
| | - Zhiqiang Shen
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- Shandong Lvdu Biotechnology Co., Ltd, Binzhou, China
- Zhiqiang Shen
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25
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Pewlaoo S, Phanthong S, Kong-Ngoen T, Santajit S, Tunyong W, Buranasinsup S, Kaeoket K, Thavorasak T, Pumirat P, Sookrung N, Chaicumpa W, Indrawattana N. Development of a Rapid Reverse Transcription-Recombinase Polymerase Amplification Couple Nucleic Acid Lateral Flow Method for Detecting Porcine Epidemic Diarrhoea Virus. BIOLOGY 2022; 11:biology11071018. [PMID: 36101399 PMCID: PMC9312133 DOI: 10.3390/biology11071018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Porcine epidemic diarrhea virus infection is an important acute diarrheal disease of swine especially in infected piglets can caused severe diarrhea, dehydration with difficulty in digesting milk curd, leading to death. The diagnosis of this viral infection is essential for monitoring and managing the disease. There is surprisingly little evidence such as easy rapid detection in the field. In this study, we developed rapid the reverse transcription-recombinase polymerase amplification couple nucleic acid lateral flow for Porcine epidemic diarrhea virus detection targeted the membrane gene in the genome sequence of the virus. Herein, the results shown that the established assay is simple and rapid, increases high sensitivity and specificity, and can be applied in the field. Abstract Porcine epidemic diarrhea virus (PEDV) infection is an important acute diarrheal disease of swine that results in economic and industrial losses worldwide. The clinical manifestations in infected piglets are severe diarrhea, dehydration with milk curd indigestion, leading to death. The diagnosis of PEDV is essential for monitoring and managing the disease. PEDV can be detected and identified by serology and the nucleic acid of the virus in clinical samples. Therefore, a novel isothermal amplification and detection technique, reverse transcription-recombinase polymerase amplification couple nucleic acid lateral flow (RT-RPA-NALF) was developed for the rapid detection of PEDV. Qualitative reverse transcription-polymerase chain reaction (RT-qPCR) was established as the gold standard assay to compare results. Specific primer pairs and probes were designed, and RT-RPA conditions were optimized to amplify the M gene of PEDV. The established RT-RPA-NALF assay could finish in 25 min at a temperature of 42 °C and the amplicon interpreted by visual detection. The developed RT-RPA-NALF assay was specific to the M gene of PEDV, did not detect other common swine diarrhea pathogens, and showed minimal detection at 102 TCID50/mL PEDV. The RT-RPA-NALF assay can detect PEDV in 5 simulated fecal samples. Furthermore, in 60 clinical fecal samples, the results of RT-RPA-NALF correlated with RT-qPCR assay, which provides sensitivity of 95.65% and specificity of 100%, with a coincident rate of 98.33%. The rapid RT-RPA-NALF is simple and rapid, increases high sensitivity, and can be used in the field.
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Affiliation(s)
- Seatthanan Pewlaoo
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
| | - Siratcha Phanthong
- Siriraj Center of Research Excellence in Allergy and Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.P.); (N.S.)
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.T.); (W.C.)
| | - Thida Kong-Ngoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
| | - Sirijan Santajit
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand;
- Research Center in Tropical Pathobiology, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Witawat Tunyong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
| | - Shutipen Buranasinsup
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Kampon Kaeoket
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Techit Thavorasak
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.T.); (W.C.)
| | - Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
| | - Nitat Sookrung
- Siriraj Center of Research Excellence in Allergy and Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.P.); (N.S.)
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.T.); (W.C.)
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
- Correspondence: ; Tel.: +66-2-354-9100 (ext. 1598)
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26
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Sullivan BP, Chou YS, Bender AT, Martin CD, Kaputa ZG, March H, Song M, Posner JD. Quantitative isothermal amplification on paper membranes using amplification nucleation site analysis. LAB ON A CHIP 2022; 22:2352-2363. [PMID: 35548880 PMCID: PMC9202034 DOI: 10.1039/d2lc00007e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and viral RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.
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Affiliation(s)
- Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Yu-Shan Chou
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Coleman D Martin
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Zoe G Kaputa
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Hugh March
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Minyung Song
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
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27
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Mota DS, Guimarães JM, Gandarilla AMD, Filho JCBS, Brito WR, Mariúba LAM. Recombinase polymerase amplification in the molecular diagnosis of microbiological targets and its applications. Can J Microbiol 2022; 68:383-402. [PMID: 35394399 DOI: 10.1139/cjm-2021-0329] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the introduction of the polymerase chain reaction (PCR) technique in 1983, nucleic acid amplification has permeated all fields of biological science, particularly clinical research. Despite its importance, PCR has been restricted to specialized centers and its use in laboratories with few resources is limited. In recent decades, there has been a notable increase in the development of new isothermal technologies for molecular diagnosis with the hope of overcoming the traditional limitations of the laboratory. Among these technologies, recombinase polymerase amplification (RPA) has a wide application potential because it does not require thermocyclers and has high sensitivity, specificity, simplicity, and detection speed. This technique has been used for DNA and RNA amplification in various pathogenic organisms such as viruses, bacteria, and parasites. In addition, RPA has been successfully implemented in different detection strategies, making it a promising alternative for performing diagnoses in environments with scarce resources and a high burden of infectious diseases. In this study, we present a review of the use of RPA in clinical settings and its implementation in various research areas.
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Affiliation(s)
- D S Mota
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J M Guimarães
- Centro Multiusuário para Análises de Fenômenos Biomédicos, Universidade do Estado do Amazonas (UEA), Manaus, AM, 69065-00, Brazil
| | - A M D Gandarilla
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J C B S Filho
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - W R Brito
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - L A M Mariúba
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
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28
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Zhang JY, Zhang Y, Bender AT, Sullivan BP, Olanrewaju AO, Lillis L, Boyle D, Drain PK, Posner JD. HIV pre-exposure prophylaxis adherence test using reverse transcription isothermal amplification inhibition assay. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1361-1370. [PMID: 35297917 PMCID: PMC8991996 DOI: 10.1039/d2ay00008c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Current HIV antiretroviral therapy (ART) or pre-exposure prophylaxis (PrEP) therapy adherence monitoring relies on either patient self-reported adherence or monitored drug dispensing, which are not reliable. We report a proof-of-concept adherence monitoring assay which directly measures nucleotide reverse transcriptase inhibitor (NRTI) concentration using a reverse transcription isothermal amplification inhibition assay. We measure the concentration of Tenofovir diphosphate (TFV-DP) - an NRTI that functions as a deoxyadenosine triphosphate (dATP) analog and long-term adherence marker for PrEP - by measuring the inhibition of the reverse transcription of an RNA template. The completion or inhibition of reverse transcription is evaluated by recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification assay commonly used for point-of-care diagnostics. We present and validate a model that predicts the amplification probability as a function of dATP and TFV-DP concentrations, nucleotide insertion sites on the RNA template, and RNA template concentration. The model can be used to rationally design and optimize the assay to operate at clinically relevant TFV-DP concentrations. We provide statistical analysis that demonstrates how the assay may be used as a qualitative or semi-quantitative tool for measuring adherence to NRTI drugs and used to support patient compliance. Due to its simple instrumentation and short runtime (<1 hour), this assay has the potential for implementation in low-complexity laboratories or point-of-care settings, which may improve access to ART and PrEP adherence monitoring.
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Affiliation(s)
- Jane Y Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
| | - Yu Zhang
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
| | | | | | | | - Paul K Drain
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
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29
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Weidmann M, Graf E, Lichterfeld D, Abd El Wahed A, Bekaert M. Efficient Screening of Long Oligonucleotides Against Hundred Thousands of SARS-CoV-2 Genome Sequences. FRONTIERS IN VIROLOGY 2022; 2. [DOI: 10.3389/fviro.2022.835707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
An unprecedented use of high-throughput sequencing for routine monitoring of SARS-CoV-2 viruses in patient samples has created a dataset of over 6 million SARS-CoV-2 genomes. To monitor genomes, deposited in the GISAID database, and to track the continuous sequence evolution of molecular assay oligonucleotide target sequences. A simple pipeline tool for non-experts was developed to mine this database for nucleotide changes in oligonucleotides and tested with the long oligonucleotides of a Recombinase polymerase amplification (RPA) assay targeting the RNA-dependent RNA polymerase (RdRP) gene of the SARS-CoV-2. Results indicate the emergence of a single nucleotide change in the reverse oligonucleotide from 0.03 to 26.23% (January to May 2021) in Alpha variant genomes, which however reduced to 17.64% by September after which the Alpha variant was completely displaced by the Delta variant. For all other variants, no relevant nucleotide changes were observed. The oligonucleotide screening pipeline allows efficient screening of nucleotide changes in oligonucleotides of all sizes in minutes.
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30
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Development and Application of Recombinase Polymerase Amplification Assays for Rapid Detection of Escherichia coli O157 in Food. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02250-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Palmieri D, Javorina A, Siddiqui J, Gardner A, Fries A, Chapleau RR, Starr C, Fishel R, Miles WO. Mass COVID-19 patient screening using UvsX and UvsY mediated DNA recombination and high throughput parallel sequencing. Sci Rep 2022; 12:4082. [PMID: 35260723 PMCID: PMC8902726 DOI: 10.1038/s41598-022-08034-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 03/01/2022] [Indexed: 01/08/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV), is a highly infectious RNA virus. A percentage of patients develop coronavirus disease 2019 (COVID-19) after infection, whose symptoms include fever, cough, shortness of breath and fatigue. Acute and life-threatening respiratory symptoms are experienced by 10-20% of symptomatic patients, particularly those with underlying medical conditions. One of the main challenges in the containment of COVID-19 is the identification and isolation of asymptomatic/pre-symptomatic individuals. A number of molecular assays are currently used to detect SARS-CoV-2. Many of them can accurately test hundreds or even thousands of patients every day. However, there are presently no testing platforms that enable more than 10,000 tests per day. Here, we describe the foundation for the REcombinase Mediated BaRcoding and AmplificatioN Diagnostic Tool (REMBRANDT), a high-throughput Next Generation Sequencing-based approach for the simultaneous screening of over 100,000 samples per day. The REMBRANDT protocol includes direct two-barcoded amplification of SARS-CoV-2 and control amplicons using an isothermal reaction, and the downstream library preparation for Illumina sequencing and bioinformatics analysis. This protocol represents a potentially powerful approach for community screening of COVID-19 that may be modified for application to any infectious or non-infectious genome.
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Affiliation(s)
- Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Amanda Javorina
- Public Health and Preventive Medicine Department, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Jalal Siddiqui
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Anne Gardner
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Anthony Fries
- Public Health and Preventive Medicine Department, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Richard R Chapleau
- Public Health and Preventive Medicine Department, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Clarise Starr
- Public Health and Preventive Medicine Department, US Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, OH, 45433, USA
| | - Richard Fishel
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Wayne O Miles
- Department of Cancer Biology and Genetics, College of Medicine and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
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Mayran C, Foulongne V, Van de Perre P, Fournier-Wirth C, Molès JP, Cantaloube JF. Rapid Diagnostic Test for Hepatitis B Virus Viral Load Based on Recombinase Polymerase Amplification Combined with a Lateral Flow Read-Out. Diagnostics (Basel) 2022; 12:diagnostics12030621. [PMID: 35328174 PMCID: PMC8946908 DOI: 10.3390/diagnostics12030621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 01/27/2023] Open
Abstract
Hepatitis B (HBV) infection is a major public health concern. Perinatal transmission of HBV from mother to child represents the main mode of transmission. Despite the existence of effective immunoprophylaxis, the preventive strategy is inefficient in neonates born to mothers with HBV viral loads above 2 × 105 IU/mL. To prevent mother-to-child transmission, it is important to identify highly viremic pregnant women and initiate antiviral therapy to decrease their viral load. We developed a simple innovative molecular approach avoiding the use of automatic devices to screen highly viremic pregnant women. This method includes rapid DNA extraction coupled with an isothermal recombinase polymerase amplification (RPA) combined with direct visual detection on a lateral flow assay (LFA). We applied our RPA-LFA approach to HBV DNA-positive plasma samples with various loads and genotypes. We designed a triage test by adapting the analytical sensitivity to the recommended therapeutic decision threshold of 2 × 105 IU/mL. The sensitivity and specificity were 98.6% (95% CI: 92.7−99.9%) and 88.2% (95% CI: 73.4−95.3%), respectively. This assay performed excellently, with an area under the ROC curve value of 0.99 (95% CI: 0.99−1.00, p < 0.001). This simple method will open new perspectives in the development of point-of-care testing to prevent HBV perinatal transmission.
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Hsieh K, Melendez JH, Gaydos CA, Wang TH. Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections. LAB ON A CHIP 2022; 22:476-511. [PMID: 35048928 PMCID: PMC9035340 DOI: 10.1039/d1lc00665g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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Hull IT, Kline EC, Gulati GK, Kotnik JH, Panpradist N, Shah KG, Wang Q, Frenkel L, Lai J, Stekler J, Lutz BR. Isothermal Amplification with a Target-Mimicking Internal Control and Quantitative Lateral Flow Readout for Rapid HIV Viral Load Testing in Low-Resource Settings. Anal Chem 2022; 94:1011-1021. [PMID: 34920665 PMCID: PMC9219584 DOI: 10.1021/acs.analchem.1c03960] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Point-of-care diagnostics often use isothermal nucleic acid amplification for qualitative detection of pathogens in low-resource healthcare settings but lack sufficient precision for quantitative applications such as HIV viral load monitoring. Although viral load (VL) monitoring is an essential component of HIV treatment, commercially available tests rely on relatively high-resource chemistries like real-time polymerase chain reaction and are thus used on an infrequent basis for millions of people living with HIV in low-income countries. To address the constraints of low-resource settings on nucleic acid quantification, we describe a recombinase polymerase amplification and lateral flow detection approach that quantifies HIV-1 DNA or RNA by comparison to a competitive internal amplification control (IAC) of a known copy number, which may be set to any useful threshold (in our case, a clinically relevant threshold for HIV treatment failure). The IAC is designed to amplify alongside the HIV target with a similar efficiency, allowing for normalization of the assay to variation or inhibition and enabling an endpoint readout that is compatible with commercially available kits for nucleic acid lateral flow detection and interpretable with minimal instrumentation or by the naked eye. We find that this approach can reliably differentiate ≤600 or ≥1400 copies of HIV DNA from a 1000-copy threshold when lateral flow strips are imaged with a conventional office scanner and analyzed with free densitometry software. We further demonstrate a user-friendly adaptation of this analysis to process cell phone photographs with an automated script. Alternatively, we show via a survey that 21 minimally trained volunteers could reliably resolve ≥10-fold (log10) differences of HIV DNA or RNA by naked eye interpretation of lateral flow results. This amplification and detection workflow requires minimal instrumentation, takes just 30 min to complete, and when combined with a suitable sample preparation method, may enable HIV VL testing while the patient waits or a self-test, which has the potential to improve care. This approach may be adapted for other applications that require quantitative analysis of a nucleic acid target in low-resource settings.
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Affiliation(s)
- Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
| | - Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
| | - Gaurav K. Gulati
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
| | - Jack Henry Kotnik
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
| | - Kamal G. Shah
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
| | - Lisa Frenkel
- Department of Pediatrics, University of Washington, Seattle, WA 98195-9300, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195-7470, USA
- Department of Global Health, University of Washington, Seattle, WA 98195-1620, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98145-5005, USA
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
| | - Joanne Stekler
- Department of Medicine, University of Washington, Seattle, WA 98195-6420, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA
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35
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Sullivan BP, Chou YS, Bender AT, Martin CD, Kaputa ZG, March H, Song M, Posner JD. Quantitative Isothermal Amplification on Paper Membranes using Amplification Nucleation Site Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.11.475898. [PMID: 35043115 PMCID: PMC8764744 DOI: 10.1101/2022.01.11.475898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3,000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.
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36
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Cassedy A, Della Bartola M, Parle-McDermott A, Mullins E, O'Kennedy R. A one-step reverse transcription recombinase polymerase amplification assay for lateral flow-based visual detection of PVY. Anal Biochem 2021; 642:114526. [PMID: 34922917 DOI: 10.1016/j.ab.2021.114526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 12/12/2022]
Abstract
Potato virus Y (PVY) is an abundant and damaging virus which reduces crop yield and marketability. Accurate detection of this economically important virus both in-field and in seed potato is considered essential in the control of PVY spread. Current detection methods are focused on immunodetection and PCR-based methods, however, identification of PVY through isothermal amplification is a promising avenue for developing accessible, on-site diagnostics with quick turnaround times. In this work, a rapid recombinase polymerase amplification assay was developed which could readily amplify PVY nucleic acids with good sensitivity and specificity. Additionally, this assay was shown to be capable of amplification directly from RNA in a one-step amplification process, without the need for prior reverse transcription. The assay was coupled with lateral flow technology to provide a rapid visual confirmation of amplification. This nucleic-acid lateral flow immunoassay could feasibly be employed in-field, or at any location where testing is required, to aid in the detection and control of PVY.
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Affiliation(s)
- Arabelle Cassedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | | | | | - Ewen Mullins
- Crop Science Department, Teagasc, Oak Park, Carlow, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland; Hamad Bin Khalifa University, Education City, Doha, Qatar; Qatar Foundation, Education City, Doha, Qatar.
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37
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Wang XF, Chen WQ, Guo JL, Peng C, Chen XY, Xu XL, Wei W, Yang L, Ca J, Xu JF. A Fast, Visual, and Instrument-free Platform Involving Rapid DNA Extraction, Chemical Heating, and Recombinase Aided Amplification for On-Site Nucleic Acid Detection. Front Bioeng Biotechnol 2021; 9:764306. [PMID: 34881235 PMCID: PMC8645684 DOI: 10.3389/fbioe.2021.764306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/04/2021] [Indexed: 11/25/2022] Open
Abstract
The nucleic acid-based technique has been widely utilized in many fields including for on-site detection. However, traditional molecular detection techniques encounter limitations like relying on instruments, time consuming or complex operation, and cannot meet the demands of on-site testing. In this study, a rapid DNA extraction method (RDEM), recombinase aided amplification (RAA), and chemical heating packet (CHP) are integrated and termed as RRC platform for on-site detection of nucleic acid. For demonstration purposes, SHZD32-1 (a new transgenic soybean line from China) was detected using the novel platform to demonstrate its feasibility and capability for on-site detection. Using the RDEM, high-quality DNA appropriate for molecular detection was quickly extracted in 3–5 min. The heat energy generated by CHP was met the temperature requirements of RAA. Using the RRC platform, the whole detection process can be accomplished within only 30 min, and the results can be visually detected with glasses under blue light. No special or expensive instrument was needed for the detection process. This study provides a novel approach for on-site detection of nucleic acids besides providing valuable insight on related future research.
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Affiliation(s)
- Xiao Fu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
| | - Wen Qiang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,College of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Jian Li Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
| | - Xiao Yun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
| | - Xiao Li Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Ca
- College of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Jun Feng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, China
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38
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Lateral flow assays (LFA) as an alternative medical diagnosis method for detection of virus species: The intertwine of nanotechnology with sensing strategies. Trends Analyt Chem 2021; 145:116460. [PMID: 34697511 PMCID: PMC8529554 DOI: 10.1016/j.trac.2021.116460] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Viruses are responsible for multiple infections in humans that impose huge health burdens on individuals and populations worldwide. Therefore, numerous diagnostic methods and strategies have been developed for prevention, management, and decreasing the burden of viral diseases, each having its advantages and limitations. Viral infections are commonly detected using serological and nucleic acid-based methods. However, these conventional and clinical approaches have some limitations that can be resolved by implementing other detector devices. Therefore, the search for sensitive, selective, portable, and costless approaches as efficient alternative clinical methods for point of care testing (POCT) analysis has gained much attention in recent years. POCT is one of the ultimate goals in virus detection, and thus, the tests need to be rapid, specific, sensitive, accessible, and user-friendly. In this review, after a brief overview of viruses and their characteristics, the conventional viral detection methods, the clinical approaches, and their advantages and shortcomings are firstly explained. Then, LFA systems working principles, benefits, classification are discussed. Furthermore, the studies regarding designing and employing LFAs in diagnosing different types of viruses, especially SARS-CoV-2 as a main concern worldwide and innovations in the LFAs' approaches and designs, are comprehensively discussed here. Furthermore, several strategies addressed in some studies for overcoming LFA limitations like low sensitivity are reviewed. Numerous techniques are adopted to increase sensitivity and perform quantitative detection. Employing several visualization methods, using different labeling reporters, integrating LFAs with other detection methods to benefit from both LFA and the integrated detection device advantages, and designing unique membranes to increase reagent reactivity, are some of the approaches that are highlighted.
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39
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112424. [PMID: 34834787 PMCID: PMC8621059 DOI: 10.3390/plants10112424] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 05/27/2023]
Abstract
Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.
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40
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Dronina J, Samukaite-Bubniene U, Ramanavicius A. Advances and insights in the diagnosis of viral infections. J Nanobiotechnology 2021; 19:348. [PMID: 34717656 PMCID: PMC8556785 DOI: 10.1186/s12951-021-01081-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.
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Affiliation(s)
- Julija Dronina
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Arunas Ramanavicius
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania.
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41
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Li H, Feng J, Wang Y, Liu G, Chen X, Fu L. Instant and Multiple DNA Extraction Method by Microneedle Patch for Rapid and on-Site Detection of Food Allergen-Encoding Genes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6879-6887. [PMID: 34105975 DOI: 10.1021/acs.jafc.1c01077] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA-based detection methods are highly promising for risk assessment in the food sector, such as tracing the existence of food allergens. However, due to the complexity of food matrices, cumbersome protocols are often needed to isolate the DNA components, which hinder the achievement of rapid and on-site detection. Herein, an instant and multiple DNA extraction method was developed based on the poly(vinyl alcohol) microneedle (MN) patch. With simple press and peel-off operations within 1 min, samples suitable for DNA-based analysis such as polymerase chain reaction (PCR) could be collected. By further combining with the recombinase polymerase amplification assay, rapid screening of the allergenic risks in complex samples such as shrimp ball and cheesecake could be achieved within 30 min. The MN-based DNA extraction method not only was a potential alternative to the traditional DNA extraction method but provided a transformative approach in realizing rapid, on-site detection of foodborne hazards in collaborating with fast DNA-based assays.
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Affiliation(s)
- Huan Li
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Jiesi Feng
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Yanbo Wang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Guangming Liu
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen 361021, P. R. China
| | - Xiaojing Chen
- College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Linglin Fu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
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42
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Qu Y, Wang Q, Li Y, Wang Y, Yin J, Ren Y, Liu C, Liu X, Wang Y, Zeng W. Development of a real-time recombinase polymerase amplification assay for rapid detection of Aeromonas hydrophila. JOURNAL OF FISH DISEASES 2021; 44:469-477. [PMID: 33152130 DOI: 10.1111/jfd.13291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
Aeromonas hydrophila is ubiquitous in the aquaculture industry and a constant cause of severe disease and economic losses. The early diagnosis of these infections is crucial for disease surveillance and prevention. We developed a real-time recombinase polymerase amplification (real-time RPA) assay for detection of A. hydrophila using the haemolysin gene. The assay was performed at 37°C for 20 min and was highly specific with no cross-reaction with other fish pathogens or with other Aeromonas species. The assay detection limit was 102 copies of the Aeromonas hydrophila per reaction. Compared with traditional culture-based method or real-time PCR, the diagnostic sensitivity and specificity of the real-time RPA were 73.7 and 100%, as well as 64.7 and 93%. Our newly developed real-time RPA was specific and sensitive and can be used in large-scale and point-of-care field investigations of A. hydrophila infections to enable earlier diagnoses.
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Affiliation(s)
- Yang Qu
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qing Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yingying Li
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yingying Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiyuan Yin
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yan Ren
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chun Liu
- Innovative Institute of Animal Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiaofang Liu
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yahui Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Weiwei Zeng
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
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Evaluation of a real-time recombinase polymerase amplification assay for rapid detection of Schistosoma haematobium infection in resource-limited setting. Acta Trop 2021; 216:105847. [PMID: 33497617 DOI: 10.1016/j.actatropica.2021.105847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/27/2022]
Abstract
Accurate diagnosis of urogenital schistosomiasis is vital for surveillance/control programs as well as achieving the WHO 2012-2020 road map for the total eradication of schistosomiasis. Recombinase polymerase amplification (RPA) has emerged as a rapid and simple molecular tool adaptable for fewer resources with diagnostic accuracy similar to polymerase chain reaction (PCR). This rapid molecular assay employs the use of enzymes for the amplification of nucleic acid taget at a constant temperature. The aim of this study was to validate a real-time RPA assay targeting the Dra 1 repittitive sequence of Schistosoma (S.) haematobium and evaluate its use in urogenital schistosomiasis diagnosis. S. haematobium Dra 1 molecular DNA standard was applied to determine the assay's analytical sensitivity. DNA extracts of S. haematobium, other Schistosoma species, protozoa and bacteria species were used to determine the specificity of the RPA assay. Clinical performance of the assay was validated with a panel of 135 urine samples from volunteers of schistosomiasis endemic communities. The developed assay was evaluated with urine samples extracted by just boiling and with SpeedXtract® DNA extraction kit. A specific fragment of S. haematobium Dra 1 repetitive sequence was amplified within 15 minutes at a constant 42˚C using the developed S. haematobium RPA assay. The detection limit was 15 copies of Dra1 molecular DNA standard per reaction. There was no cross-reaction with other protozoan and bacterial species except Schistosoma species, S. mansoni and S. japonicum. Using 135 urine samples, Schistosoma RPA assay had a clinical sensitivity and specificity of 98.4% (95% CI, 91.6-100) and 100% (95% CI, 94.9-99) respectively when compared to S. haematobium Dra 1 qPCR assay. The diagnostic performance of S. haematobium real-time RPA assay was not affected by the use of crude DNA extracted samples. The S. haematobium RPA assay can serve as an alternative to PCR, especially in low resource settings.
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Zhang L, Peng J, Chen J, Xu L, Zhang Y, Li Y, Zhao J, Xiang L, Ge Y, Cheng W. Highly Sensitive Detection of Low-Abundance BRAF V600E Mutation in Fine-Needle Aspiration Samples by Zip Recombinase Polymerase Amplification. Anal Chem 2021; 93:5621-5628. [PMID: 33764743 DOI: 10.1021/acs.analchem.1c00405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Papillary thyroid carcinoma (PTC) is the most common thyroid cancer with high incidence in endocrine tumors, which emphasizes the significance of accurate diagnostics. Still, the commonly used cytological method (fine-needle aspiration (FNA) cytology) and molecular diagnostic methods (such as PCR and sequencing) are limited in terms of diagnostic time, sensitivity, and user-friendliness. In this study, we introduce a novel Zip recombinase polymerase amplification (Z-RPA) strategy to efficiently detect rare mutant alleles in PTC fine-needle aspiration samples, which is sensitive, fast, and simple to manipulate. Using Zip nucleic acid (ZNA) probes to clamp the mutation region, the phi 29 polymerase could selectively displace mismatched ZNA probes and start amplification, while leaving complementary ZNA probes untouched and blocking amplification according to genotype. We demonstrated the good sensitivity and specificity of this strategy with optimized conditions and design, which enabled detection of BRAF V600E mutation in a total 4 ng of genomic DNA within 40 min (≈1 copy). Robust behavior in clinical specimen analysis was also demonstrated. The Z-RPA strategy provides a pragmatic approach to rapidly, sensitively, and easily detect BRAF V600E mutation in clinical fine-needle aspiration samples, which is a promising method for early cancer diagnosis and treatment guideline.
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Affiliation(s)
- Lutan Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China.,United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen 361000, P. R. China
| | - Jian Peng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Lulu Xu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Yangli Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Ying Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Jie Zhao
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Linguo Xiang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Yunsheng Ge
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen 361000, P. R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
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Gaitho D, Kinoti F, Mwaniki L, Kemunto D, Ogoti V, Njigua C, Kubo E, Langat A, Mecha J. Factors associated with the timely uptake of initial HIV virologic test among HIV-exposed infants attending clinics within a faith-based HIV program in Kenya; a cross-sectional study. BMC Public Health 2021; 21:569. [PMID: 33757463 PMCID: PMC7986293 DOI: 10.1186/s12889-021-10587-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 03/08/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Early infant diagnosis (EID) of HIV, followed by effective care including antiretroviral therapy (ART), reduces infant mortality by 76% and HIV progression by 75%. In 2015, 50% of 1.2 million HIV-exposed infants (HEI) in 21 priority countries received a virologic test within the recommended 2 months of birth. We sought to identify factors associated with timely uptake of virologic EID among HEI and gain insight into missed opportunities. METHODS This was a cross-sectional study that used de-identified data from electronic medical records of 54 health facilities within the Christian Health Association of Kenya (CHAK) HIV Project database. All HEI who had their first HIV virologic test done between January 2015 and December 2017 were included in the study and categorized as either having the test within or after 8 weeks of birth. Multivariate linear mixed effects regression model was used to determine factors associated with uptake of the first HIV EID polymerase chain reaction (PCR). Predictor variables studied include sex, birth weight, the entry point into care, provision of ART prophylaxis for the infant, maternal ART at time of EID, mode of delivery, and place of delivery. RESULTS We included 2020 HEI of whom 1018 (50.4%) were female. A majority, 1596 (79.0%) had their first HIV PCR within 2 months of birth at a median age of 6.4 weeks (interquartile range 6-7.4). Overall, HIV positivity rate at initial test among this cohort was 1.2%. Delayed HIV PCR testing for EID was more likely to yield a positive result [adjusted odds ratio (aOR) = 1.29 (95% confidence interval (CI) 1.09-1.52) p = 0.003]. Infants of mothers not on ART at the time of HIV PCR test and infants who had not received prophylaxis to prevent vertical HIV transmission had significant increased odds of a delayed initial test [aOR = 1.27 (95% CI = 1.18-1.37) p = < 0.0001] and [aOR = 1.43 (95% CI 1.27-1.61) p = < 0.001] respectively. CONCLUSION An initial HIV PCR test done after 8 weeks of birth is likely to yield a positive result. Barriers to accessing ART for treatment among HIV-infected pregnant and breastfeeding women, and prophylaxis for the HEI were associated with delayed EID. In order to ensure timely EID, programs need to incorporate both facility and community strategy interventions to ensure all pregnant women seek antenatal care and deliver within health facilities.
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Affiliation(s)
- Douglas Gaitho
- Christian Health Association of Kenya (CHAK), P.O. Box 30690 – 00100, GPO, Nairobi, Kenya
| | - Freda Kinoti
- Department of Clinical Medicine & Therapeutics, University of Nairobi, P.O. Box 19676 – 00202, Nairobi, Kenya
| | - Lawrence Mwaniki
- Christian Health Association of Kenya (CHAK), P.O. Box 30690 – 00100, GPO, Nairobi, Kenya
| | - Diana Kemunto
- Christian Health Association of Kenya (CHAK), P.O. Box 30690 – 00100, GPO, Nairobi, Kenya
| | - Victor Ogoti
- Christian Health Association of Kenya (CHAK), P.O. Box 30690 – 00100, GPO, Nairobi, Kenya
| | - Catherine Njigua
- Christian Health Association of Kenya (CHAK), P.O. Box 30690 – 00100, GPO, Nairobi, Kenya
| | - Elizabeth Kubo
- Christian Health Association of Kenya (CHAK), P.O. Box 30690 – 00100, GPO, Nairobi, Kenya
| | - Agnes Langat
- Division of Global HIV and TB, Centers for Disease Control and Prevention Kenya, P.O. Box 606 – 00621, Village Market, Nairobi, Kenya
| | - Jared Mecha
- Department of Clinical medicine & Therapeutics, College of Health Sciences – University of Nairobi, P.O. Box 19676 – 00202, Nairobi, Kenya
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Huang P, Jin H, Zhao Y, Li E, Yan F, Chi H, Wang Q, Han Q, Mo R, Song Y, Bi J, Jiao C, Li W, He H, Wang H, Ma A, Feng N, Wang J, Wang T, Yang S, Gao Y, Xia X, Wang H. Nucleic acid visualization assay for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) by targeting the UpE and N gene. PLoS Negl Trop Dis 2021; 15:e0009227. [PMID: 33647020 PMCID: PMC7951983 DOI: 10.1371/journal.pntd.0009227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 03/11/2021] [Accepted: 02/11/2021] [Indexed: 12/26/2022] Open
Abstract
Since its first emergence in 2012, cases of infection with Middle East respiratory syndrome coronavirus (MERS-CoV) have continued to occur. At the end of January 2020, 2519 laboratory confirmed cases with a case-fatality rate of 34.3% have been reported. Approximately 84% of human cases have been reported in the tropical region of Saudi Arabia. The emergence of MERS-CoV has highlighted need for a rapid and accurate assay to triage patients with a suspected infection in a timely manner because of the lack of an approved vaccine or an effective treatment for MERS-CoV to prevent and control potential outbreaks. In this study, we present two rapid and visual nucleic acid assays that target the MERS-CoV UpE and N genes as a panel that combines reverse transcription recombinase polymerase amplification with a closed vertical flow visualization strip (RT-RPA-VF). This test panel was designed to improve the diagnostic accuracy through dual-target screening after referencing laboratory testing guidance for MERS-CoV. The limit of detection was 1.2×101 copies/μl viral RNA for the UpE assay and 1.2 copies/μl viral RNA for the N assay, with almost consistent with the sensitivity of the RT-qPCR assays. The two assays exhibited no cross-reactivity with multiple CoVs, including the bat severe acute respiratory syndrome related coronavirus (SARSr-CoV), the bat coronavirus HKU4, and the human coronaviruses 229E, OC43, HKU1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, the panel does not require sophisticated equipment and provides rapid detection within 30 min. This panel displays good sensitivity and specificity and may be useful to rapidly detect MERS-CoV early during an outbreak and for disease surveillance.
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Affiliation(s)
- Pei Huang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hongli Jin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Entao Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hang Chi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Qi Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Qiuxue Han
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruo Mo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Yumeng Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jinhao Bi
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Cuicui Jiao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wujian Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongbin He
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hongmei Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Aimin Ma
- Changchun Medical College, Changchun, China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jianzhong Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hualei Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
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47
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Kumar Y. Isothermal amplification-based methods for assessment of microbiological safety and authenticity of meat and meat products. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107679] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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48
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Zhao L, Wang J, Sun XX, Wang J, Chen Z, Xu X, Dong M, Guo YN, Wang Y, Chen P, Gao W, Geng Y. Development and Evaluation of the Rapid and Sensitive RPA Assays for Specific Detection of Salmonella spp. in Food Samples. Front Cell Infect Microbiol 2021; 11:631921. [PMID: 33718280 PMCID: PMC7946851 DOI: 10.3389/fcimb.2021.631921] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella spp. is among the main foodborne pathogens which cause serious foodborne diseases. An isothermal real-time recombinase polymerase amplification (RPA) and lateral flow strip detection (LFS RPA) were used to detect Salmonella spp. targeting the conserved sequence of invasion protein A (invA). The Real-time RPA was performed in a portable florescence scanner at 39°C for 20 min. The LFS RPA was performed in an incubator block at 39°C for 15 min, under the same condition that the amplifications could be inspected by the naked eyes on the LFS within 5 min. The detection limit of Salmonella spp. DNA using real-time RPA was 1.1 × 101 fg, which was the same with real-time PCR but 10 times higher than that of LFS RPA assay. Moreover, the practicality of discovering Salmonella spp. was validated with artificially contaminated lamb, chicken, and broccoli samples. The analyzing time dropped from 60 min to proximately 5–12 min on the basis of the real-time and LFS RPA assays compared with the real-time PCR assay. Real-time and LFS RPA assays’ results were equally reliable. There was no cross-reactivity with other pathogens in both assays. In addition, the assays had good stability. All of these helped to show that the developed RPA assays were simple, rapid, sensitive, credible, and could be a potential point-of-need (PON) test required mere resources.
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Affiliation(s)
- Liwei Zhao
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Jianchang Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Xiao Xia Sun
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Jinfeng Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Zhimin Chen
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Xiangdong Xu
- School of Public Health, Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, China
| | - Mengyuan Dong
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Ya-Nan Guo
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yuanyuan Wang
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Pingping Chen
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Weijuan Gao
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yunyun Geng
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
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Xie J, Yang X, Duan L, Chen K, Liu P, Zhan W, Zhang C, Zhao H, Wei M, Tang Y, Luo M. One-Step Reverse-Transcription Recombinase Polymerase Amplification Using Lateral Flow Strips for the Detection of Coxsackievirus A6. Front Microbiol 2021; 12:629533. [PMID: 33613499 PMCID: PMC7889601 DOI: 10.3389/fmicb.2021.629533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
Hand, foot, and mouth disease (HFMD) is a common infectious disease affecting mainly children under 5 years of age. Coxsackievirus A6 (CVA-6), a major causative pathogen of HFMD, has caused outbreaks in recent years. Currently, no effective vaccine or antiviral treatments are available. In this study, one-step reverse-transcription recombinase polymerase amplification (RT-RPA), combined with a disposable lateral flow strip (LFS) assay, was developed to detect CVA-6. This assay can be performed in less than 35 min at 37°C without expensive instruments, and the result can be observed directly with the naked eye. The sensitivity of the RT-RPA-LFS was 10 copies per reaction, which was comparable to that of the conventional real-time quantitative polymerase chain reaction (qPCR) assays. Moreover, the assay specificity was 100%. The clinical performance of the RT-RPA-LFS assay was evaluated using 142 clinical samples, and the coincidence rate between RT-RPA-LFS and qPCR was 100%. Therefore, our RT-RPA-LFS assay provides a simple and rapid approach for point-of-care CVA-6 diagnosis.
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Affiliation(s)
- Jia Xie
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaohan Yang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lei Duan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Keyi Chen
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Pan Liu
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wenli Zhan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Changbin Zhang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hongyu Zhao
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Mengru Wei
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yuan Tang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Mingyong Luo
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
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50
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Li G, Wu M, Li J, Cai W, Xie Y, Si G, Xiao L, Cong F, He D. Rapid detection of porcine deltacoronavirus and porcine epidemic diarrhea virus using the duplex recombinase polymerase amplification method. J Virol Methods 2021; 292:114096. [PMID: 33600848 DOI: 10.1016/j.jviromet.2021.114096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/04/2021] [Accepted: 02/01/2021] [Indexed: 01/07/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) have emerged and spread throughout the porcine industry in many countries and are economically important pathogens causing diarrhea in sows and acute death in newborn piglets. Therefore, a sensitive diagnostic method would be beneficial for the prevention and control of PEDV and PDCoV infection. However, traditional detection methods have a number of drawbacks. This research aimed to establish a rapid detection method of duplex recombinant enzyme-mediated thermostatic amplification (RT-RPA) for PEDV and PDCoV. In this study, eight pairs of primers were designed for each virus according to the conserved domains of both PEDV and PDCoV from the NCBI Genbank, and one pair of primers was selected for each virus following the test results. After optimization of the reaction time, reaction temperature and primer concentration ratio, the duplex RT-RPA assay amplified a 226-bp fragment specifically for PEDV and a 321-bp fragment specifically for PDCoV. Meanwhile, the specificity and sensitivity of the primers and clinical samples were tested to verify the establishment of the RT-RPA method. The sensitivities of the duplex RT-RPA method for PEDV and PDCoV were 1 × 102 copies/μL. The results were consistent with PCR results and showed that a detection method for PEDV and PDCoV duplex RT-RPA was successfully established. In summary, the duplex recombinase polymerase amplification method could offer a promising alternative to the duplex RT-qPCR for detection of PEDV and PDCoV.
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Affiliation(s)
- Gen Li
- College of Veterinary Medicine of South China Agricultural University, Guangzhou, 510640, China
| | - Miaoli Wu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong, Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Jinhui Li
- College of Veterinary Medicine of South China Agricultural University, Guangzhou, 510640, China
| | - Weiyou Cai
- College of Veterinary Medicine of South China Agricultural University, Guangzhou, 510640, China
| | - Yongsheng Xie
- College of Veterinary Medicine of South China Agricultural University, Guangzhou, 510640, China
| | - Guangbing Si
- College of Veterinary Medicine of South China Agricultural University, Guangzhou, 510640, China
| | - Li Xiao
- Guangdong Laboratory Animals Monitoring Institute and Guangdong, Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Feng Cong
- Guangdong Laboratory Animals Monitoring Institute and Guangdong, Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Dongsheng He
- College of Veterinary Medicine of South China Agricultural University, Guangzhou, 510640, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, 510640, China; Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, Guangzhou, 510640, China.
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