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Thippornchai N, Pengpanich S, Jaroenram W, Kosoltanapiwat N, Sukphopetch P, Kiatpathomchai W, Leaungwutiwong P. A colorimetric reverse-transcription loop-mediated isothermal amplification method targeting the L452R mutation to detect the Delta variant of SARS-CoV-2. Sci Rep 2024; 14:21961. [PMID: 39304686 DOI: 10.1038/s41598-024-72417-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 09/06/2024] [Indexed: 09/22/2024] Open
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered global difficulties for both individuals and economies, with new variants continuing to emerge. The Delta variant of SARS-CoV-2 remains most prevalent worldwide, and it affects the efficacy of coronavirus disease 2019 (COVID-19) vaccination. Expedited testing to detect the Delta variant of SARS-CoV-2 and monitor viral transmission is necessary. This study aimed to develop and evaluate a colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) technique targeting the L452R mutation in the S gene for the specific detection of the Delta variant. In the test, positivity was indicated as a color change from purple to yellow. The assay's 95% limit of detection was 57 copies per reaction for the L452R (U1355G)-specific standard plasmid. Using 126 clinical samples, our assay displayed 100% specificity, 97.06% sensitivity, and 98.41% accuracy in identifying the Delta variant of SARS-CoV-2 compared to real-time RT-PCR. To our knowledge, this is the first colorimetric RT-LAMP assay that can differentiate the Delta variant from its generic SARS-CoV-2, enabling it as an approach for studying COVID-19 demography and facilitating proper effective control measure establishment to fight against the reemerging variants of SARS-CoV-2 in the future.
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Affiliation(s)
- Narin Thippornchai
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Sukanya Pengpanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani, 12120, Thailand
| | - Wansadaj Jaroenram
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani, 12120, Thailand
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Passanesh Sukphopetch
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Wansika Kiatpathomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Rd., Klong Neung, Klong Luang, Pathum Thani, 12120, Thailand.
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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Ly YT, Leuko S, Moeller R. An overview of the bacterial microbiome of public transportation systems-risks, detection, and countermeasures. Front Public Health 2024; 12:1367324. [PMID: 38528857 PMCID: PMC10961368 DOI: 10.3389/fpubh.2024.1367324] [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: 01/08/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
When we humans travel, our microorganisms come along. These can be harmless but also pathogenic, and are spread by touching surfaces or breathing aerosols in the passenger cabins. As the pandemic with SARS-CoV-2 has shown, those environments display a risk for infection transmission. For a risk reduction, countermeasures such as wearing face masks and distancing were applied in many places, yet had a significant social impact. Nevertheless, the next pandemic will come and additional countermeasures that contribute to the risk reduction are needed to keep commuters safe and reduce the spread of microorganisms and pathogens, but also have as little impact as possible on the daily lives of commuters. This review describes the bacterial microbiome of subways around the world, which is mainly characterized by human-associated genera. We emphasize on healthcare-associated ESKAPE pathogens within public transport, introduce state-of-the art methods to detect common microbes and potential pathogens such as LAMP and next-generation sequencing. Further, we describe and discuss possible countermeasures that could be deployed in public transportation systems, as antimicrobial surfaces or air sterilization using plasma. Commuting in public transport can harbor risks of infection. Improving the safety of travelers can be achieved by effective detection methods, microbial reduction systems, but importantly by hand hygiene and common-sense hygiene guidelines.
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Affiliation(s)
| | | | - Ralf Moeller
- Department of Radiation Biology, Institute for Aerospace Medicine, German Aerospace Center, Cologne, Germany
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3
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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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4
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Pourakbari R, Gholami M, Shakerimoghaddam A, Khiavi FM, Mohammadimehr M, Khomartash MS. Comparison of RT-LAMP and RT-qPCR assays for detecting SARS-CoV-2 in the extracted RNA and direct swab samples. J Virol Methods 2024; 324:114871. [PMID: 38103738 DOI: 10.1016/j.jviromet.2023.114871] [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: 10/07/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infected patients is critical for infection control. Loop-mediated isothermal amplification (LAMP) has been demonstrated to be a rapid, simple, reliable, cost-effective and sensitive method to detect SARS-CoV-2 in a variety of samples in considerably less time than Real-Time PCR. In this study, we developed and optimized a rapid detection method for SARS-CoV-2 based on RT-LAMP method utilizing a specific primer set targeting the ORF1a gene and then examined its sensitivity and efficiency using a serially diluted viral RNA sample with a known concentration. Furthermore, the sensitivity of the RT-LAMP to detect SARS-CoV-2 in direct swab samples with varying Ct values were compared to a commercial molecular RT-qPCR based detection kit. According to our findings the optimal incubation time for RT-LAMP assay was 45 min. There was a complete agreement between RT-LAMP and RT-qPCR in diagnosing the viral genome in the diluted extracted RNA sample. However, it had a lower sensitivity (71%) to detect the viral genome in direct swab samples compared to RT-qPCR. In conclusion, due to its simplicity, rapidness, sensitivity, and specificity, RT-LAMP has tremendous potential as a point-of-care tool; nevertheless, more research is needed to utilize it for detecting SARS-CoV-2, particularly in direct swab samples.
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Affiliation(s)
- Ramin Pourakbari
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran.; Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Mohammad Gholami
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Ali Shakerimoghaddam
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran.; Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Farhad Motavalli Khiavi
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran.; Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Mojgan Mohammadimehr
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran
| | - Mehdi Shakouri Khomartash
- Infectious Diseases Research Center, Aja University of Medical Sciences, Tehran, Iran.; Medical Biotechnology Research Center, Aja University of Medical Sciences, Tehran, Iran..
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5
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Sritong N, Ngo WW, Ejendal KFK, Linnes JC. Development of an integrated sample amplification control for salivary point-of-care pathogen testing. Anal Chim Acta 2024; 1287:342072. [PMID: 38182338 DOI: 10.1016/j.aca.2023.342072] [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: 10/03/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed. RESULTS We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 min without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples. SIGNIFICANCE IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Winston Wei Ngo
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Karin F K Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA; Department of Public Health, Purdue University, West Lafayette, IN, USA.
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6
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Liu Y, Li Y, Hang Y, Wang L, Wang J, Bao N, Kim Y, Jang HW. Rapid assays of SARS-CoV-2 virus and noble biosensors by nanomaterials. NANO CONVERGENCE 2024; 11:2. [PMID: 38190075 PMCID: PMC10774473 DOI: 10.1186/s40580-023-00408-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024]
Abstract
The COVID-19 outbreak caused by SARS-CoV-2 in late 2019 has spread rapidly across the world to form a global epidemic of respiratory infectious diseases. Increased investigations on diagnostic tools are currently implemented to assist rapid identification of the virus because mass and rapid diagnosis might be the best way to prevent the outbreak of the virus. This critical review discusses the detection principles, fabrication techniques, and applications on the rapid detection of SARS-CoV-2 with three categories: rapid nuclear acid augmentation test, rapid immunoassay test and biosensors. Special efforts were put on enhancement of nanomaterials on biosensors for rapid, sensitive, and low-cost diagnostics of SARS-CoV-2 virus. Future developments are suggested regarding potential candidates in hospitals, clinics and laboratories for control and prevention of large-scale epidemic.
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Affiliation(s)
- Yang Liu
- School of Public Health, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
- Department of Materials Science and Engineering, Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
- NantongEgens Biotechnology Co., LTD, Nantong, 226019, Jiangsu, People's Republic of China
| | - Yilong Li
- School of Public Health, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Yuteng Hang
- School of Public Health, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Lei Wang
- NantongEgens Biotechnology Co., LTD, Nantong, 226019, Jiangsu, People's Republic of China
| | - Jinghan Wang
- Department of Materials Science and Engineering, Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ning Bao
- School of Public Health, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Youngeun Kim
- Department of Materials Science and Engineering, Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Ho Won Jang
- Department of Materials Science and Engineering, Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea.
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7
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Sritong N, Ngo WW, Ejendal KFK, Linnes JC. Development of an Integrated Sample Amplification Control for Salivary Point-of-Care Pathogen Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.03.23296477. [PMID: 37873363 PMCID: PMC10593008 DOI: 10.1101/2023.10.03.23296477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed. Results We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 minutes without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples. Significance IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Winston Wei Ngo
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Karin F. K. Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Jacqueline C. Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Department of Public Health, Purdue University, West Lafayette, IN, USA
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8
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Muhsin SA, He Y, Al-Amidie M, Sergovia K, Abdullah A, Wang Y, Alkorjia O, Hulsey RA, Hunter GL, Erdal ZK, Pletka RJ, George HS, Wan XF, Almasri M. A microfluidic biosensor architecture for the rapid detection of COVID-19. Anal Chim Acta 2023; 1275:341378. [PMID: 37524456 PMCID: PMC10251744 DOI: 10.1016/j.aca.2023.341378] [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: 03/26/2023] [Accepted: 05/15/2023] [Indexed: 08/02/2023]
Abstract
The lack of enough diagnostic capacity to detect severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has been one of the major challenges in the control the 2019 COVID pandemic; this led to significant delay in prompt treatment of COVID-19 patients or accurately estimate disease situation. Current methods for the diagnosis of SARS-COV-2 infection on clinical specimens (e.g. nasal swabs) include polymerase chain reaction (PCR) based methods, such as real-time reverse transcription (rRT) PCR, real-time reverse transcription loop-mediated isothermal amplification (rRT-LAMP), and immunoassay based methods, such as rapid antigen test (RAT). These conventional PCR methods excel in sensitivity and specificity but require a laboratory setting and typically take up to 6 h to obtain the results whereas RAT has a low sensitivity (typically at least 3000 TCID50/ml) although with the results with 15 min. We have developed a robust micro-electro-mechanical system (MEMS) based impedance biosensor fit for rapid and accurate detection of SARS-COV-2 of clinical samples in the field with minimal training. The biosensor consisted of three regions that enabled concentrating, trapping, and sensing the virus present in low quantities with high selectivity and sensitivity in 40 min using an electrode coated with a specific SARS-COV-2 antibody cross-linker mixture. Changes in the impedance value due to the binding of the SARS-COV-2 antigen to the antibody will indicate positive or negative result. The testing results showed that the biosensor's limit of detection (LoD) for detection of inactivated SARS-COV-2 antigen in phosphate buffer saline (PBS) was as low as 50 TCID50/ml. The biosensor specificity was confirmed using the influenza virus while the selectivity was confirmed using influenza polyclonal sera. Overall, the results showed that the biosensor is able to detect SARS-COV-2 in clinical samples (swabs) in 40 min with a sensitivity of 26 TCID50/ml.
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Affiliation(s)
- Sura A Muhsin
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Missouri, 411 S 6th St, Columbia, Mo, 65211, USA
| | - Ying He
- Center for Influenza and Emerging Infectious Diseases, Department of Molecular Microbiology and Immunology, School of Medicine, Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Muthana Al-Amidie
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Missouri, 411 S 6th St, Columbia, Mo, 65211, USA
| | - Karen Sergovia
- Center for Influenza and Emerging Infectious Diseases, Department of Molecular Microbiology and Immunology, School of Medicine, Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Amjed Abdullah
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Missouri, 411 S 6th St, Columbia, Mo, 65211, USA
| | - Yang Wang
- Center for Influenza and Emerging Infectious Diseases, Department of Molecular Microbiology and Immunology, School of Medicine, Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Omar Alkorjia
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Missouri, 411 S 6th St, Columbia, Mo, 65211, USA
| | - Robert A Hulsey
- Black and Veatch, 11401 Lamar, Overland Park, KS, 66211, USA
| | - Gary L Hunter
- Black and Veatch, 201 Brookfield Parkway, Suite 150, Greenville, SC, 29607, USA
| | - Zeynep K Erdal
- Black and Veatch, 201 Brookfield Parkway, Suite 150, Greenville, SC, 29607, USA
| | - Ryan J Pletka
- Black and Veatch, 2999 Oak Road, Suite 490, Walnut Creek, CA, 94597, USA
| | - Hyleme S George
- Black and Veatch, 11401 Lamar, Overland Park, KS, 66211, USA
| | - Xiu-Feng Wan
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Missouri, 411 S 6th St, Columbia, Mo, 65211, USA; Center for Influenza and Emerging Infectious Diseases, Department of Molecular Microbiology and Immunology, School of Medicine, Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
| | - Mahmoud Almasri
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Missouri, 411 S 6th St, Columbia, Mo, 65211, USA.
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Borah Slater K, Ahmad M, Poirier A, Stott A, Siedler BS, Brownsword M, Mehat J, Urbaniec J, Locker N, Zhao Y, La Ragione R, Silva SRP, McFadden J. Development of a loop-mediated isothermal amplification (LAMP)-based electrochemical test for rapid detection of SARS-CoV-2. iScience 2023; 26:107570. [PMID: 37664622 PMCID: PMC10470312 DOI: 10.1016/j.isci.2023.107570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/10/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Rapid, reliable, sensitive, portable, and accurate diagnostics are required to control disease outbreaks such as COVID-19 that pose an immense burden on human health and the global economy. Here we developed a loop-mediated isothermal amplification (LAMP)-based electrochemical test for the detection of SARS-CoV-2 that causes COVID-19. The test is based on the oxidation-reduction reaction between pyrophosphates (generated from positive LAMP reaction) and molybdate that is detected by cyclic voltammetry using inexpensive and disposable carbon screen printed electrodes. Our test showed higher sensitivity (detecting as low as 5.29 RNA copies/μL) compared to the conventional fluorescent reverse transcriptase (RT)-LAMP. We validated our tests using human serum and saliva spiked with SARS-CoV-2 RNA and clinical (saliva and nasal-pharyngeal) swab samples demonstrating 100% specificity and 93.33% sensitivity. Our assay provides a rapid, specific, and sensitive test with an electrochemical readout in less than 45 min that could be adapted for point-of-care settings.
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Affiliation(s)
- Khushboo Borah Slater
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Muhammad Ahmad
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Aurore Poirier
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - Ash Stott
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Bianca Sica Siedler
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Matthew Brownsword
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Jai Mehat
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Joanna Urbaniec
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nicolas Locker
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Yunlong Zhao
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Roberto La Ragione
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK
| | - S. Ravi P. Silva
- Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, UK
| | - Johnjoe McFadden
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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10
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Simon DS, Yew CW, Kumar VS. Multiplexed Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Nucleic Acid-Based Lateral Flow Dipstick as a Rapid Diagnostic Method to Detect SARS-CoV-2. Microorganisms 2023; 11:1233. [PMID: 37317207 PMCID: PMC10223058 DOI: 10.3390/microorganisms11051233] [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: 04/14/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
Due to the high reproduction rate of COVID-19, it is important to identify and isolate infected patients at the early stages of infection. The limitations of current diagnostic methods are speed, cost, and accuracy. Furthermore, new viral variants have emerged with higher rates of infectivity and mortality, many with mutations at various primer binding sites, which may evade detection via conventional PCR kits. Therefore, a rapid method that is sensitive, specific, and cost-effective is needed for a point-of-care molecular test. Accordingly, we developed a rapid molecular SARS-CoV-2 detection kit with high specificity and sensitivity, RT-PCR, taking advantage of the loop-mediated isothermal amplification (LAMP) technique. Four sets of six primers were designed based on conserved regions of the SARS-CoV-2 genome: two outer, two inner and two loop primers. Using the optimized protocol, SARS-CoV-2 genes were detected as quickly as 10 min but were most sensitive at 30 min, detecting as little as 100 copies of template DNA. We then coupled the RT-LAMP with a lateral flow dipstick (LFD) for multiplex detection. The LFD could detect two genic amplifications on a single strip, making it suitable for multiplexed detection. The development of a multiplexed RT-LAMP-LFD reaction on crude VTM samples would be suitable for the point-of-care diagnosis of COVID-19 in diagnostic laboratories as well as in private homes.
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Affiliation(s)
| | | | - Vijay Subbiah Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (D.S.S.); (C.-W.Y.)
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Wu Y, Liu Z, Mao S, Liu B, Tong Z. Identify the Virus-like Models for COVID-19 as Bio-Threats: Combining Phage Display, Spectral Detection and Algorithms Analysis. Int J Mol Sci 2023; 24:ijms24043209. [PMID: 36834622 PMCID: PMC9967019 DOI: 10.3390/ijms24043209] [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: 12/21/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The rapid identification and recognition of COVID-19 have been challenging since its outbreak. Multiple methods were developed to realize fast monitoring early to prevent and control the pandemic. In addition, it is difficult and unrealistic to apply the actual virus to study and research because of the highly infectious and pathogenic SARS-CoV-2. In this study, the virus-like models were designed and produced to replace the original virus as bio-threats. Three-dimensional excitation-emission matrix fluorescence and Raman spectroscopy were employed for differentiation and recognition among the produced bio-threats and other viruses, proteins, and bacteria. Combined with PCA and LDA analysis, the identification of the models for SARS-CoV-2 was achieved, reaching a correction of 88.9% and 96.3% after cross-validation, respectively. This idea might provide a possible pattern for detecting and controlling SARS-CoV-2 from the perspective of combining optics and algorithms, which could be applied in the early-warning system against COVID-19 or other bio-threats in the future.
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Affiliation(s)
- Yuting Wu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Zhiwei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Sihan Mao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Bing Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Zhaoyang Tong
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
- Correspondence:
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Wilner OI, Yesodi D, Weizmann Y. Point-of-care nucleic acid tests: assays and devices. NANOSCALE 2023; 15:942-952. [PMID: 36515009 DOI: 10.1039/d2nr05385c] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The COVID-19 pandemic (caused by the SARS_CoV_2 virus) has emphasized the need for quick, easy-to-operate, reliable, and affordable diagnostic tests and devices at the Point-of-Care (POC) for homes/fields/clinics. Such tests and devices will contribute significantly to the fight against the COVID-19 pandemic and any future infectious disease epidemic. Often, academic research studies and those from industry lack knowledge of each other's developments. Here, we introduced DNA Polymerase Chain Reaction (PCR) and isothermal amplification reactions and reviewed the current commercially available POC nucleic acid diagnostic devices. In addition, we reviewed the history and the recent advancements in an effort to develop reliable, quick, portable, cost-effective, and automatic point-of-care nucleic acid diagnostic devices, from sample to result. The purpose of this paper is to bridge the gap between academia and industry and to share important knowledge on this subject.
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Affiliation(s)
- Ofer I Wilner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Doron Yesodi
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Yossi Weizmann
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
- Ilse Katz Institute for Nanotechnology Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
- Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Aldossary AM, Tawfik EA, Altammami MA, Alquait AA, Booq RY, Sendy BK, Alarawi MS, Gojobori T, Altamimi AM, Alaifan TA, Albarrag AM, Alyamani EJ. Development and Validation of Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) as a Simple and Rapid Diagnostic Tool for SARS-CoV-2 Detection. Diagnostics (Basel) 2022; 12:diagnostics12092232. [PMID: 36140632 PMCID: PMC9498013 DOI: 10.3390/diagnostics12092232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 12/23/2022] Open
Abstract
Since the COVID-19 pandemic outbreak in the world, many countries have searched for quick diagnostic tools to detect the virus. There are many ways to design diagnostic assays; however, each may have its limitations. A quick, sensitive, specific, and simple approach is essential for highly rapidly transmitted infections, such as SARS-CoV-2. This study aimed to develop a rapid and cost-effective diagnostic tool using a one-step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) approach. The results were observed using the naked eye within 30–60 min using turbidity or colorimetric analysis. The sensitivity, specificity, and lowest limit of detection (LoD) for SARS-CoV-2 RNA against the RT-LAMP assay were assessed. This assay was also verified and validated against commercial quantitative RT-PCR used by health authorities in Saudi Arabia. Furthermore, a quick and direct sampling from the saliva, or buccal cavity, was applied after simple modification, using proteinase K and heating at 98 °C for 5 min to avoid routine RNA extraction. This rapid single-tube diagnostic tool detected COVID-19 with an accuracy rate of 95% for both genes (ORF1a and N) and an LoD for the ORF1a and N genes as 39 and 25 copies/reaction, respectively. It can be potentially used as a high-throughput national screening for different respiratory-based infections within the Middle East region, such as the MERS virus or major zoonotic pathogens such as Mycobacterium paratuberculosis and Brucella spp., particularly in remote and rural areas where lab equipment is limited.
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Affiliation(s)
- Ahmad M. Aldossary
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Essam A. Tawfik
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Musaad A. Altammami
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Azzam A. Alquait
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Rayan Y. Booq
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Bandar K. Sendy
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
| | - Mohammed S. Alarawi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Asmaa M. Altamimi
- Public Health Laboratory, Public Health Authority, Riyadh 13354, Saudi Arabia
| | - Taghreed A. Alaifan
- Public Health Laboratory, Public Health Authority, Riyadh 13354, Saudi Arabia
| | - Ahmed M. Albarrag
- Public Health Laboratory, Public Health Authority, Riyadh 13354, Saudi Arabia
| | - Essam J. Alyamani
- National Center of Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 12354, Saudi Arabia
- Correspondence:
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