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Lane D, Allsopp R, Holmes CW, Slingsby OC, Jukes-Jones R, Bird P, Anderson NL, Razavi M, Yip R, Pearson TW, Pope M, Khunti K, Doykov I, Hällqvist J, Mills K, Skipp P, Carling R, Ng L, Shaw J, Gupta P, Jones DJL. A high throughput immuno-affinity mass spectrometry method for detection and quantitation of SARS-CoV-2 nucleoprotein in human saliva and its comparison with RT-PCR, RT-LAMP, and lateral flow rapid antigen test. Clin Chem Lab Med 2024; 62:1206-1216. [PMID: 38253336 DOI: 10.1515/cclm-2023-0243] [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: 03/06/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
OBJECTIVES Many reverse transcription polymerase chain reaction (RT-PCR) methods exist that can detect SARS-CoV-2 RNA in different matrices. RT-PCR is highly sensitive, although viral RNA may be detected long after active infection has taken place. SARS-CoV-2 proteins have shorter detection windows hence their detection might be more meaningful. Given salivary droplets represent a main source of transmission, we explored the detection of viral RNA and protein using four different detection platforms including SISCAPA peptide immunoaffinity liquid chromatography-mass spectrometry (SISCAPA-LC-MS) using polyclonal capture antibodies. METHODS The SISCAPA-LC MS method was compared to RT-PCR, RT-loop-mediated isothermal amplification (RT-LAMP), and a lateral flow rapid antigen test (RAT) for the detection of virus material in the drool saliva of 102 patients hospitalised after infection with SARS-CoV-2. Cycle thresholds (Ct) of RT-PCR (E gene) were compared to RT-LAMP time-to-positive (TTP) (NE and Orf1a genes), RAT optical densitometry measurements (test line/control line ratio) and to SISCAPA-LC-MS for measurements of viral protein. RESULTS SISCAPA-LC-MS showed low sensitivity (37.7 %) but high specificity (89.8 %). RAT showed lower sensitivity (24.5 %) and high specificity (100 %). RT-LAMP had high sensitivity (83.0 %) and specificity (100.0 %). At high initial viral RNA loads (<20 Ct), results obtained using SISCAPA-LC-MS correlated with RT-PCR (R2 0.57, p-value 0.002). CONCLUSIONS Detection of SARS-CoV-2 nucleoprotein in saliva was less frequent than the detection of viral RNA. The SISCAPA-LC-MS method allowed processing of multiple samples in <150 min and was scalable, enabling high throughput.
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Affiliation(s)
- Dan Lane
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Rebecca Allsopp
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Christopher W Holmes
- Clinical Microbiology, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | - Rebekah Jukes-Jones
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
| | - Paul Bird
- Clinical Microbiology, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | | | - Richard Yip
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | | | - Matt Pope
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Kamlesh Khunti
- Leicester Diabetes Centre, Leicester General Hospital, University of Leicester, Leicester, UK
| | - Ivan Doykov
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Jenny Hällqvist
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Paul Skipp
- Centre for Proteomic Research, University of Southampton, Southampton, UK
| | - Rachel Carling
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
- GKT School Medical Education, Kings College London, London, UK
| | - Leong Ng
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Jacqui Shaw
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Pankaj Gupta
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Donald J L Jones
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
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Xu Z, Ma X, Wang X, Zhang R, Zhang T, Ma M, Shi F, Chen C. Rapid and sensitive visual detection of avian leukosis virus by reverse transcription loop-mediated isothermal amplification combined with a lateral flow immunochromatographic strip assay. Arch Virol 2024; 169:94. [PMID: 38594417 DOI: 10.1007/s00705-024-05977-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/15/2023] [Indexed: 04/11/2024]
Abstract
Considering that avian leukosis virus (ALV) infection has inflicted massive economic losses on the poultry breeding industry in most countries, its early diagnosis remains an important measure for timely treatment and control of the disease, for which a rapid and sensitive point-of-care test is required. We established a user-friendly, economical, and rapid visualization method for ALV amplification products based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) combined with an immunochromatographic strip in a lateral flow device (LFD). Using the ALVp27 gene as the target, five RT-LAMP primers and one fluorescein-isothiocyanate-labeled probe were designed. After 60 min of RT-LAMP amplification at 64 °C, the products could be visualized directly using the LFD. The detection limit of this assay for ALV detection was 102 RNA copies/μL, and the sensitivity was 100 times that of reverse transcription polymerase chain reaction (RT-PCR), showing high specificity and sensitivity. To verify the clinical practicality of this assay for detecting ALV, the gold standard RT-PCR method was used for comparison, and consistent results were obtained with both assays. Thus, the assay described here can be used for rapid detection of ALV in resource-limited environments.
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Affiliation(s)
- Zhihua Xu
- College of Life Science, Shihezi University, Shihezi, 832003, China
| | - Xiaoyu Ma
- College of Life Science, Shihezi University, Shihezi, 832003, China
| | - Xuejing Wang
- College of Life Science, Shihezi University, Shihezi, 832003, China
| | - Renyin Zhang
- College of Life Science, Shihezi University, Shihezi, 832003, China
| | - Tieying Zhang
- College of Life Science, Shihezi University, Shihezi, 832003, China
| | - Mingze Ma
- College of Life Science, Shihezi University, Shihezi, 832003, China
| | - Feng Shi
- College of Life Science, Shihezi University, Shihezi, 832003, China.
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, Xinjiang, China.
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3
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Atta S, Zhao Y, Li JQ, Vo-Dinh T. Dual-Modal Colorimetric and Surface-Enhanced Raman Scattering (SERS)-Based Lateral Flow Immunoassay for Ultrasensitive Detection of SARS-CoV-2 Using a Plasmonic Gold Nanocrown. Anal Chem 2024; 96:4783-4790. [PMID: 38471066 DOI: 10.1021/acs.analchem.3c04361] [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: 03/14/2024]
Abstract
The 2019 coronavirus disease (COVID-19) outbreak created an unprecedented need for rapid, sensitive, and cost-effective point-of-care diagnostic tests to prevent and mitigate the spread of the SARS-CoV-2 virus. Herein, we demonstrated an advanced lateral flow immunoassay (LFIA) platform with dual-functional [colorimetric and surface-enhanced Raman scattering (SERS)] detection of the spike 1 (S1) protein of SARS-CoV-2. The nanosensor was integrated with a specially designed core-gap-shell morphology consisting of a gold shell decorated with external nanospheres, a structure referred to as gold nanocrown (GNC), labeled with a Raman reporter molecule 1,3,3,1',3',3'-hexamethyl-2,2'-indotricarbocyanine iodide (HITC) to produce a strong colorimetric signal as well as an enhanced SERS signal. Among the different plasmonics-active GNC nanostructures, the GNC-2 morphology, which has a shell decorated with an optimum number and size of nanospheres, produces an intense dark-blue colorimetric signal and ultrahigh SERS signal. The limit of detection (LOD) of the S1 protein via colorimetric detection LFIA was determined to be 91.24 pg/mL. On the other hand, the LOD for the SERS LFIA method was more than three orders of magnitude lower at 57.21 fg/mL. Furthermore, we analyzed the performance of the GNC-2 nanosensor for directly analyzing the S1 protein spiked in saliva samples without any sample pretreatment and achieving the LOD as low as 39.65 fg/mL using SERS-based plasmonics-enhanced LFIA, indicating ultrahigh detection sensitivity. Overall, our GNC nanosensor showed excellent sensitivity, reproducibility, and rapid detection of the SARS-CoV-2 S1 protein, demonstrating excellent potential as a promising point-of-care platform for the early detection of respiratory virus infections.
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Affiliation(s)
- Supriya Atta
- Fitzpatrick Institute for Photonics, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Yuanhao Zhao
- Fitzpatrick Institute for Photonics, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Joy Qiaoyi Li
- Fitzpatrick Institute for Photonics, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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Ganesh PS, Elugoke SE, Lee SH, Kim SY, Ebenso EE. Smart and emerging point of care electrochemical sensors based on nanomaterials for SARS-CoV-2 virus detection: Towards designing a future rapid diagnostic tool. CHEMOSPHERE 2024; 352:141269. [PMID: 38307334 DOI: 10.1016/j.chemosphere.2024.141269] [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: 11/20/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
In the recent years, researchers from all over the world have become interested in the fabrication of advanced and innovative electrochemical and/or biosensors for respiratory virus detection with the use of nanotechnology. These fabricated sensors demonstrated a number of benefits, including precision, affordability, accessibility, and miniaturization which makes them a promising test method for point-of-care (PoC) screening for SARS-CoV-2 viral infection. In order to comprehend the principles of electrochemical sensing and the role of various types of sensing interfaces, we comprehensively explored the underlying principles of electroanalytical methods and terminologies related to it in this review. In addition, it is addressed how to fabricate electrochemical sensing devices incorporating nanomaterials as graphene, metal/metal oxides, metal organic frameworks (MOFs), MXenes, quantum dots, and polymers. We took an effort to carefully compile current developments, advantages, drawbacks, possible solutions in nanomaterials based electrochemical sensors.
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Affiliation(s)
- Pattan Siddappa Ganesh
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Saheed Eluwale Elugoke
- Centre for Material Science, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa; Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa
| | - Seok-Han Lee
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Eno E Ebenso
- Centre for Material Science, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa; Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa.
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5
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El-Daly MM. Advances and Challenges in SARS-CoV-2 Detection: A Review of Molecular and Serological Technologies. Diagnostics (Basel) 2024; 14:519. [PMID: 38472991 DOI: 10.3390/diagnostics14050519] [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: 01/05/2024] [Revised: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The urgent need for accurate COVID-19 diagnostics has led to the development of various SARS-CoV-2 detection technologies. Real-time reverse transcriptase polymerase chain reaction (RT-qPCR) remains a reliable viral gene detection technique, while other molecular methods, including nucleic acid amplification techniques (NAATs) and isothermal amplification techniques, provide diverse and effective approaches. Serological assays, detecting antibodies in response to viral infection, are crucial for disease surveillance. Saliva-based immunoassays show promise for surveillance purposes. The efficiency of SARS-CoV-2 antibody detection varies, with IgM indicating recent exposure and IgG offering prolonged detectability. Various rapid tests, including lateral-flow immunoassays, present opportunities for quick diagnosis, but their clinical significance requires validation through further studies. Challenges include variations in specificity and sensitivity among testing platforms and evolving assay sensitivities over time. SARS-CoV-2 antigens, particularly the N and S proteins, play a crucial role in diagnostic methods. Innovative approaches, such as nanozyme-based assays and specific nucleotide aptamers, offer enhanced sensitivity and flexibility. In conclusion, ongoing advancements in SARS-CoV-2 detection methods contribute to the global effort in combating the COVID-19 pandemic.
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Affiliation(s)
- Mai M El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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6
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Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.
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Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
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7
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Momenifar N, Pirouzfar M, Hashemian Z, Daneshvar Amoli A. Development of an optimized RT-LAMP test for the detection of SARS-CoV-2. Biologicals 2023; 84:101716. [PMID: 37801803 DOI: 10.1016/j.biologicals.2023.101716] [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] [Received: 09/10/2022] [Revised: 06/17/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
SARS-COV-2 is the causative agent of an acute respiratory syndrome called Coronavirus disease 2019 (COVID-19) with a varying mortality rate from 2019 to 2022. There are several measures for control and prevention of Covid-19 including using mask, vaccine injections, as well as screening the potential cases. We aimed to design and develop a molecular method (RT-LAMP) for detecting coronavirus in biological samples that is cheaper, faster and easier than conventional molecular methods. In this study, various reaction components were explored to make the optimal combination of an RT-LAMP master mix composition. The results revealed the ability of this RT-LAMP test in specifically identifying 100 copies of mixture of N and E genes in just 30-45 min. This study demonstrated the reliable performance of the RT-LAMP method for the detection of SARS-COV-2 in biological samples. Given the significant advantages of this method compared to the gold standard qRT-PCR, it can be employed as a promising tool for the diagnosis of coronavirus as well as other pathogenic viruses.
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Affiliation(s)
- Navid Momenifar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Mohammad Pirouzfar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Zohreh Hashemian
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
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8
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Chan AHY, Ngu SF, Lau LSK, Tsun OKL, Ngan HYS, Cheung ANY, Chan KKL. Evaluation of an Isothermal Amplification HPV Assay on Self-Collected Vaginal Samples as Compared to Clinician-Collected Cervical Samples. Diagnostics (Basel) 2023; 13:3297. [PMID: 37958193 PMCID: PMC10647996 DOI: 10.3390/diagnostics13213297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/14/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
This study aimed to evaluate the concordance of HPV results between the SentisTM HPV assay (Sentis) (BGI Group, Shenzhen, China), an isothermal amplification-based HPV assay, on self-collected and clinician-collected samples and the agreement of Sentis on self-collected samples with the BD OnclarityTM HPV assay (Onclarity) (Becton, Dickinson, and Company, Franklin Lakes, New Jersey, USA), a PCR-based HPV assay, on clinician-collected samples. This was a prospective study of 104 women attending the colposcopy clinic for abnormal smears. After informed consent, participants self-collected vaginal samples before having clinician-collected cervical samples. Self-collected samples underwent HPV testing with Sentis (Self-Sentis HPV) and clinician-collected samples were tested with Sentis (Clinician-Sentis HPV) and Onclarity (Clinician-Onclarity), which was used as a reference standard. The concordance was assessed using Cohen's kappa. The prevalence of HPV and the acceptability of self-sampling were also evaluated. The concordance rate between Self-Sentis HPV and Clinician-Sentis HPV was 89.8% with a kappa of 0.769. The concordance rate between Self-Sentis HPV and Clinician-Onclarity was 84.4% with a kappa of 0.643. The prevalence of HPV was 26.0% on Clinician-Onclarity, 29.3% on Clinician-Sentis HPV, and 35.6% on Self-Sentis HPV. Overall, 65% of participants would undergo self-sampling again. This was attributed to mainly not feeling embarrassed (68%) and being convenient (58%). Our study showed a substantial agreement between Self-Sentis HPV with Clinician-Sentis HPV and Clinician-Onclarity. Self-sampling was also shown to be a generally well-accepted method of screening.
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Affiliation(s)
- Aaron H. Y. Chan
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong; (A.H.Y.C.); (L.S.K.L.); (H.Y.S.N.); (K.K.L.C.)
| | - Siew-Fei Ngu
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong; (A.H.Y.C.); (L.S.K.L.); (H.Y.S.N.); (K.K.L.C.)
| | - Lesley S. K. Lau
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong; (A.H.Y.C.); (L.S.K.L.); (H.Y.S.N.); (K.K.L.C.)
| | - Obe K. L. Tsun
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong; (O.K.L.T.); (A.N.Y.C.)
| | - Hextan Y. S. Ngan
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong; (A.H.Y.C.); (L.S.K.L.); (H.Y.S.N.); (K.K.L.C.)
| | - Annie N. Y. Cheung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong; (O.K.L.T.); (A.N.Y.C.)
| | - Karen K. L. Chan
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong; (A.H.Y.C.); (L.S.K.L.); (H.Y.S.N.); (K.K.L.C.)
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Seder I, Coronel-Tellez R, Helalat SH, Sun Y. Fully integrated sample-in-answer-out platform for viral detection using digital reverse transcription recombinase polymerase amplification (dRT-RPA). Biosens Bioelectron 2023; 237:115487. [PMID: 37352758 DOI: 10.1016/j.bios.2023.115487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023]
Abstract
Recombinase polymerase amplification (RPA) is one of the most promising diagnostic methods for pathogen detection, owing to the simplified isothermal amplification technique. Using one-step digital reverse transcription RPA (dRT-RPA) to detect viral RNA provides a fast diagnosis and absolute quantification. Here, we present a chip that purifies, digitalizes, and detects viral RNA of SARS-CoV-2 in a fully automated and sensitive manner. The chip purifies the RNA using the surface charge concept of magnet bead-RNA binding, then mixes the RNA with the amplification reagents, digitalizes the amplification mixture, and performs dRT-RPA. RNA-bead complex is transported among purification buffers that are separated by an oil phase. For reagent manipulation and mixing, a magnetic valve system is integrated on the chip, where an external magnet controls the reagent direction and time of addition. Besides, a novel vacuum system is suggested to drive and regulate the reagents into two fluid systems simultaneously in ∼2 min. We also developed a cost-effective way to perform fluorescent detection for dRT-RPA on chip by using EvaGreen® dye. With integrated heating and optical detection system, the on-chip dRT-RPA presents a sample-to-answer detection platform for absolute viral RNA quantitation in 37 min and a sensitivity as low as 10 RNA copies/μL. Hence, this platform is expected to be a useful tool for accurate and automated diagnosis of infectious diseases.
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Affiliation(s)
- Islam Seder
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800, Kgs. Lyngby, Denmark
| | - Rodrigo Coronel-Tellez
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800, Kgs. Lyngby, Denmark
| | - Seyed Hossein Helalat
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800, Kgs. Lyngby, Denmark
| | - Yi Sun
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800, Kgs. Lyngby, Denmark.
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10
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Laman A, Das D, Priye A. Miniaturized Non-Contact Heating and Transmitted Light Imaging Using an Inexpensive and Modular 3D-Printed Platform for Molecular Diagnostics. SENSORS (BASEL, SWITZERLAND) 2023; 23:7718. [PMID: 37765775 PMCID: PMC10535971 DOI: 10.3390/s23187718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
The ability to simultaneously heat and image samples using transmitted light is crucial for several biological applications. However, existing techniques such as heated stage microscopes, thermal cyclers equipped with imaging capabilities, or non-contact heating systems are often bulky, expensive, and complex. This work presents the development and characterization of a Miniaturized Optically-clear Thermal Enclosure (MOTE) system-an open-source, inexpensive, and low-powered modular system-capable of convectively heating samples while simultaneously imaging them with transmitted light. We develop and validate a computational fluid dynamics (CFD) model to design and optimize the heating chamber. The model simulates velocity and temperature profiles within the heating chamber for various chamber materials and sizes. The computational model yielded an optimal chamber dimension capable of achieving a stable temperature ranging from ambient to 95 °C with a spatial discrepancy of less than 1.5 °C, utilizing less than 8.5 W of power. The dual-functionality of the MOTE system, enabling synchronous heating and transmitted light imaging, was demonstrated through the successful execution of paper-based LAMP reactions to detect λ DNA samples in real-time down to 10 copies/µL of the target concentration. The MOTE system offers a promising and flexible platform for various applications, from molecular diagnostics to biochemical analyses, cell biology, genomics, and education.
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Affiliation(s)
- Alex Laman
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH 45221, USA;
| | - Debayan Das
- Chemical Engineering Department, NIT Durgapur, Mahatma Gandhi Rd., A-Zone, Durgapur 713209, West Bengal, India;
| | - Aashish Priye
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH 45221, USA;
- Digital Futures, University of Cincinnati, Cincinnati, OH 45221, USA
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Yadav SK, Verma D, Yadav U, Kalkal A, Priyadarshini N, Kumar A, Mahato K. Point-of-Care Devices for Viral Detection: COVID-19 Pandemic and Beyond. MICROMACHINES 2023; 14:1744. [PMID: 37763907 PMCID: PMC10535693 DOI: 10.3390/mi14091744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
The pandemic of COVID-19 and its widespread transmission have made us realize the importance of early, quick diagnostic tests for facilitating effective cure and management. The primary obstacles encountered were accurately distinguishing COVID-19 from other illnesses including the flu, common cold, etc. While the polymerase chain reaction technique is a robust technique for the determination of SARS-CoV-2 in patients of COVID-19, there arises a high demand for affordable, quick, user-friendly, and precise point-of-care (POC) diagnostic in therapeutic settings. The necessity for available tests with rapid outcomes spurred the advancement of POC tests that are characterized by speed, automation, and high precision and accuracy. Paper-based POC devices have gained increasing interest in recent years because of rapid, low-cost detection without requiring external instruments. At present, microfluidic paper-based analysis devices have garnered public attention and accelerated the development of such POCT for efficient multistep assays. In the current review, our focus will be on the fabrication of detection modules for SARS-CoV-2. Here, we have included a discussion on various strategies for the detection of viral moieties. The compilation of these strategies would offer comprehensive insight into the detection of the causative agent preparedness for future pandemics. We also provide a descriptive outline for paper-based diagnostic platforms, involving the determination mechanisms, as well as a commercial kit for COVID-19 as well as their outlook.
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Affiliation(s)
- Sumit K. Yadav
- Department of Biotechnology, Vinoba Bhave University, Hazaribagh 825301, Jharkhand, India
| | - Damini Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ujala Yadav
- Department of Life Sciences, Central University of Jharkhand, Ranchi 835205, Jharkhand, India
| | - Ashish Kalkal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Nivedita Priyadarshini
- Department of Zoology, DAV PG College Siwan, Jai Prakash University, Chhapra 841226, Bihar, India
| | - Ashutosh Kumar
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46637, USA
| | - Kuldeep Mahato
- Department of Nanoengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, San Diego, CA 92093, USA
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12
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Khanthaphixay B, Wu L, Yoon JY. Microparticle-Based Detection of Viruses. BIOSENSORS 2023; 13:820. [PMID: 37622906 PMCID: PMC10452130 DOI: 10.3390/bios13080820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
Surveillance of viral pathogens in both point-of-care and clinical settings is imperative to preventing the widespread propagation of disease-undetected viral outbreaks can pose dire health risks on a large scale. Thus, portable, accessible, and reliable biosensors are necessary for proactive measures. Polymeric microparticles have recently gained popularity for their size, surface area, and versatility, which make them ideal biosensing tools. This review cataloged recent investigations on polymeric microparticle-based detection platforms across eight virus families. These microparticles were used as labels for detection (often with fluorescent microparticles) and for capturing viruses for isolation or purification (often with magnetic microparticles). We also categorized all methods by the characteristics, materials, conjugated receptors, and size of microparticles. Current approaches were compared, addressing strengths and weaknesses in the context of virus detection. In-depth analyses were conducted for each virus family, categorizing whether the polymeric microparticles were used as labels, for capturing, or both. We also summarized the types of receptors conjugated to polymeric microparticles for each virus family.
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Affiliation(s)
| | | | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 75721, USA; (B.K.); (L.W.)
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13
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Wang Y, Fu L, Tao D, Han X, Xu B, Deng M, Li S, Zhao C, Li X, Zhao S, Gong P, Yang Y, Khazalwa EM, Ma Y, Ruan J, Li C, Xie S. Development of a Naked Eye CRISPR-Cas12a and -Cas13a Multiplex Point-of-Care Detection of Genetically Modified Swine. ACS Synth Biol 2023; 12:2051-2060. [PMID: 37432138 DOI: 10.1021/acssynbio.3c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The Rapid Visual CRISPR (RAVI-CRISPR) assay employs Cas12a and Cas13a enzymes for precise gene detection in a sample. However, RAVI-CRISPR is limited in single-tube multiplex detection applications due to the lack of specific single-strand (ss) DNA-fluorescently quenched (ssDNA-FQ) and RNA-fluorescently quenched (ssRNA-FQ) reporter cleavage mechanisms. We report the development of a sensitive and specific dual-gene Cas12a and Cas13a diagnostic system. To optimize the application for field testing, we designed a portable multiplex fluorescence imaging assay that could distinguish test results with the naked eye. Herein, dual gene amplified products from multiplex recombinase polymerase amplification (RPA) were simultaneously detected in a single tube using Cas12a and Cas13a enzymes. The resulting orthogonal DNA and RNA collateral cleavage specifically distinguishes individual and mixed ssDNA-FQ and ssRNA-FQ reporters using the green-red-yellow, fluorescent signal conversion reaction system, detectable with portable blue and ultraviolet (UV) light transilluminators. As a proof-of-concept, reliable multiplex RAVI-CRISPR detection of genome-edited pigs was demonstrated, exhibiting 100% sensitivity and specificity for the analysis of CD163 knockout, lactoferrin (LF) knock-in, and wild-type pig samples. This portable naked-eye multiplex RAVI-CRISPR detection platform can provide accurate point-of-care screening of genetically modified animals and infectious diseases in resource-limited settings.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Lanting Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Dagang Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xiaosong Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Manfei Deng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Sheng Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Changzhi Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Ping Gong
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan 430208, P. R. China
| | - Yu Yang
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan 430208, P. R. China
| | | | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Jinxue Ruan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China
- Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, P. R. China
- Key Laboratory of Prevention and Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Wuhan 430070, P. R. China
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14
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Fu Q, Pang X, Su Z, Yang Y, Liu Y, Zhang Z, Fu Y, Wang J, Zhou J. Rapid On-Site Detection of SARS-CoV-2 Using RT-LAMP Assay with a Portable Low-Cost Device. BIOSENSORS 2023; 13:724. [PMID: 37504122 PMCID: PMC10377351 DOI: 10.3390/bios13070724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/29/2023]
Abstract
Emerging infectious diseases pose a serious threat to human health and affect social stability. In recent years, the epidemic situation of emerging infectious diseases is very serious; among these infectious diseases, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected many countries and regions in a short time. The prevention and treatment of these diseases require rapid on-site detection methods. However, the common detection method, RT-PCR, requires expensive instruments, complex operations, and professional operators. Here, we developed a portable low-cost assay for rapid on-site detection of viral nucleic acid using reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The SARS-CoV-2 RNA can be successfully amplified within 15 min in a thermos, and the detection result is read rapidly in a portable low-cost device with a sensitivity of 100 copies/µL. The portable low-cost device consists of a black box, a laser or LED and a filter, costing only a few cents. The rapid on-site detection method can provide strong support for the control of biological threats such as infectious diseases. It is also an emergency detection method for low-resource settings, relieving the huge pressure on health care.
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Affiliation(s)
- Quanying Fu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Xueyuan Pang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenning Su
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuxiao Yang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yiren Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Ziyue Zhang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yuqiu Fu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Jiasi Wang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianhua Zhou
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
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15
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García-Sorribes S, Lara-Hernández F, Manzano-Blasco I, Abadía-Otero J, Albert E, Mulet A, Briongos-Figuero LS, Gabella-Martín M, Torres I, Signes-Costa J, Navarro D, Martín-Escudero JC, García-García AB, Chaves FJ. Sample Treatment with Trypsin for RT-LAMP COVID-19 Diagnosis. BIOLOGY 2023; 12:900. [PMID: 37508333 PMCID: PMC10376771 DOI: 10.3390/biology12070900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023]
Abstract
The SARS-CoV-2 coronavirus is responsible for the COVID-19 pandemic resulting in a global health emergency. Given its rapid spread and high number of infected individuals, a diagnostic tool for a rapid, simple, and cost-effective detection was essential. In this work, we developed a COVID-19 diagnostic test, that incorporates a human internal control, based on the Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). When working with synthetic SARS-CoV-2 RNA, the optimized RT-LAMP assay has a sensitivity of 10 viral copies and can be detected by fluorescence in less than 15 min or by the naked eye in 25 min using colorimetric RT-LAMP. To avoid the RNA extraction step, a pre-treatment of the sample was optimized. Subsequently, a validation was performed on 268 trypsin treated samples (including nasopharyngeal, buccal, and nasal exudates) and amplified with colorimetric RT-LAMP to evaluate its sensitivity and specificity in comparison with RT-qPCR of extracted samples. The validation results showed a sensitivity and specificity of 100% for samples with Ct ≤ 30. The rapid, simple, and inexpensive RT-LAMP SARS-CoV-2 extraction-free procedure developed may be an alternative test that could be applied for the detection of SARS-CoV-2 or adapted to detect other viruses present in saliva or nasopharyngeal samples with higher sensitivity and specificity of the antibody test.
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Affiliation(s)
| | | | - Iris Manzano-Blasco
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Jessica Abadía-Otero
- Internal Medicine Service, Rio Hortega University Hospital, 47012 Valladolid, Spain
| | - Eliseo Albert
- Microbiology Service, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | - Alba Mulet
- Pulmonary Department, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | | | | | - Ignacio Torres
- Microbiology Service, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | - Jaime Signes-Costa
- Pulmonary Department, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | - David Navarro
- Microbiology Service, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | - Juan-Carlos Martín-Escudero
- Internal Medicine Service, Rio Hortega University Hospital, 47012 Valladolid, Spain
- Medicine Department, Valladolid University, 47002 Valladolid, Spain
| | - Ana-Bárbara García-García
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
- CIBERDEM, ISCIII, 28029 Madrid, Spain
| | - Felipe Javier Chaves
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
- CIBERDEM, ISCIII, 28029 Madrid, Spain
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16
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Abir FF, Chowdhury MEH, Tapotee MI, Mushtak A, Khandakar A, Mahmud S, Hasan MA. PCovNet+: A CNN-VAE anomaly detection framework with LSTM embeddings for smartwatch-based COVID-19 detection. ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE 2023; 122:106130. [PMID: 37006447 PMCID: PMC10047244 DOI: 10.1016/j.engappai.2023.106130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/20/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
The world is slowly recovering from the Coronavirus disease 2019 (COVID-19) pandemic; however, humanity has experienced one of its According to work by Mishra et al. (2020), the study's first phase included a cohort of 5,262 subjects, with 3,325 Fitbit users constituting the majority. However, among this large cohort of 5,262 subjects, most significant trials in modern times only to learn about its lack of preparedness in the face of a highly contagious pathogen. To better prepare the world for any new mutation of the same pathogen or the newer ones, technological development in the healthcare system is a must. Hence, in this work, PCovNet+, a deep learning framework, was proposed for smartwatches and fitness trackers to monitor the user's Resting Heart Rate (RHR) for the infection-induced anomaly. A convolutional neural network (CNN)-based variational autoencoder (VAE) architecture was used as the primary model along with a long short-term memory (LSTM) network to create latent space embeddings for the VAE. Moreover, the framework employed pre-training using normal data from healthy subjects to circumvent the data shortage problem in the personalized models. This framework was validated on a dataset of 68 COVID-19-infected subjects, resulting in anomalous RHR detection with precision, recall, F-beta, and F-1 score of 0.993, 0.534, 0.9849, and 0.6932, respectively, which is a significant improvement compared to the literature. Furthermore, the PCovNet+ framework successfully detected COVID-19 infection for 74% of the subjects (47% presymptomatic and 27% post-symptomatic detection). The results prove the usability of such a system as a secondary diagnostic tool enabling continuous health monitoring and contact tracing.
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Affiliation(s)
- Farhan Fuad Abir
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL, United States
| | | | - Malisha Islam Tapotee
- Department of Electrical and Electronic Engineering, University of Dhaka, Dhaka 1000, Bangladesh
| | - Adam Mushtak
- Clinical Imaging Department, Hamad Medical Corporation, Doha, Qatar
| | - Amith Khandakar
- Department of Electrical Engineering, Qatar University, Doha 2713, Qatar
| | - Sakib Mahmud
- Department of Electrical Engineering, Qatar University, Doha 2713, Qatar
| | - Md Anwarul Hasan
- Department of Mechanical and Industrial Engineering, Qatar University, Doha 2713, Qatar
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17
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Zouaghi N, Aziz S, Shah I, Aamouche A, Jung DW, Lakssir B, Ressami EM. Miniaturized Rapid Electrochemical Immunosensor Based on Screen Printed Carbon Electrodes for Mycobacterium tuberculosis Detection. BIOSENSORS 2023; 13:589. [PMID: 37366954 PMCID: PMC10296126 DOI: 10.3390/bios13060589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/17/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
In 2019, over 21% of an estimated 10 million new tuberculosis (TB) patients were either not diagnosed at all or diagnosed without being reported to public health authorities. It is therefore critical to develop newer and more rapid and effective point-of-care diagnostic tools to combat the global TB epidemic. PCR-based diagnostic methods such as Xpert MTB/RIF are quicker than conventional techniques, but their applicability is restricted by the need for specialized laboratory equipment and the substantial cost of scaling-up in low- and middle-income countries where the burden of TB is high. Meanwhile, loop-mediated isothermal amplification (LAMP) amplifies nucleic acids under isothermal conditions with a high efficiency, helps in the early detection and identification of infectious diseases, and can be performed without the need for sophisticated thermocycling equipment. In the present study, the LAMP assay was integrated with screen-printed carbon electrodes and a commercial potentiostat for real time cyclic voltammetry analysis (named as the LAMP-Electrochemical (EC) assay). The LAMP-EC assay was found to be highly specific to TB-causing bacteria and capable of detecting even a single copy of the Mycobacterium tuberculosis (Mtb) IS6110 DNA sequence. Overall, the LAMP-EC test developed and evaluated in the present study shows promise to become a cost-effective tool for rapid and effective diagnosis of TB.
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Affiliation(s)
- Noura Zouaghi
- LISA Laboratory, National Applied Science School, Cadi Ayyad University, Marrakech 40000, Morocco; (N.Z.); (A.A.)
- Moroccan Foundation for Advanced Science, Innovation and Research, Digitalization & Microelectronics Smart Devices Laboratory, Rabat Design Center, Rabat 10112, Morocco; (B.L.); (E.M.R.)
| | - Shahid Aziz
- Department of Mechanical Engineering, Jeju National University, 102 Jejudaehak-ro, Jeju-Si 63243, Republic of Korea;
- Institute of Basic Sciences, Jeju National University, 102 Jejudaehak-ro, Jeju-Si 63243, Republic of Korea
| | - Imran Shah
- Department of Aerospace Engineering, College of Aeronautical Engineering, National University of Sciences and Technology, Risalpur 24090, Pakistan;
| | - Ahmed Aamouche
- LISA Laboratory, National Applied Science School, Cadi Ayyad University, Marrakech 40000, Morocco; (N.Z.); (A.A.)
| | - Dong-won Jung
- Faculty of Applied Energy System, Major of Mechanical Engineering, Jeju National University, 102 Jejudaehak-ro, Jeju-Si 63243, Republic of Korea
| | - Brahim Lakssir
- Moroccan Foundation for Advanced Science, Innovation and Research, Digitalization & Microelectronics Smart Devices Laboratory, Rabat Design Center, Rabat 10112, Morocco; (B.L.); (E.M.R.)
| | - El Mostafa Ressami
- Moroccan Foundation for Advanced Science, Innovation and Research, Digitalization & Microelectronics Smart Devices Laboratory, Rabat Design Center, Rabat 10112, Morocco; (B.L.); (E.M.R.)
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18
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Zhu Z, Guo Y, Wang C, Yang Z, Li R, Zeng Z, Li H, Zhang D, Yang L. An ultra-sensitive one-pot RNA-templated DNA ligation rolling circle amplification-assisted CRISPR/Cas12a detector assay for rapid detection of SARS-CoV-2. Biosens Bioelectron 2023; 228:115179. [PMID: 36878066 PMCID: PMC9974209 DOI: 10.1016/j.bios.2023.115179] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 01/28/2023] [Accepted: 02/22/2023] [Indexed: 03/04/2023]
Abstract
Rapid, sensitive, and one-pot diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an extremely important role in point-of-care testing (POCT). Herein, we report an ultra-sensitive and rapid one-pot enzyme-catalyzed rolling circle amplification-assisted CRISPR/FnCas12a assay, termed OPERATOR. OPERATOR employs a single well-designed single-strand padlock DNA, containing a protospacer adjacent motif (PAM) site and a sequence complementary to the target RNA which procedure converts and amplifies genomic RNA to DNA by RNA-templated DNA ligation and multiply-primed rolling circle amplification (MRCA). The MRCA amplicon of single-stranded DNA is cleaved by the FnCas12a/crRNA complex and detected via a fluorescence reader or lateral flow strip. OPERATOR presents outstanding advantages including ultra-sensitivity (1.625 copies per reaction), high specificity (100%), rapid reaction speed (∼30 min), easy operation, low cost, and on-spot visualization. Furthermore, we established a POCT platform by combining OPERATOR with rapid RNA release and a lateral flow strip without professional equipment. The high performance of OPERATOR in SARS-CoV-2 tests was confirmed using both reference materials and clinical samples, and the results suggest that is readily adaptable for point-of-care testing of other RNA viruses.
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Affiliation(s)
- Zaobing Zhu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Yongkun Guo
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Chen Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, PR China
| | - Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Zhiqi Zeng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510180, PR China
| | - Hui Li
- Zhuhai Huirui Biotechnology Co. Ltd, PR China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Litao Yang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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19
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Iwasaki Y, Takei Y, Yamada M, Sugino S, Saito K, Aoyagi T, Oshima K, Kanamori H, Baba H, Takei K, Tokuda K, Kodama EN, Kamo T, Kamio T, Kasai T, Ogawa S, Yamauchi M. Circulating Extracellular Vesicle Levels in Patients with Coronavirus Disease 2019 Coagulopathy: A Prospective Cohort Study. J Clin Med 2023; 12:jcm12103460. [PMID: 37240566 DOI: 10.3390/jcm12103460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is associated with coagulopathy. However, the underlying mechanisms are not completely understood. We evaluated the association between COVID-19 coagulopathy and extracellular vesicle (EV) levels. We hypothesized that several EV levels would be higher in COVID-19 coagulopathy patients than in non-coagulopathy patients. This prospective observational study was conducted in four tertiary care faculties in Japan. We enrolled 99 COVID-19 patients (48 with coagulopathy and 51 without coagulopathy) aged ≥20 years who required hospitalization, and 10 healthy volunteers; we divided the patients into coagulopathy and non-coagulopathy groups according to the D-dimer levels (≥1 μg/mL and <1 μg/mL, respectively). We used flow cytometry to measure the tissue-factor-bearing, endothelium-derived, platelet-derived, monocyte-derived, and neutrophil-derived EV levels in platelet-free plasma. The EV levels were compared between the two COVID-19 groups as well as among the coagulopathy patients, non-coagulopathy patients, and healthy volunteers. No significant difference was found in EV levels between the two groups. Meanwhile, the cluster of differentiation (CD) 41 + EV levels were significantly higher in COVID-19 coagulopathy patients than in healthy volunteers (549.90 [255.05-984.65] vs. 184.3 [150.1-254.1] counts/µL, p = 0.011). Therefore, CD41+ EVs might play an essential role in COVID-19 coagulopathy development.
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Affiliation(s)
- Yudai Iwasaki
- Department of Anesthesiology and Perioperative Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Yusuke Takei
- Department of Anesthesiology and Perioperative Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Shigekazu Sugino
- Department of Anesthesiology and Perioperative Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Koji Saito
- Department of Anesthesiology and Perioperative Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Tetsuji Aoyagi
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Kengo Oshima
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Hiroaki Baba
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Kentarou Takei
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Koichi Tokuda
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Eichi N Kodama
- Division of Infectious Diseases, International Research Institute of Disaster Science, Graduate School of Medicine, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
| | - Tetsuro Kamo
- Department of Emergency Medicine and Critical Care Medicine, Tochigi Prefectural Emergency and Critical Care Center, Imperial Gift Foundation Saiseikai, Utsunomiya Hospital, Utsunomiya-shi 321-0974, Tochigi, Japan
| | - Tadashi Kamio
- Department of Intensive Care, Shonan Kamakura General Hospital, 1370-1 Okamoto, Kamakura 247-8533, Kanagawa, Japan
| | - Takehiko Kasai
- Department of Emergency Medicine, Sapporo Medical University, South 1 West 17, Sapporo 060-8556, Hokkaido, Japan
| | - Satoru Ogawa
- Department of Pain Management and Palliative Care Medicine, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Kyoto, Japan
| | - Masanori Yamauchi
- Department of Anesthesiology and Perioperative Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Miyagi, Japan
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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Li A, Wang Q, Huang Y, Hu L, Li S, Wang Q, Yu Y, Zhang H, Tang DYY, Show PL, Feng S. Can egg yolk antibodies terminate the CSBV infection in apiculture? Virus Res 2023; 328:199080. [PMID: 36882131 DOI: 10.1016/j.virusres.2023.199080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023]
Abstract
Chinese sacbrood virus (CSBV) is the most severe pathogen of Apis cerana, which leads to serious fatal diseases in bee colonies and eventual catastrophe for the Chinese beekeeping industry. Additionally, CSBV can potentially infect Apis mellifera by bridging the species barrier and significantly affect the productivity of the honey industry. Although several approaches, such as feeding royal jelly, traditional Chinese medicine, and double-stranded RNA treatments, have been employed to suppress CSBV infection, their practical applicabilities are constrained due to their poor effectiveness. In recent years, specific egg yolk antibodies (EYA) have been increasingly utilized in passive immunotherapy for infectious diseases without any side effects. According to both laboratory research and practical use, EYA have demonstrated superior protection for bees against CSBV infection. This review provided an in-depth analysis of the issues and drawbacks in this field in addition to provide a thorough summary of current advancements in CSBV studies. Some promising strategies for the synergistic study of EYA against CSBV, including the exploitation of novel antibody drugs, novel TCM monomer/formula determination, and development of nucleotide drugs, are also proposed in this review. Furthermore, the prospects for the future perspectives of EYA research and applications are presented. Collectively, EYA would terminate CSBV infection soon, as well as will provide scientific guidance and references to control and manage other viral infections in apiculture.
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Affiliation(s)
- Aifang Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, China
| | - Qianfang Wang
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, Henan 471023, China
| | - Yu Huang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, China
| | - Lina Hu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, China
| | - Shuxuan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, China
| | - Qianqian Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, China
| | - Yangfan Yu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, China
| | - Haizhou Zhang
- Luoyang Fengzaokang Biotechnological Co. Ltd., Luoyang, Henan 471000, China
| | - Doris Ying Ying Tang
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor Darul Ehsan 43500, Malaysia
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor Darul Ehsan 43500, Malaysia; Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China; Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai 602105, India.
| | - Shuying Feng
- Medical College, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, China; Luoyang Fengzaokang Biotechnological Co. Ltd., Luoyang, Henan 471000, China.
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Szobi A, Buranovská K, Vojtaššáková N, Lovíšek D, Özbaşak HÖ, Szeibeczederová S, Kapustian L, Hudáčová Z, Kováčová V, Drobná D, Putaj P, Bírová S, Čirková I, Čarnecký M, Kilián P, Jurkáček P, Čabanová V, Boršová K, Sláviková M, Vaňová V, Klempa B, Čekan P, Paul ED. Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system. Commun Biol 2023; 6:233. [PMID: 36864129 PMCID: PMC9979146 DOI: 10.1038/s42003-023-04612-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Sensitive and rapid point-of-care assays have been crucial in the global response to SARS-CoV-2. Loop-mediated isothermal amplification (LAMP) has emerged as an important diagnostic tool given its simplicity and minimal equipment requirements, although limitations exist regarding sensitivity and the methods used to detect reaction products. We describe the development of Vivid COVID-19 LAMP, which leverages a metallochromic detection system utilizing zinc ions and a zinc sensor, 5-Br-PAPS, to circumvent the limitations of classic detection systems dependent on pH indicators or magnesium chelators. We make important strides in improving RT-LAMP sensitivity by establishing principles for using LNA-modified LAMP primers, multiplexing, and conducting extensive optimizations of reaction parameters. To enable point-of-care testing, we introduce a rapid sample inactivation procedure without RNA extraction that is compatible with self-collected, non-invasive gargle samples. Our quadruplexed assay (targeting E, N, ORF1a, and RdRP) reliably detects 1 RNA copy/µl of sample (=8 copies/reaction) from extracted RNA and 2 RNA copies/µl of sample (=16 copies/reaction) directly from gargle samples, making it one of the most sensitive RT-LAMP tests and even comparable to RT-qPCR. Additionally, we demonstrate a self-contained, mobile version of our assay in a variety of high-throughput field testing scenarios on nearly 9,000 crude gargle samples. Vivid COVID-19 LAMP can be an important asset for the endemic phase of COVID-19 as well as preparing for future pandemics.
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Affiliation(s)
- Adrián Szobi
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Katarína Buranovská
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Nina Vojtaššáková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Daniel Lovíšek
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Halil Önder Özbaşak
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Sandra Szeibeczederová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Liudmyla Kapustian
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Zuzana Hudáčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- Stanford University, 730 Escondido Rd., Stanford, CA, 94305, USA
| | - Viera Kováčová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
- University of Cologne, Institute for Biological Physics, Zülpicher Str. 77, 50937, Köln, Germany
| | - Diana Drobná
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Piotr Putaj
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Stanislava Bírová
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Ivana Čirková
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Martin Čarnecký
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Kilián
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA
| | - Peter Jurkáček
- AstonITM s.r.o., Račianska 153, 831 54, Bratislava, Slovakia
| | - Viktória Čabanová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Kristína Boršová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Veronika Vaňová
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 845 05, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
| | - Evan D Paul
- MultiplexDX, s.r.o., Comenius University Science Park, Ilkovičova 8, 841 04, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Suite 450, Rockville, MD, 20850, USA.
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Moon SH, Kim SC, Kim BW, Park GJ, Chai HS, Kim YM, Kim HS, Park HS. SARS-CoV-2 molecular diagnostic point-of-care testing based on loop-mediated isothermal amplification: A prospective, single-center validation study. Heliyon 2023; 9:e14564. [PMID: 36942218 PMCID: PMC10014123 DOI: 10.1016/j.heliyon.2023.e14564] [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: 11/08/2022] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Objectives Rapid and accurate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests are crucial for controlling the spread of infections in emergency settings. This study evaluated the diagnostic accuracy of a point-of-care (POC) test based on loop-mediated isothermal amplification (LAMP) that produces rapid results within 30 min. Methods We prospectively included adult patients (age >19 years) who were diagnosed with SARS-CoV-2 infection within the last 3 days and symptomatic patients who had visited the emergency room. Posterior nasopharyngeal (PNP) swabs and throat swabs collected by physicians were used to test the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy, and Cohen's Kappa coefficient (k) of the POC index and reference reverse transcription quantitative polymerase chain reaction (RT-qPCR) test devices. Results Of the 352 participants, 102 (29.0%) tested positive via the RT-PCR-based reference test device; the RT-LAMP-based POC test had a sensitivity of 70.6% and specificity of 98.0%, with 93.5% PPV, 89.1% NPV, 35.5% PLR, and 3.4% NLR. Cohen's k correlation of results from the two devices was 0.74. The cycle threshold value between the positive and negative POC test results differed (17.6 vs. 24.6, p < 0.001). Conclusions The RT-LAMP POC test in the emergency medical setting has a fair predictive value in high viral load cases in terms of infectivity.
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Affiliation(s)
- Sung Hun Moon
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Sang-Chul Kim
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
- Department of Emergency Medicine, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowongu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Byung Woo Kim
- Department of Paramedic Science, Korea National University of Transportation, 61, Daehak-ro, Jeungpyeong-gun, Chungcheongbuk-do, 27909, Republic of Korea
| | - Gwan-Jin Park
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Hyun-Seok Chai
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Young Min Kim
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Hee Sung Kim
- Department of Internal Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
- College of Medicine and Medical Research Institute, Chungbuk National University, 1 Chungdae-ro, Seowongu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Hee Sue Park
- Department of Laboratory Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowongu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
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24
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Abavisani M, Khayami R, Hoseinzadeh M, Kodori M, Kesharwani P, Sahebkar A. CRISPR-Cas system as a promising player against bacterial infection and antibiotic resistance. Drug Resist Updat 2023; 68:100948. [PMID: 36780840 DOI: 10.1016/j.drup.2023.100948] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/25/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
The phenomenon of antibiotic resistance (AR) and its increasing global trends and destructive waves concerns patients and the healthcare system. In order to combat AR, it is necessary to explore new strategies when the current antibiotics fail to be effective. Thus, knowing the resistance mechanisms and appropriate diagnosis of bacterial infections may help enhance the sensitivity and specificity of novel strategies. On the other hand, resistance to antimicrobial compounds can spread from resistant populations to susceptible ones. Antimicrobial resistance genes (ARGs) significantly disseminate AR via horizontal and vertical gene transfer. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is a member of the bacterial immune system with the ability to remove the ARGs; therefore, it can be introduced as an effective and innovative strategy in the battle against AR. Here, we reviewed CRISPR-based bacterial diagnosis technologies. Moreover, the strategies to battle AR based on targeting bacterial chromosomes and resistance plasmids using the CRISPR-Cas system have been explained. Besides, we have presented the limitations of CRISPR delivery and potential solutions to help improve the future development of CRISPR-based platforms.
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Affiliation(s)
- Mohammad Abavisani
- Student research committee, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran; Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran
| | - Reza Khayami
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran
| | - Melika Hoseinzadeh
- Student research committee, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran
| | - Mansoor Kodori
- Non communicable Diseases Research Center, Bam University of Medical sciences, Bam, the Islamic Republic of Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India; Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Chennai, India
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran; Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran.
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25
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Li Q, Zhou X, Wang Q, Liu W, Chen C. Microfluidics for COVID-19: From Current Work to Future Perspective. BIOSENSORS 2023; 13:163. [PMID: 36831930 PMCID: PMC9953302 DOI: 10.3390/bios13020163] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/07/2023] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
Spread of coronavirus disease 2019 (COVID-19) has significantly impacted the public health and economic sectors. It is urgently necessary to develop rapid, convenient, and cost-effective point-of-care testing (POCT) technologies for the early diagnosis and control of the plague's transmission. Developing POCT methods and related devices is critical for achieving point-of-care diagnosis. With the advantages of miniaturization, high throughput, small sample requirements, and low actual consumption, microfluidics is an essential technology for the development of POCT devices. In this review, according to the different driving forces of the fluid, we introduce the common POCT devices based on microfluidic technology on the market, including paper-based microfluidic, centrifugal microfluidic, optical fluid, and digital microfluidic platforms. Furthermore, various microfluidic-based assays for diagnosing COVID-19 are summarized, including immunoassays, such as ELISA, and molecular assays, such as PCR. Finally, the challenges of and future perspectives on microfluidic device design and development are presented. The ultimate goals of this paper are to provide new insights and directions for the development of microfluidic diagnostics while expecting to contribute to the control of COVID-19.
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Affiliation(s)
- Qi Li
- Department of Pharmacy, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410017, China
| | - Xingchen Zhou
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410017, China
| | - Qian Wang
- Department of Pharmacy, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410017, China
| | - Wenfang Liu
- Department of Pharmacy, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410017, China
| | - Chuanpin Chen
- Department of Pharmacy, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410017, China
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Shan Y, Wang B, Huang H, Yan K, Li W, Wang S, Liu F. Portable high-throughput multimodal immunoassay platform for rapid on-site COVID-19 diagnostics. Anal Chim Acta 2023; 1238:340634. [PMID: 36464448 PMCID: PMC9671405 DOI: 10.1016/j.aca.2022.340634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/21/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a causal agent of Coronavirus Disease 2019 (COVID-19) has led to the global pandemic. Though the real-time reverse transcription polymerase chain reaction (RT-PCR) acting as a gold-standard method has been widely used for COVID-19 diagnostics, it can hardly support rapid on-site applications or monitor the stage of disease development as well as to identify the infection and immune status of rehabilitation patients. To suit rapid on-site COVID-19 diagnostics under various application scenarios with an all-in-one device and simple detection reagents, we propose a high-throughput multimodal immunoassay platform with fluorescent, colorimetric, and chemiluminescent immunoassays on the same portable device and a multimodal reporter probe using quantum dot (QD) microspheres modified with horseradish peroxidase (HRP) coupled with goat anti-human IgG. The recombinant nucleocapsid protein fixed on a 96-well plate works as the capture probe. In the condition with the target under detection, both reporter and capture probes can be bound by such target. When illuminated by excitation light, fluorescence signals from QD microspheres can be collected for target quantification often at a fast speed. Additionally, when pursuing simple detection without using any sensing devices, HRP-catalyzed TMB colorimetric immunoassay is employed; and when pursuing highly sensitive detection, HRP-catalyzed luminol chemiluminescent immunoassay is established. Verified by the anti-SARS-CoV-2 N humanized antibody, the sensitivities of colorimetric, fluorescent, and chemiluminescent immunoassays are respectively 20, 80, and 640 times more sensitive than that of the lateral flow colloidal gold immunoassay strip. Additionally, such a platform can simultaneously detect multiple samples at the same time thus supporting high-throughput sensing; and all these detecting operations can be implemented on-site within 50 min relying on field-operable processing and field-portable devices. Such a high-throughput multimodal immunoassay platform can provide a new all-in-one solution for rapid on-site diagnostics of COVID-19 for different detecting purposes.
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Affiliation(s)
- Yanke Shan
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Bin Wang
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Huachuan Huang
- School of Manufacture Science and Engineering, Key Laboratory of Testing Technology for Manufacturing Process, Ministry of Education, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, China
| | - Keding Yan
- Advanced Institute of Micro-Nano Intelligent Sensing (AIMNIS), School of Electronic Information Engineering, Xi'an Technological University, Xi'an, Shaanxi, 710032, China
| | - Wenzhi Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710000, China.
| | - Shouyu Wang
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China; OptiX+ Laboratory, Wuxi, Jiangsu, China.
| | - Fei Liu
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
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Crego-Vicente B, Fernández-Soto P, García-Bernalt Diego J, Febrer-Sendra B, Muro A. Development of a Duplex LAMP Assay with Probe-Based Readout for Simultaneous Real-Time Detection of Schistosoma mansoni and Strongyloides spp. -A Laboratory Approach to Point-Of-Care. Int J Mol Sci 2023; 24:ijms24010893. [PMID: 36614336 PMCID: PMC9821331 DOI: 10.3390/ijms24010893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is the most popular technology for point-of-care testing applications due its rapid, sensitive and specific detection with simple instrumentation compared to PCR-based methods. Many systems for reading the results of LAMP amplifications exist, including real-time fluorescence detection using fluorophore-labelled probes attached to oligonucleotide sequences complementary to the target nucleic acid. This methodology allows the simultaneous detection of multiple targets (multiplexing) in one LAMP assay. A method for multiplexing LAMP is the amplification by release of quenching (DARQ) technique by using a 5'-quencher modified LAMP primer annealed to 3'-fluorophore-labelled acting as detection oligonucleotide. The main application of multiplex LAMP is the rapid and accurate diagnosis of infectious diseases, allowing differentiation of co-infecting pathogens in a single reaction. Schistosomiasis, caused among other species by Schistosoma mansoni and strongyloidiasis, caused by Strongyloides stercoralis, are the most common helminth-parasite infections worldwide with overlapping distribution areas and high possibility of coinfections in the human population. It would be of great interest to develop a duplex LAMP to detect both pathogens in the same reaction. In this study, we investigate the use of our two previously developed and well-stablished LAMP assays for S. mansoni and Strongyloides spp. DNA detection in a new duplex real-time eight-primer system based on a modified DARQ probe method that can be performed in a portable isothermal fluorimeter with minimal laboratory resources. We also applied a strategy to stabilize the duplexed DARQ-LAMP mixtures at room temperature for use as ready-to-use formats facilitating analysis in field settings as point-of-care diagnostics for schistosomiasis and strongyloidiasis.
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COVID-19 diagnostics: Molecular biology to nanomaterials. Clin Chim Acta 2023; 538:139-156. [PMID: 36403665 PMCID: PMC9673061 DOI: 10.1016/j.cca.2022.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022]
Abstract
The SARS-CoV-2 pandemic has claimed around 6.4 million lives worldwide. The disease symptoms range from mild flu-like infection to life-threatening complications. The widespread infection demands rapid, simple, and accurate diagnosis. Currently used methods include molecular biology-based approaches that consist of conventional amplification by RT-PCR, isothermal amplification-based techniques such as RT-LAMP, and gene editing tools like CRISPR-Cas. Other methods include immunological detection including ELISA, lateral flow immunoassay, chemiluminescence, etc. Radiological-based approaches are also being used. Despite good analytical performance of these current methods, there is an unmet need for less costly and simpler tests that may be performed at point of care. Accordingly, nanomaterial-based testing has been extensively pursued. In this review, we discuss the currently used diagnostic techniques for SARS-CoV-2, their usefulness, and limitations. In addition, nanoparticle-based approaches have been highlighted as another potential means of detection. The review provides a deep insight into the current diagnostic methods and future trends to combat this deadly menace.
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Chen X, Zhou Q, Yuan W, Shi Y, Dong S, Luo X. Visual and rapid identification of Chlamydia trachomatis and Neisseria gonorrhoeae using multiplex loop-mediated isothermal amplification and a gold nanoparticle-based lateral flow biosensor. Front Cell Infect Microbiol 2023; 13:1067554. [PMID: 36926514 PMCID: PMC10011439 DOI: 10.3389/fcimb.2023.1067554] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
Sexually transmitted chlamydia and gonorrhea infections caused by the bacteria Chlamydia trachomatis and Neisseria gonorrhoeae remain a major public health concern worldwide, particularly in less developed nations. It is crucial to use a point of care (POC) diagnostic method that is quick, specific, sensitive, and user-friendly to treat and control these infections effectively. Here, a novel molecular diagnostic assay, combining multiplex loop-mediated isothermal amplification (mLAMP) with a visual gold nanoparticles-based lateral flow biosensor (AuNPs-LFB) was devised and used for highly specific, sensitive, rapid, visual, and easy identification of C. trachomatis and N. gonorrhoeae. Two unique independent primer pairs were successful designed against the ompA and orf1 genes of C. trachomatis and N. gonorrhoeae, respectively. The optimal mLAMP-AuNPs-LFB reaction conditions were determined to be 67°C for 35 min. The detection procedure, involving crude genomic DNA extraction (~5 min), LAMP amplification (35 min), and visual results interpretation (<2 min), can be completed within 45 min. Our assay has a detection limit of 50 copies per test, and we did not observe any cross-reactivity with any other bacteria in our testing. Hence, our mLAMP-AuNPs-LFB assay can potentially be used for POC testing to detect C. trachomatis and N. gonorrhoeae in clinical settings, particularly in underdeveloped regions.
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Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- Clinical Medical Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- *Correspondence: Xinhua Luo, ; Shilei Dong, ; Xu Chen,
| | - Qingxue Zhou
- Clinical Laboratory, Hangzhou Women’s Hospital, Hangzhou, Zhejiang, China
| | - Wei Yuan
- Department of Quality Control, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| | - Yuanfang Shi
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China
- *Correspondence: Xinhua Luo, ; Shilei Dong, ; Xu Chen,
| | - Xinhua Luo
- Department of Infectious Disease, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
- *Correspondence: Xinhua Luo, ; Shilei Dong, ; Xu Chen,
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Zhao Y, Zeng Y, Lu R, Wang Z, Zhang X, Wu N, Zhu T, Wang Y, Zhang C. Rapid point-of-care detection of BK virus in urine by an HFman probe-based loop-mediated isothermal amplification assay and a finger-driven microfluidic chip. PeerJ 2023; 11:e14943. [PMID: 36915661 PMCID: PMC10007963 DOI: 10.7717/peerj.14943] [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: 10/11/2022] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Background BK virus (BKV)-associated nephropathy (BKVN) is one of the leading causes of renal dysfunction and graft loss in renal transplant recipients. Early monitoring of BKV in urine is crucial to minimize the deleterious effects caused by this virus on preservation of graft function. Methods We report a simple, rapid, sensitive loop-mediated isothermal amplification (LAMP) assay using an HFman probe for detecting BKV in urine. To evaluate the performance of the assay, a comparison of the HFman probe-based LAMP (HF-LAMP) assay with two qPCR assays was performed using urine samples from 132 HIV-1 infected individuals. We further evaluated the performance of HF-LAMP directly using the urine samples from these HIV-1 infected individuals and 30 kidney transplant recipients without DNA extraction. Furthermore, we combined the HF-LAMP assay with a portable finger-driven microfluidic chip for point-of-care testing (POCT). Results The assay has high specificity and sensitivity with a limit of detection (LOD) of 12 copies/reaction and can be completed within 30 min. When the DNA was extracted, the HF-LAMP assay showed an equivalent and potentially even higher sensitivity (93.5%) than the qPCR assays (74.2-87.1%) for 132 urine samples from HIV-1 infected individuals. The HF-LAMP assay can be applied in an extraction-free format and can be completed within 45 min using a simple heat block. Although some decreased performance was seen on urine samples from HIV-1 infected individuals, the sensitivity, specificity, and accuracy of the extraction-free BKV HF-LAMP assay were 95%, 100%, and 96.7% for 30 clinical urine samples from kidney transplant recipients, respectively. Conclusion The assay has high specificity and sensitivity. Combined with a portable finger-driven microfluidic chip for easy detection, this method shows great potential for POCT detection of BKV.
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Affiliation(s)
- Yongjuan Zhao
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Yi Zeng
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Renfei Lu
- Nantong Third Hospital Affiliated to Nantong University, Nantong, China
| | - Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Engineering Medicine, Beihang University, Beijing, China
| | | | - Nannan Wu
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Tongyu Zhu
- Shanghai Medical College, Shanghai, China.,Zhongshan Hospital, Shanghai, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Engineering Medicine, Beihang University, Beijing, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Shanghai, China
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Li M, Ge H, Sun Z, Fu J, Cao L, Feng X, Meng G, Peng Y, Liu Y, Zhao C. A loop-mediated isothermal amplification-enabled analytical assay for the detection of SARS-CoV-2: A review. Front Cell Infect Microbiol 2022; 12:1068015. [PMID: 36619749 PMCID: PMC9816412 DOI: 10.3389/fcimb.2022.1068015] [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: 10/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The number of words: 4645, the number of figures: 4, the number of tables: 1The outbreak of COVID-19 in December 2019 caused a global pandemic of acute respiratory disease, and with the increasing virulence of mutant strains and the number of confirmed cases, this has resulted in a tremendous threat to global public health. Therefore, an accurate diagnosis of COVID-19 is urgently needed for rapid control of SARS-CoV-2 transmission. As a new molecular biology technology, loop-mediated isothermal amplification (LAMP) has the advantages of convenient operation, speed, low cost and high sensitivity and specificity. In the past two years, rampant COVID-19 and the continuous variation in the virus strains have demanded higher requirements for the rapid detection of pathogens. Compared with conventional RT-PCR and real-time RT-PCR methods, genotyping RT-LAMP method and LAMP plus peptide nucleic acid (PNA) probe detection methods have been developed to correctly identified SARS-CoV-2 variants, which is also why LAMP technology has attracted much attention. LAMP detection technology combined with lateral flow assay, microfluidic technology and other sensing technologies can effectively enhance signals by nucleic acid amplification and help to give the resulting output in a faster, more convenient and user-friendly way. At present, LAMP plays an important role in the detection of SARS-CoV-2.
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Affiliation(s)
- Mingna Li
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Hongjuan Ge
- College of public health, Jilin Medical University, Jilin, China
| | - Zhe Sun
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Jangshan Fu
- College of public health, Jilin Medical University, Jilin, China
| | - Lele Cao
- College of public health, Jilin Medical University, Jilin, China
| | - Xinrui Feng
- College of public health, Jilin Medical University, Jilin, China,Medical college, Yanbian University, Jilin, China
| | - Guixian Meng
- College of medical laboratory, Jilin Medical University, Jilin, China
| | - Yubo Peng
- Business School, The University of Adelaide, Adelaide, SA, Australia
| | - Yan Liu
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
| | - Chen Zhao
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
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Mostafa M, Barhoum A, Sehit E, Gewaid H, Mostafa E, Omran MM, Abdalla MS, Abdel-Haleem FM, Altintas Z, Forster RJ. Current trends in COVID-19 diagnosis and its new variants in physiological fluids: Surface antigens, antibodies, nucleic acids, and RNA sequencing. Trends Analyt Chem 2022; 157:116750. [PMID: 36060607 PMCID: PMC9425703 DOI: 10.1016/j.trac.2022.116750] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/21/2022] [Accepted: 07/24/2022] [Indexed: 12/15/2022]
Abstract
Rapid, highly sensitive, and accurate virus circulation monitoring techniques are critical to limit the spread of the virus and reduce the social and economic burden. Therefore, point-of-use diagnostic devices have played a critical role in addressing the outbreak of COVID-19 (SARS-CoV-2) viruses. This review provides a comprehensive overview of the current techniques developed for the detection of SARS-CoV-2 in various body fluids (e.g., blood, urine, feces, saliva, tears, and semen) and considers the mutations (i.e., Alpha, Beta, Gamma, Delta, Omicron). We classify and comprehensively discuss the detection methods depending on the biomarker measured (i.e., surface antigen, antibody, and nucleic acid) and the measurement techniques such as lateral flow immunoassay (LFIA), enzyme-linked immunosorbent assay (ELISA), reverse transcriptase-polymerase chain reaction (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), microarray analysis, clustered regularly interspaced short palindromic repeats (CRISPR) and biosensors. Finally, we addressed the challenges of rapidly identifying emerging variants, detecting the virus in the early stages of infection, the detection sensitivity, selectivity, and specificity, and commented on how these challenges can be overcome in the future.
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Affiliation(s)
- Menna Mostafa
- NanoStruc Research Group, Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt
| | - Ahmed Barhoum
- National Centre for Sensor Research, School of Chemical Sciences, Dublin City University, D09 V209, Dublin, Ireland
| | - Ekin Sehit
- Institute of Chemistry, Technical University of Berlin, 10623, Berlin, Germany
- Institute of Materials Science, Faculty of Engineering, Kiel University, 24143, Kiel, Germany
| | - Hossam Gewaid
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St, Dublin, D02R590, Ireland
| | - Eslam Mostafa
- Borg Pharmaceutical Industries, Refaat Hassan St, Al Abageyah, El-Khalifa, Cairo Governorate, 16, Egypt
| | - Mohamed M Omran
- Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt
| | - Mohga S Abdalla
- Chemistry Department, Faculty of Science, Helwan University, 11795, Cairo, Egypt
| | - Fatehy M Abdel-Haleem
- Chemistry Department, Faculty of Science, Cairo University, 12613, Giza, Egypt
- Center for Hazards Mitigation, Environmental Studies and Research (CHMESR), Cairo University, 12613, Giza, Egypt
| | - Zeynep Altintas
- Institute of Chemistry, Technical University of Berlin, 10623, Berlin, Germany
- Institute of Materials Science, Faculty of Engineering, Kiel University, 24143, Kiel, Germany
| | - Robert J Forster
- National Centre for Sensor Research, School of Chemical Sciences, Dublin City University, D09 V209, Dublin, Ireland
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Xie L, Li J, Ai Y, He H, Chen X, Yin M, Li W, Huang W, Luo MY, He J. Current strategies for SARS-CoV-2 molecular detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4625-4642. [PMID: 36349688 DOI: 10.1039/d2ay01313d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.
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Affiliation(s)
- Lei Xie
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Junlin Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Ying Ai
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510080, China
| | - Haolan He
- Guangzhou Eighth People's Hospital, Guangzhou 510080, China
| | - Xiuyun Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Mingyu Yin
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wanxi Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wenguan Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Min-Yi Luo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Jinyang He
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
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Sinha Mahapatra P, Ganguly R, Ghosh A, Chatterjee S, Lowrey S, Sommers AD, Megaridis CM. Patterning Wettability for Open-Surface Fluidic Manipulation: Fundamentals and Applications. Chem Rev 2022; 122:16752-16801. [PMID: 36195098 DOI: 10.1021/acs.chemrev.2c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Effective manipulation of liquids on open surfaces without external energy input is indispensable for the advancement of point-of-care diagnostic devices. Open-surface microfluidics has the potential to benefit health care, especially in the developing world. This review highlights the prospects for harnessing capillary forces on surface-microfluidic platforms, chiefly by inducing smooth gradients or sharp steps of wettability on substrates, to elicit passive liquid transport and higher-order fluidic manipulations without off-the-chip energy sources. A broad spectrum of the recent progress in the emerging field of passive surface microfluidics is highlighted, and its promise for developing facile, low-cost, easy-to-operate microfluidic devices is discussed in light of recent applications, not only in the domain of biomedical microfluidics but also in the general areas of energy and water conservation.
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Affiliation(s)
- Pallab Sinha Mahapatra
- Micro Nano Bio-Fluidics group, Department of Mechanical Engineering, Indian Institute of Technology Madras, Chennai600036, India
| | - Ranjan Ganguly
- Department of Power Engineering, Jadavpur University, Kolkata700098, India
| | - Aritra Ghosh
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois60607, United States
| | - Souvick Chatterjee
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois60607, United States
| | - Sam Lowrey
- Department of Physics, University of Otago, Dunedin9016, New Zealand
| | - Andrew D Sommers
- Department of Mechanical and Manufacturing Engineering, Miami University, Oxford, Ohio45056, United States
| | - Constantine M Megaridis
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois60607, United States
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Atçeken N, Yigci D, Ozdalgic B, Tasoglu S. CRISPR-Cas-Integrated LAMP. BIOSENSORS 2022; 12:1035. [PMID: 36421156 PMCID: PMC9688180 DOI: 10.3390/bios12111035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Pathogen-specific point-of-care (PoC) diagnostic tests have become an important need in the fight against infectious diseases and epidemics in recent years. PoC diagnostic tests are designed with the following parameters in mind: rapidity, accuracy, sensitivity, specificity, and ease of use. Molecular techniques are the gold standard for pathogen detection due to their accuracy and specificity. There are various limitations in adapting molecular diagnostic methods to PoC diagnostic tests. Efforts to overcome limitations are focused on the development of integrated molecular diagnostics by utilizing the latest technologies available to create the most successful PoC diagnostic platforms. With this point of view, a new generation technology was developed by combining loop-mediated isothermal amplification (LAMP) technology with clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) technology. This integrated approach benefits from the properties of LAMP technology, namely its high efficiency, short turnaround time, and the lack of need for a complex device. It also makes use of the programmable function of CRISPR-Cas technology and the collateral cleavage activity of certain Cas proteins that allow for convenient reporter detection. Thus, this combined technology enables the development of PoC diagnostic tests with high sensitivity, specificity, and ease of use without the need for complicated devices. In this review, we discuss the advantages and limitations of the CRISPR/Cas combined LAMP technology. We review current limitations to convert CRISPR combined LAMP into pathogen-specific PoC platforms. Furthermore, we point out the need to design more useful PoC platforms using microfabrication technologies by developing strategies that overcome the limitations of this new technology, reduce its complexity, and reduce the risk of contamination.
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Affiliation(s)
- Nazente Atçeken
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Defne Yigci
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Berin Ozdalgic
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Department of Mechanical Engineering, Engineering Faculty, Koç University, Istanbul 34450, Turkey
- School of Medical Services & Techniques, Dogus University, Istanbul 34775, Turkey
| | - Savas Tasoglu
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Department of Mechanical Engineering, Engineering Faculty, Koç University, Istanbul 34450, Turkey
- Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Istanbul 34684, Turkey
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Istanbul 34450, Turkey
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36
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Ganesh PS, Kim SY. A comparison of conventional and advanced electroanalytical methods to detect SARS-CoV-2 virus: A concise review. CHEMOSPHERE 2022; 307:135645. [PMID: 35817176 PMCID: PMC9270057 DOI: 10.1016/j.chemosphere.2022.135645] [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: 05/12/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Respiratory viruses are a serious threat to human wellbeing that can cause pandemic disease. As a result, it is critical to identify virus in a timely, sensitive, and precise manner. The present novel coronavirus-2019 (COVID-19) disease outbreak has increased these concerns. The research of developing various methods for COVID-19 virus identification is one of the most rapidly growing research areas. This review article compares and addresses recent improvements in conventional and advanced electroanalytical approaches for detecting COVID-19 virus. The popular conventional methods such as polymerase chain reaction (PCR), loop mediated isothermal amplification (LAMP), serology test, and computed tomography (CT) scan with artificial intelligence require specialized equipment, hours of processing, and specially trained staff. Many researchers, on the other hand, focused on the invention and expansion of electrochemical and/or bio sensors to detect SARS-CoV-2, demonstrating that they could show a significant role in COVID-19 disease control. We attempted to meticulously summarize recent advancements, compare conventional and electroanalytical approaches, and ultimately discuss future prospective in the field. We hope that this review will be helpful to researchers who are interested in this interdisciplinary field and desire to develop more innovative virus detection methods.
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Affiliation(s)
- Pattan-Siddappa Ganesh
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education (KoreaTech), Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Sang-Youn Kim
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education (KoreaTech), Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
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Mao G, Ye S, Yin W, Yang Y, Ji X, He J, Liu Y, Dai J, He Z, Ma Y. Ratiometric fluorescent Si-FITC nanoprobe for immunoassay of SARS-CoV-2 nucleocapsid protein. NANO RESEARCH 2022; 16:2859-2865. [PMID: 36196429 PMCID: PMC9523638 DOI: 10.1007/s12274-022-5005-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 05/26/2023]
Abstract
Coronavirus disease 2019 (COVID-19) highlights the importance of rapid and reliable diagnostic assays for the management of virus transmission. Here, we developed a one-pot hydrothermal method to prepare Si-FITC nanoparticles (NPs) for the fluorescent immunoassay of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (N protein). The synthesis of Si-FITC NPs did not need post-modification, which addressed the issue of quantum yield reduction during the coupling reaction. Si-FITC NPs showed two distinct peaks, Si fluorescence at λ em = 385 nm and FITC fluorescence at λ em = 490 nm. In the presence of KMnO4, Si fluorescence was decreased and FITC fluorescence was enhanced. Briefly, in the presence of N protein, catalase (CAT)-linked secondary antibody/reporter antibody/N protein/capture antibody immunocomplexes were formed on microplates. Subsequently, hydrogen peroxide (H2O2) and Si-FITC NPs/KMnO4 were injected into the microplate together. The decomposition of H2O2 by CAT resulted in remaining of KMnO4, which changed the fluorescence intensity ratio of Si-FITC NPs. The fluorescence intensity ratio correlated significantly with the N protein concentration ranging from 0.02 to 50.00 ng/mL, and the detection limit was 0.003 ng/mL, which was more sensitive than the commercial ELISA kit with a detection limit of 0.057 ng/mL. The N protein concentration can be accurately determined in human serum. Furthermore, the COVID-19 and non-COVID-19 patients were distinguishable by this method. Therefore, the ratiometric fluorescent immunoassay can be used for SARS-CoV-2 infection diagnosis with a high sensitivity and selectivity. Electronic Supplementary Material Supplementary material (characterization of Si-FITC NPs (FTIR, HRXPS); stability investigation of Si-FITC NPs (photostability, pH stability, anti-interference ability); stability investigation of free FITC (pH value, KMnO4); quenching mechanism of KMnO4 (UV-vis absorption spectra, fluorescence lifetime decay curves); reaction condition optimization of biotin-CAT with H2O2 (pH value, temperature, time); detection of N protein using commercial ELISA Kit; selectivity investigation of assays for SARS-CoV-2 N protein detection; determination results of SARS-CoV-2 N protein in human serum) is available in the online version of this article at 10.1007/s12274-022-5005-z.
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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
| | - 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
| | - Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, 518112 China
| | - Xinghu Ji
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072 China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, 518112 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
| | - Zhike He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072 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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Pohanka M. Progress in Biosensors for the Point-of-Care Diagnosis of COVID-19. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22197423. [PMID: 36236521 PMCID: PMC9571584 DOI: 10.3390/s22197423] [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] [Received: 09/06/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 05/31/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly virulent infection that has caused a pandemic since 2019. Early diagnosis of the disease has been recognized as one of the important approaches to minimize the pathological impact and spread of infection. Point-of-care tests proved to be substantial analytical tools, and especially lateral flow immunoassays (lateral flow tests) serve the purpose. In the last few years, biosensors have gained popularity. These are simple but highly sensitive and accurate analytical devices composed from a selective molecule such as an antibody or antigen and a sensor platform. Biosensors would be an advanced alternative to current point-of-care tests for COVID-19 diagnosis and standard laboratory methods as well. Recent discoveries related to point-of-care diagnostic tests for COVID-19, the development of biosensors for specific antibodies and specific virus parts or their genetic information are reviewed.
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Affiliation(s)
- Miroslav Pohanka
- Faculty of Military Health Sciences, University of Defense, Trebesska 1575, CZ-50001 Hradec Kralove, Czech Republic
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Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
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Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
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A comprehensive review of COVID-19 detection techniques: From laboratory systems to wearable devices. Comput Biol Med 2022; 149:106070. [PMID: 36099862 PMCID: PMC9433350 DOI: 10.1016/j.compbiomed.2022.106070] [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: 02/04/2022] [Revised: 08/03/2022] [Accepted: 08/27/2022] [Indexed: 11/30/2022]
Abstract
Screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among symptomatic and asymptomatic patients offers unique opportunities for curtailing the transmission of novel coronavirus disease 2019, commonly known as COVID-19. Molecular diagnostic techniques, namely reverse transcription loop-mediated isothermal amplification (RT-LAMP), reverse transcription-polymerase chain reaction (RT-PCR), and immunoassays, have been frequently used to identify COVID-19 infection. Although these techniques are robust and accurate, mass testing of potentially infected individuals has shown difficulty due to the resources, manpower, and costs it entails. Moreover, as these techniques are typically used to test symptomatic patients, healthcare systems have failed to screen asymptomatic patients, whereas the spread of COVID-19 by these asymptomatic individuals has turned into a crucial problem. Besides, respiratory infections or cardiovascular conditions generally demonstrate changes in physiological parameters, namely body temperature, blood pressure, and breathing rate, which signifies the onset of diseases. Such vitals monitoring systems have shown promising results employing artificial intelligence (AI). Therefore, the potential use of wearable devices for monitoring asymptomatic COVID-19 individuals has recently been explored. This work summarizes the efforts that have been made in the domains from laboratory-based testing to asymptomatic patient monitoring via wearable systems.
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Torezin Mendonça G, Cassaboni Stracke M, de Oliveira Coelho B, Bruna Soligo Sanchuki H, Klassen de Oliveira V, Klerynton Marchini F, Lucíola Zanette D, Nóbrega Aoki M, Ribeiro Viana E, Blanes L. A new RT-LAMP-on-a-Chip Instrument for SARS-CoV-2 diagnostics. Microchem J 2022; 180:107600. [PMID: 35620142 PMCID: PMC9121651 DOI: 10.1016/j.microc.2022.107600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 02/08/2023]
Abstract
This work describes the development of a Point-of-Care (POC) Lab-on-a-Chip (LOC) instrument for diagnosis of SARS-CoV-2 by Reverse-Transcription Loop-mediated isothermal amplification (RT-LAMP). The hardware is based on a Raspberry Pi computer ($35), a video camera, an Arduino Nano microcontroller, a printed circuit board as a heater and a 3D printed housing. The chips were manufactured in polymethyl methacrylate (PMMA) using a CO2 laser cutting machine and sealed with a PCR optic plastic film. The chip temperature is precisely controlled by a proportional-integral-derivative (PID) algorithm. During the RT-LAMP amplifications the chip was maintained at ∼ (65.0 ± 0.1) °C for 25 minutes and 5 minutes cooling down, totaling a 30 minutes of reaction .The software interpretation occurs in less than a second. The chip design has four 25 µL chambers, two for clinical samples and two for positive and negative control-samples. The RT-LAMP master mix solution added in the chip chambers contains the pH indicator Phenol Red, that is pink (for pH ∼ 8.0) before amplification and becomes yellow (pH ∼ 6.0) if the genetic material is amplified. The RT-LAMP SARS-CoV-2 diagnostic was made by color image recognition using the OpenCV machine vision software library. The software was programmed to automatically distinguish the HSV color parameter distribution in each one of the four chip chambers. The instrument was successfully tested for SARS-CoV-2 diagnosis, in 22 clinic samples, 11 positives and 11 negatives, achieving an assertiveness of 86% when compared to the results obtained by RT-LAMP standard reactions performed in conventional PCR equipment.
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Affiliation(s)
- Geovani Torezin Mendonça
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Mateus Cassaboni Stracke
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Bruna de Oliveira Coelho
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | | | - Fabricio Klerynton Marchini
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Dalila Lucíola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Emilson Ribeiro Viana
- Research and Characterization of Nanomaterials and Nanodevices Laboratory (LPCA-NN), Physics Department, Federal University of Technology - Paraná, 7 de setembro 3165 Avenue, Curitiba, Paraná, Brazil
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Corresponding author
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Seyit M, Avci E, Yilmaz A, Kemanci A, Caliskan A, Ozen M, Oskay A, Aybek H, Türkcuer İ. Evaluation of the Diagnostic Value of Hematologic Parameters and Ratios in SARS-CoV-2 VOC-202012/01 Mutant Population. Cureus 2022; 14:e28285. [PMID: 36158396 PMCID: PMC9494022 DOI: 10.7759/cureus.28285] [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] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
Introduction In this study, we set out to study possible differences between individuals with and without VOC 202012/01 variant by using less costly complete blood count analytes and quickly analyzing the samples and ratios derived from these analytes. For this purpose, we assessed neutrophil, lymphocyte, platelet, and Red Blood Cell Distribution Width-Standard Deviation (RDW-SD) levels among complete blood count parameters (CBC) (identification and count of red blood cell, neutrophil, eosinophil, basophil, lymphocyte, monocyte, platelet) as well as the neutrophil-lymphocyte ratio (NLR) and platelet-lymphocyte ratio (PLR). Methods A retrospective cross-sectional study was performed over the course of two months (from May to June 2021) on 212 patients who presented to the emergency department of a tertiary hospital with Covid-19 symptoms and took SARS-CoV2 PCR and CBC tests. The polymerase chain reaction (PCR)-confirmed SARS-CoV2 positive patients and their hospitalization data were gathered from the public health management system. Their VOC-202012/01 mutation status was also confirmed by this system. Results RDW-SD, RDW, NLR, and PLR indexes, as well as C-reactive protein (CRP), and lactate dehydrogenase (LDH) values, were higher in the patients with VOC-202012/01 mutation (p<0.0001) than those without mutation, while hemoglobin and hematocrit counts and ratio, as well as eosinophil and lymphocyte counts, remained lower in the patients with mutation (p<0.0001). Conclusion NLR and RLP ratios derived from hematological parameters and models based on these ratios and RDW-SD are cheaper and more widely used. Our study suggests that the hematological analytes, the ratios obtained from these analytes, and the models created through these ratios in patients presenting to the ED with COVID-19-like symptoms and having positive reverse transcription polymerase chain reaction (RT-PCR) test results were significantly different in those with and without the VOC-202012/01 mutation. The bottom line is that they can serve as reliable predictors in the assessment of patients with the VOC-202012/01 mutation.
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Abdul Ghani MA, Nordin AN, Zulhairee M, Che Mohamad Nor A, Shihabuddin Ahmad Noorden M, Muhamad Atan MKF, Ab Rahim R, Mohd Zain Z. Portable Electrochemical Biosensors Based on Microcontrollers for Detection of Viruses: A Review. BIOSENSORS 2022; 12:bios12080666. [PMID: 36005062 PMCID: PMC9406062 DOI: 10.3390/bios12080666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
With the rise of zoonotic diseases in recent years, there is an urgent need for improved and more accessible screening and diagnostic methods to mitigate future outbreaks. The recent COVID-19 pandemic revealed an over-reliance on RT-PCR, a slow, costly and lab-based method for diagnostics. To better manage the pandemic, a high-throughput, rapid point-of-care device is needed for early detection and isolation of patients. Electrochemical biosensors offer a promising solution, as they can be used to perform on-site tests without the need for centralized labs, producing high-throughput and accurate measurements compared to rapid test kits. In this work, we detail important considerations for the use of electrochemical biosensors for the detection of respiratory viruses. Methods of enhancing signal outputs via amplification of the analyte, biorecognition of elements and modification of the transducer are also explained. The use of portable potentiostats and microfluidics chambers that create a miniature lab are also discussed in detail as an alternative to centralized laboratory settings. The state-of-the-art usage of portable potentiostats for detection of viruses is also elaborated and categorized according to detection technique: amperometry, voltammetry and electrochemical impedance spectroscopy. In terms of integration with microfluidics, RT-LAMP is identified as the preferred method for DNA amplification virus detection. RT-LAMP methods have shorter turnaround times compared to RT-PCR and do not require thermal cycling. Current applications of RT-LAMP for virus detection are also elaborated upon.
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Affiliation(s)
- Muhammad Afiq Abdul Ghani
- MEMS-VLSI Research Unit, Department of Electrical and Computer Engineering, Engineering Faculty, International Islamic University Malaysia, Kuala Lumpur 53100, Federal Territory of Kuala Lumpur, Malaysia
| | - Anis Nurashikin Nordin
- MEMS-VLSI Research Unit, Department of Electrical and Computer Engineering, Engineering Faculty, International Islamic University Malaysia, Kuala Lumpur 53100, Federal Territory of Kuala Lumpur, Malaysia
- Correspondence:
| | - Munirah Zulhairee
- Electrochemical Material and Sensor (EMaS) Research Group, Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam 40450, Selangor, Malaysia
| | - Adibah Che Mohamad Nor
- Faculty of Pharmacy, Universiti Teknologi MARA, Puncak Alam Campus, Bandar Puncak Alam 42300, Selangor, Malaysia
| | | | - Muhammad Khairul Faisal Muhamad Atan
- MEMS-VLSI Research Unit, Department of Electrical and Computer Engineering, Engineering Faculty, International Islamic University Malaysia, Kuala Lumpur 53100, Federal Territory of Kuala Lumpur, Malaysia
| | - Rosminazuin Ab Rahim
- MEMS-VLSI Research Unit, Department of Electrical and Computer Engineering, Engineering Faculty, International Islamic University Malaysia, Kuala Lumpur 53100, Federal Territory of Kuala Lumpur, Malaysia
| | - Zainiharyati Mohd Zain
- Electrochemical Material and Sensor (EMaS) Research Group, Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam 40450, Selangor, Malaysia
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Wang G, Wang L, Meng Z, Su X, Jia C, Qiao X, Pan S, Chen Y, Cheng Y, Zhu M. Visual Detection of COVID-19 from Materials Aspect. ADVANCED FIBER MATERIALS 2022; 4:1304-1333. [PMID: 35966612 PMCID: PMC9358106 DOI: 10.1007/s42765-022-00179-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 05/25/2023]
Abstract
ABSTRACT In the recent COVID-19 pandemic, World Health Organization emphasized that early detection is an effective strategy to reduce the spread of SARS-CoV-2 viruses. Several diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and lateral flow immunoassay (LFIA), have been applied based on the mechanism of specific recognition and binding of the probes to viruses or viral antigens. Although the remarkable progress, these methods still suffer from inadequate cellular materials or errors in the detection and sampling procedure of nasopharyngeal/oropharyngeal swab collection. Therefore, developing accurate, ultrafast, and visualized detection calls for more advanced materials and technology urgently to fight against the epidemic. In this review, we first summarize the current methodologies for SARS-CoV-2 diagnosis. Then, recent representative examples are introduced based on various output signals (e.g., colorimetric, fluorometric, electronic, acoustic). Finally, we discuss the limitations of the methods and provide our perspectives on priorities for future test development.
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Affiliation(s)
- Gang Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Le Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Zheyi Meng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Xiaolong Su
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Chao Jia
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Xiaolan Qiao
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Shaowu Pan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Yinjun Chen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Yanhua Cheng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
| | - Meifang Zhu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620 China
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Design and Analysis of Highly Sensitive LSPR-Based Metal–Insulator–Metal Nano-Discs as a Biosensor for Fast Detection of SARS-CoV-2. PHOTONICS 2022. [DOI: 10.3390/photonics9080542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
For over 2 years, the coronavirus has been the most urgent challenge to humanity, and the development of rapid and accurate detection methods is crucial to control these viruses. Here, a 3D FDTD simulation of Au/SiO2/Au metal–insulator–metal (MIM) nanostructures as a biosensor was performed. The strong coupling between the two plasmonic interfaces in the Au/SiO2/Au cavity helped us to obtain relatively higher sensitivity. The attachment of SARS-CoV-2 changed the refractive index, which was used to detect SARS-CoV-2. Due to the higher overlapping of plasmonic mode with the environment of nano-discs, a higher sensitivity of 312.8 nm/RIU was obtained. The peak wavelength of the proposed structure shifted by approximately 47 nm when the surrounding medium refractive index changed from 1.35 (no binding) to 1.5 (full binding). Consequently, the SPR peak intensity variation can be used as another sensing mechanism to detect SARS-CoV-2. Finally, the previously reported refractive index changes for various concentrations of the SARS-CoV-2 S-glycoprotein solution were used to evaluate the performance of the designed biosensor.
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Yin B, Wan X, Sohan ASMMF, Lin X. Microfluidics-Based POCT for SARS-CoV-2 Diagnostics. MICROMACHINES 2022; 13:mi13081238. [PMID: 36014162 PMCID: PMC9413395 DOI: 10.3390/mi13081238] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/30/2022] [Accepted: 07/30/2022] [Indexed: 11/17/2022]
Abstract
A microfluidic chip is a tiny reactor that can confine and flow a specific amount of fluid into channels of tens to thousands of microns as needed and can precisely control fluid flow, pressure, temperature, etc. Point-of-care testing (POCT) requires small equipment, has short testing cycles, and controls the process, allowing single or multiple laboratory facilities to simultaneously analyze biological samples and diagnose infectious diseases. In general, rapid detection and stage assessment of viral epidemics are essential to overcome pandemic situations and diagnose promptly. Therefore, combining microfluidic devices with POCT improves detection efficiency and convenience for viral disease SARS-CoV-2. At the same time, the POCT of microfluidic chips increases user accessibility, improves accuracy and sensitivity, shortens detection time, etc., which are beneficial in detecting SARS-CoV-2. This review shares recent advances in POCT-based testing for COVID-19 and how it is better suited to help diagnose in response to the ongoing pandemic.
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Affiliation(s)
- Binfeng Yin
- School of Mechanical Engineering, Yangzhou University, Yangzhou 225127, China; (X.W.); (A.S.M.M.F.S.)
- Correspondence: (B.Y.); (X.L.); Tel.: +86-189-1118-5500 (B.Y.); +86-182-2266-7931 (X.L.)
| | - Xinhua Wan
- School of Mechanical Engineering, Yangzhou University, Yangzhou 225127, China; (X.W.); (A.S.M.M.F.S.)
| | | | - Xiaodong Lin
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
- Correspondence: (B.Y.); (X.L.); Tel.: +86-189-1118-5500 (B.Y.); +86-182-2266-7931 (X.L.)
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Li YP, Cao XJ, Luo X, Xie TA, Liu WJ, Xie SM, Lin M, Guo XG. Evaluation of RT-LAMP Assay for Rapid Detection of SARS-CoV-2. Lab Med 2022; 54:56-64. [PMID: 35849098 PMCID: PMC9384514 DOI: 10.1093/labmed/lmac030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE To evaluate the accuracy of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in community or primary-care settings. METHOD We systematically searched the Web of Science, Embase, PubMed, and Cochrane Library databases. We conducted quality evaluation using ReviewManager software (version 5.0). We then used MetaDisc software (version 1.4) and Stata software (version 12.0) to build forest plots, along with a Deeks funnel plot and a bivariate boxplot for analysis. RESULT Overall, the sensitivity, specificity, and diagnostic odds ratio were 0.79, 0.97, and 328.18, respectively. The sensitivity for the subgroup with RNA extraction appeared to be higher, at 0.88 (0.86-0.90), compared to the subgroup without RNA extraction, at 0.50 (0.45-0.55), with no significant difference in specificity. CONCLUSION RT-LAMP assay exhibited high specificity regarding current SARS-CoV-2 infection. However, its overall sensitivity was relatively moderate. Extracting RNA was found to be beneficial in improving sensitivity.
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Affiliation(s)
| | | | - Xin Luo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Tian-Ao Xie
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Wan-Jun Liu
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Shi-Ming Xie
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Clinical Medicine, The First Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Min Lin
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Chinese and Western Medicine in Clinical Medicine, The Clinical School of Chinese and Western Medicine of Guangzhou Medical University, Guangzhou, China
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Chen X, Zhou Q, Tan Y, Wang R, Wu X, Liu J, Liu R, Wang S, Dong S. Nanoparticle-Based Lateral Flow Biosensor Integrated With Loop-Mediated Isothermal Amplification for Rapid and Visual Identification of Chlamydia trachomatis for Point-of-Care Use. Front Microbiol 2022; 13:914620. [PMID: 35903464 PMCID: PMC9318599 DOI: 10.3389/fmicb.2022.914620] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Chlamydial infection, caused by Chlamydia trachomatis, is the most common bacterial sexually transmitted infection and remains a major public health problem worldwide, particularly in underdeveloped regions. Developing a rapid and sensitive point-of-care (POC) testing for accurate screening of C. trachomatis infection is critical for earlier treatment to prevent transmission. In this study, a novel diagnostic assay, loop-mediated isothermal amplification integrated with gold nanoparticle-based lateral flow biosensor (LAMP-LFB), was devised and applied for diagnosis of C. trachomatis in clinical samples. A set of LAMP primers based on the ompA gene from 14 C. trachomatis serological variants (serovar A-K, L1, L2, L3) was successfully designed and used for the development of C. trachomatis-LAMP-LFB assay. The optimal reaction system can be performed at a constant temperature of 67°C for 35 min. The total assay process, including genomic DNA extraction (~15 min), LAMP reaction (35 min), and LFB readout (~2 min), could be finished within 60 min. The C. trachomatis-LAMP-LFB could detect down to 50 copies/ml, and the specificity was 100%, no cross-reactions with other pathogens were observed. Hence, our C. trachomatis-LAMP-LFB was a rapid, reliable, sensitive, cost-effective, and easy-to-operate assay, which could offer an attractive POC testing tool for chlamydial infection screening, especially in resource starvation settings.
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Kim D, Kim SJ, Kim YK, Kwon KT, Kim S. Clinical evaluation of an innovative isothermal amplification detection system for COVID-19 diagnosis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2578-2585. [PMID: 35748579 DOI: 10.1039/d2ay00815g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A pre-integrated system design intended for a point-of-care (POC) and sample-to-result diagnostic platform with nucleic acid amplification has been developed, which is equipment/electricity-free without any permanent instruments or manual sample processing. This semi-integrated system focuses on pandemic situations that are suitable for the Affordable, Sensitive, Specific, User-friendly, Robust and rapid, Equipment-free, and Deliverable to the end-user "ASSURED" concept recommended by the World Health Organization (WHO). Nucleic acid amplification is an essential rate-limiting factor in the performance of integrated systems that involve sample preparation and detection. The ORF1ab (RdRp) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been targeted by RT-LAMP optimization and evaluation using a commercial hot-pack as a heat source that successfully achieves a femto-scale (<6.8 × 102 copies per rxn) limit of detection (LOD) within 40 min (except for the RNA extraction step). Therefore, the prototype system was assessed using COVID-19-suspected clinical samples (eighty eight) and compared with the results of a commercial real-time reverse transcription polymerase chain reaction (RT-qPCR) assay (Allplex SARS-CoV-2 Assay kit (Seegene, Seoul, Republic of Korea)). These innovative approaches achieved over 95% sensitivity and specificity. In conclusion, the developed system using a hot-pack as a heat source is a promising tool that enables the rapid identification of infectious diseases in the real world.
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Affiliation(s)
- Dami Kim
- Philmedi R&D Center, Philmedi Incorporation, Seongnam, 13211, Republic of Korea
| | - Se Jin Kim
- Philmedi R&D Center, Philmedi Incorporation, Seongnam, 13211, Republic of Korea
| | - Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Division of Infectious Diseases, Daegu 41944, Republic of Korea
| | - Ki Tae Kwon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, 41404, Republic of Korea.
| | - Sanghyo Kim
- Philmedi R&D Center, Philmedi Incorporation, Seongnam, 13211, Republic of Korea
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea.
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Mannier C, Yoon JY. Progression of LAMP as a Result of the COVID-19 Pandemic: Is PCR Finally Rivaled? BIOSENSORS 2022; 12:bios12070492. [PMID: 35884295 PMCID: PMC9312731 DOI: 10.3390/bios12070492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 06/01/2023]
Abstract
Reflecting on the past three years and the coronavirus disease 19 (COVID-19) pandemic, varying global tactics offer insights into the most effective public-health responses. In the US, specifically, rapid and widespread testing was quickly prioritized to lower restrictions sooner. Essentially, only two types of COVID-19 diagnostic tests were publicly employed during the peak pandemic: the rapid antigen test and reverse transcription polymerase chain reaction (RT-PCR). However, neither test ideally suited the situation, as rapid antigen tests are far too inaccurate, and RT-PCR tests require skilled personnel and sophisticated equipment, leading to long wait times. Loop-mediated isothermal amplification (LAMP) is another exceptionally accurate nucleic acid amplification test (NAAT) that offers far quicker time to results. However, RT-LAMP COVID-19 tests have not been embraced as extensively as rapid antigen tests or RT-PCR. This review will investigate the performance of current RT-LAMP-based COVID-19 tests and summarize the reasons behind the hesitancy to embrace RT-LAMP instead of RT-PCR. We will also look at other LAMP platforms to explore possible improvements in the accuracy and portability of LAMP, which could be applied to COVID-19 diagnostics and future public-health outbreaks.
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