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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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2
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Hong S, Park J, Bok J, Cho E, Rhee J. Assessment of measurement accuracy of amplified DNA using a colorimetric loop-mediated isothermal amplification assay. Biotechniques 2024; 76:114-118. [PMID: 38131320 DOI: 10.2144/btn-2023-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
A colorimetric loop-mediated isothermal amplification assay detects changes in pH during amplification based on color changes at a constant temperature. Currently, various studies have focused on developing and assessing molecular point-of-care testing instruments. In this study, we evaluated amplified DNA concentrations measured using the colorimetric LAMP assay of the 1POT™ Professional device (1drop Inc, Korea). Results of the 1POT analysis of clinical samples were compared with measurements obtained from the Qubit™ 4 and NanoDrop™ 2000 devices (both from Thermo Fisher Scientific, MA, USA). These results showed a correlation of 0.98 (95% CI: 0.96-0.99) and 0.96 (95% CI: 0.92-0.98) between 1POT and the Qubit and NanoDrop. 1POT can measure amplified DNA accurately and is suitable for on-site molecular diagnostics.
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Affiliation(s)
- Seongsoo Hong
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Jeongho Park
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Jaekyung Bok
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Euna Cho
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Joowon Rhee
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
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3
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Nawab M, Riaz SK, Ismail E, Ahamed A, Tariq A, Malik MFA, Qusty NF, Bantun F, Slama P, Umair M, Haque S, Bonilla-Aldana DK, Rodriguez-Morales AJ. Integrated approach for detection of SARS-CoV-2 and its variant by utilizing LAMP and ARMS-PCR. Ann Clin Microbiol Antimicrob 2024; 23:11. [PMID: 38303011 PMCID: PMC10836012 DOI: 10.1186/s12941-023-00665-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024] Open
Abstract
Global impact of COVID-19 pandemic has heightened the urgency for efficient virus detection and identification of variants such as the Q57H mutation. Early and efficient detection of SARS-CoV-2 among densely populated developing countries is paramount objective. Although RT-PCR assays offer accuracy, however, dependence on expansive kits and availability of allied health resources pose an immense challenge for developing countries. In the current study, RT-LAMP based detection of SARS-Cov-2 with subsequent confirmation of Q57H variant through ARMS-PCR was performed. Among the 212 collected samples, 134 yielded positive results, while 78 tested negative using RT-LAMP. Oropharyngeal swabs of suspected individuals were collected and processed for viral RNA isolation. Isolated viral RNA was processed further by using either commercially available WarmStart Master Mix or our in house developed LAMP master mix separately. Subsequently, the end results of each specimen were evaluated by colorimetry. For LAMP assays, primers targeting three genes (ORF1ab, N and S) were designed using PrimerExplorer software. Interestingly, pooling of these three genes in single reaction tube increased sensitivity (95.5%) and specificity (93.5%) of LAMP assay. SARS-CoV-2 positive specimens were screened further for Q57H mutation using ARMS-PCR. Based on amplicon size variation, later confirmed by sequencing, our data showed 18.5% samples positive for Q57H mutation. Hence, these findings strongly advocate use of RT-LAMP-based assay for SARS-CoV-2 screening within suspected general population. Furthermore, ARMS-PCR also provides an efficient mean to detect prevalent mutations against SARS-Cov-2.
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Affiliation(s)
- Maryam Nawab
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Syeda Kiran Riaz
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Eiman Ismail
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Alfar Ahamed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aaysha Tariq
- Molecular Diagnostic Unit, Clinical Pathology Department, PAEC General Hospital, Islamabad, Pakistan
| | | | - Naeem F Qusty
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, PO Box 7607, Makkah, Al Abdeyah, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, 61300, Czech Republic
| | - Massab Umair
- Department of Virology, National Institute of Health (NIH), Islamabad, Pakistan
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102 2801, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, 13306, United Arab Emirates
| | | | - Alfonso J Rodriguez-Morales
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102 2801, Lebanon
- Master Program on Clinical Epidemiology and Biostatistics, Faculty of Health Sciences, Universidad Científica del Sur, Lima, 15046, Peru
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chilmi S, Kesuma TA, Wibawa PA, Susianti H, Iskandar A, Wulanda IA, Wahono CS, Handono K. The Long-Term Serological Profile of CoronaVac Vaccine Based on Comorbidities and History of SARS-CoV-2 Infection in Indonesia. Jpn J Infect Dis 2024; 77:40-46. [PMID: 37914294 DOI: 10.7883/yoken.jjid.2023.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
CoronaVac is one of the most widely administered COVID-19 vaccines in Indonesia. Previous studies have documented its effectiveness in protecting against COVID-19 in several countries. This study aimed to assess the long-term immunogenicity of CoronaVac in individuals with comorbidities or a history of SARS-CoV-2 infection. The total anti-N Ig and anti-S-RBD Ig levels at 7 and 26 weeks after the second dose of vaccine were documented in 194 health workers. The participants were divided into groups based on their comorbidities and history of SARS-CoV-2 infection. The antibody titers did not differ according to comorbidity status or history of SARS-CoV-2 infection. The total anti-nucleocapsid Ig and total anti-S-RBD Ig levels were significantly lower in individuals without a history of SARS-CoV-2 infection. These results indicate that CoronaVac induces a lower specific antibody response than natural infection and less long-term immunogenicity.
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Affiliation(s)
- Syahrul Chilmi
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Tanti Adelia Kesuma
- Residency of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Purwa Adrianta Wibawa
- Residency of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Hani Susianti
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Agustin Iskandar
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Indah Adhita Wulanda
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Caesarius Singgih Wahono
- Department of Internal Medicine, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Kusworini Handono
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
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Alsaeed M, Alhamid G, Tombuloglu H, Kabanja JH, Karagoz A, Tombuloglu G, Rabaan AA, Al-Suhaimi E, Unver T. Ultrasensitive and fast detection of SARS-CoV-2 using RT-LAMP without pH-dependent dye. Funct Integr Genomics 2024; 24:16. [PMID: 38242999 DOI: 10.1007/s10142-024-01297-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
This study investigates the performance of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the colorimetric detection of SARS-CoV-2 using fluorometric dye, namely, calcein. The detection limit (LoD) with the N-ID1 primer set resulted in superior performance, corresponding to ~ 2 copies/reaction or ~ 0.1 copies/μL of the RNA sample. The color development can be observed by the naked eye, using an ultraviolet (UV) transilluminator or a hand-UV light without the requirement of expensive devices. The average time-to-reaction (TTR) value was 26.2 min in high-copy number samples, while it was about 50 min in rRT-PCR. A mobile application was proposed to quantify the positive and negative results based on the three-color spaces (RGB, Lab, and HSB). Compared to rRT-PCR (n = 67), this assay allows fast and sensitive visual detection of SARS-CoV-2, with high sensitivity (90.9%), selectivity (100%), and accuracy (94.03%). Besides, the assay was sensitive regardless of variants. Since this assay uses a fluorescent dye for visual observation, it can be easily adapted in RT-LAMP assays with high sensitivity. Thus, it can be utilized in low-source centers and field testing such as conferences, sports meetings, refugee camps, companies, and schools.
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Affiliation(s)
- Moneerah Alsaeed
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Galyah Alhamid
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.
| | - Juma H Kabanja
- Department of Pathology & Laboratory Medicine, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Aysel Karagoz
- Quality Assurance Department, Turk Pharmaceutical and Serum Ind. Inc., Ankara, Turkey
| | - Guzin Tombuloglu
- Department of Biophysics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan
| | - Ebtesam Al-Suhaimi
- Vice Presidency for Scientific Research and Innovation, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Turgay Unver
- Ficus Biotechnology, Ankara, Turkey
- Faculty of Engineering, Ostim Technical University, 06374, Ankara, Turkey
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Das D, Lin CW, Chuang HS. On-chip screening of SARS-CoV-2 cDNA by LAMP-integrated rotational diffusometry. Talanta 2024; 267:125253. [PMID: 37776805 DOI: 10.1016/j.talanta.2023.125253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/10/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023]
Abstract
The unprecedented pandemic has raised the demand for prompt, precise, and large-scale virus detection techniques to control the transmission of contagious illnesses. In this study, a loop-mediated isothermal amplification (LAMP) based on-chip platform was developed to address this challenge using rotational diffusometry and functionalized Janus particles. A recombinant plasmid containing a cDNA sequence of the SARS-CoV-2 non-structural protein 2 (nsp2) gene was employed here as a proof-of-concept for COVID-19 detection. Specifically, designed primers and the functionalized Janus particles were simultaneously loaded on a microfluidic chip to perform the LAMP reaction on a hot plate. The optimal Janus particle concentrations for diffusometric analysis were thoroughly validated, and the performance of the on-chip LAMP reaction was assessed using thermal image analysis. Utilization of the highly sensitive rotational diffusometry achieved a limit of detection of 1 pg/μL in just 10 min with a sample volume of 20 μL. Our method delivered a tenfold higher sensitivity than the conventional method by utilizing only half of its usual required time. Overall, this study proposes a potential nucleic acid (NA) amplification device to aid the rapid diagnosis of various diseases by modifying the primers for different target genes.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung, 413, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, 701, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan, 701, Taiwan.
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8
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Ho M, Sathishkumar N, Sklavounos AA, Sun J, Yang I, Nichols KP, Wheeler AR. Digital microfluidics with distance-based detection - a new approach for nucleic acid diagnostics. Lab Chip 2023; 24:63-73. [PMID: 37987330 DOI: 10.1039/d3lc00683b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
There is great enthusiasm for using loop-mediated isothermal amplification (LAMP) in point-of-care nucleic acid amplification tests (POC NAATs), as an alternative to PCR. While isothermal amplification techniques like LAMP eliminate the need for rapid temperature cycling in a portable format, these systems are still plagued by requirements for dedicated optical detection apparatus for analysis and manual off-chip sample processing. Here, we developed a new microfluidic system for LAMP-based POC NAATs to address these limitations. The new system combines digital microfluidics (DMF) with distance-based detection (DBD) for direct signal readout. This is the first report of the use of (i) LAMP or (ii) DMF with DBD - thus, we describe a number of characterization steps taken to determine optimal combinations of reagents, materials, and processes for reliable operation. For example, DBD was found to be quite sensitive to background signals from low molecular weight LAMP products; thus, a Capto™ adhere bead-based clean-up procedure was developed to isolate the desirable high-molecular-weight products for analysis. The new method was validated by application to detection of SARS-CoV-2 in saliva. The method was able to distinguish between saliva containing no virus, saliva containing a low viral load (104 genome copies per mL), and saliva containing a high viral load (108 copies per mL), all in an automated system that does not require detection apparatus for analysis. We propose that the combination of DMF with distance-based detection may be a powerful one for implementing a variety of POC NAATs or for other applications in the future.
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Affiliation(s)
- Man Ho
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - N Sathishkumar
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Jianxian Sun
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Ivy Yang
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | | | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
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Botto MM, Borsellini A, Lamers MH. A four-point molecular handover during Okazaki maturation. Nat Struct Mol Biol 2023; 30:1505-1515. [PMID: 37620586 DOI: 10.1038/s41594-023-01071-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 07/17/2023] [Indexed: 08/26/2023]
Abstract
DNA replication introduces thousands of RNA primers into the lagging strand that need to be removed for replication to be completed. In Escherichia coli when the replicative DNA polymerase Pol IIIα terminates at a previously synthesized RNA primer, DNA Pol I takes over and continues DNA synthesis while displacing the downstream RNA primer. The displaced primer is subsequently excised by an endonuclease, followed by the sealing of the nick by a DNA ligase. Yet how the sequential actions of Pol IIIα, Pol I polymerase, Pol I endonuclease and DNA ligase are coordinated is poorly defined. Here we show that each enzymatic activity prepares the DNA substrate for the next activity, creating an efficient four-point molecular handover. The cryogenic-electron microscopy structure of Pol I bound to a DNA substrate with both an upstream and downstream primer reveals how it displaces the primer in a manner analogous to the monomeric helicases. Moreover, we find that in addition to its flap-directed nuclease activity, the endonuclease domain of Pol I also specifically cuts at the RNA-DNA junction, thus marking the end of the RNA primer and creating a 5' end that is a suitable substrate for the ligase activity of LigA once all RNA has been removed.
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Affiliation(s)
- Margherita M Botto
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands
- Department of Molecular and Cellular Biology, Geneva University, Geneva, Switzerland
| | - Alessandro Borsellini
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands
- Department of Structural Biology, Human Technopole, Milan, Italy
| | - Meindert H Lamers
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands.
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10
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Poirier AC, Riaño Moreno RD, Takaindisa L, Carpenter J, Mehat JW, Haddon A, Rohaim MA, Williams C, Burkhart P, Conlon C, Wilson M, McClumpha M, Stedman A, Cordoni G, Branavan M, Tharmakulasingam M, Chaudhry NS, Locker N, Fernando A, Balachandran W, Bullen M, Collins N, Rimer D, Horton DL, Munir M, La Ragione RM. VIDIIA Hunter diagnostic platform: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostics approved for medical use in the UK. Front Mol Biosci 2023; 10:1144001. [PMID: 37842636 PMCID: PMC10572354 DOI: 10.3389/fmolb.2023.1144001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: Accurate and rapid diagnostics paired with effective tracking and tracing systems are key to halting the spread of infectious diseases, limiting the emergence of new variants and to monitor vaccine efficacy. The current gold standard test (RT-qPCR) for COVID-19 is highly accurate and sensitive, but is time-consuming, and requires expensive specialised, lab-based equipment. Methods: Herein, we report on the development of a SARS-CoV-2 (COVID-19) rapid and inexpensive diagnostic platform that relies on a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and a portable smart diagnostic device. Automated image acquisition and an Artificial Intelligence (AI) deep learning model embedded in the Virus Hunter 6 (VH6) device allow to remove any subjectivity in the interpretation of results. The VH6 device is also linked to a smartphone companion application that registers patients for swab collection and manages the entire process, thus ensuring tests are traced and data securely stored. Results: Our designed AI-implemented diagnostic platform recognises the nucleocapsid protein gene of SARS-CoV-2 with high analytical sensitivity and specificity. A total of 752 NHS patient samples, 367 confirmed positives for coronavirus disease (COVID-19) and 385 negatives, were used for the development and validation of the test and the AI-assisted platform. The smart diagnostic platform was then used to test 150 positive clinical samples covering a dynamic range of clinically meaningful viral loads and 250 negative samples. When compared to RT-qPCR, our AI-assisted diagnostics platform was shown to be reliable, highly specific (100%) and sensitive (98-100% depending on viral load) with a limit of detection of 1.4 copies of RNA per µL in 30 min. Using this data, our CE-IVD and MHRA approved test and associated diagnostic platform has been approved for medical use in the United Kingdom under the UK Health Security Agency's Medical Devices (Coronavirus Test Device Approvals, CTDA) Regulations 2022. Laboratory and in-silico data presented here also indicates that the VIDIIA diagnostic platform is able to detect the main variants of concern in the United Kingdom (September 2023). Discussion: This system could provide an efficient, time and cost-effective platform to diagnose SARS-CoV-2 and other infectious diseases in resource-limited settings.
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Affiliation(s)
- Aurore C. Poirier
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | | | - Leona Takaindisa
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Jessie Carpenter
- VIDIIA Ltd., Surrey Technology Centre, Guildford, United Kingdom
| | - Jai W. Mehat
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
| | - Abi Haddon
- Berkshire and Surrey Pathology Services, Molecular Diagnostics, Royal Surrey County Hospital, Guildford, United Kingdom
| | - Mohammed A. Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom
| | - Craig Williams
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom
| | - Peter Burkhart
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom
| | - Chris Conlon
- GB Electronics (UK) Ltd, Worthing, United Kingdom
| | | | | | - Anna Stedman
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Guido Cordoni
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Manoharanehru Branavan
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom
| | | | - Nouman S. Chaudhry
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom
| | - Nicolas Locker
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
| | - Anil Fernando
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom
| | - Wamadeva Balachandran
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark Bullen
- GB Electronics (UK) Ltd, Worthing, United Kingdom
| | - Nadine Collins
- Berkshire and Surrey Pathology Services, Molecular Diagnostics, Royal Surrey County Hospital, Guildford, United Kingdom
| | - David Rimer
- VIDIIA Ltd., Surrey Technology Centre, Guildford, United Kingdom
| | - Daniel L. Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom
| | - Roberto M. La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
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11
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Hongjaisee S, Kham-Kjing N, Musikul P, Daengkaokhew W, Kongson N, Guntala R, Jaiyapan N, Kline E, Panpradist N, Ngo-Giang-Huong N, Khamduang W. A Single-Tube Colorimetric Loop-Mediated Isothermal Amplification for Rapid Detection of SARS-CoV-2 RNA. Diagnostics (Basel) 2023; 13:3040. [PMID: 37835783 PMCID: PMC10572433 DOI: 10.3390/diagnostics13193040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Since SARS-CoV-2 is a highly transmissible virus, a rapid and accurate diagnostic method is necessary to prevent virus spread. We aimed to develop and evaluate a new rapid colorimetric reverse transcription loop--mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection in a single closed tube. Nasopharyngeal and throat swabs collected from at-risk individuals testing for SARS-CoV-2 were used to assess the sensitivity and specificity of a new RT-LAMP assay against a commercial qRT-PCR assay. Total RNA extracts were submitted to the RT-LAMP reaction under optimal conditions and amplified at 65 °C for 30 min using three sets of specific primers targeting the nucleocapsid gene. The reaction was detected using two different indicator dyes, hydroxynaphthol blue (HNB) and cresol red. A total of 82 samples were used for detection with HNB and 94 samples with cresol red, and results were compared with the qRT-PCR assay. The sensitivity of the RT-LAMP-based HNB assay was 92.1% and the specificity was 93.2%. The sensitivity of the RT-LAMP-based cresol red assay was 80.3%, and the specificity was 97%. This colorimetric feature makes this assay highly accessible, low-cost, and user-friendly, which can be deployed for massive scale-up and rapid diagnosis of SARS-CoV-2 infection, particularly in low-resource settings.
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Affiliation(s)
- Sayamon Hongjaisee
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand;
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
| | - Nang Kham-Kjing
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Piyagorn Musikul
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Wannaporn Daengkaokhew
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Nuntita Kongson
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | | | - Nitipoom Jaiyapan
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
| | - Enos Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA;
| | - Nuttada Panpradist
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA;
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Nicole Ngo-Giang-Huong
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle (MIVEGEC), Agropolis University Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Pour le Développement (IRD), 34394 Montpellier, France
- International Joint Laboratory PRESTO, Chiang Mai 50200, Thailand
| | - Woottichai Khamduang
- LUCENT International Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (N.P.); (N.N.-G.-H.)
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (P.M.); (W.D.); (N.K.); (N.J.)
- International Joint Laboratory PRESTO, Chiang Mai 50200, Thailand
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12
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Jee H, Choi M, Park IS, Lee J, Jang WS, Lim CS. Simple Point-of-Care Nucleic Acid Amplification Test for Rapid SARS-CoV-2 Infection Diagnosis. Diagnostics (Basel) 2023; 13:3001. [PMID: 37761368 PMCID: PMC10529522 DOI: 10.3390/diagnostics13183001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
After three years of the SARS-CoV-2 pandemic, the demand for developing field-deployable point-of-care (PoC) molecular diagnostic tests has increased. Although RT-qPCR is the molecular diagnostic gold standard and is accurate, it is not readily applied to point-of-care testing (POCT). Meanwhile, rapid diagnostic kits have the disadvantage of low sensitivity. Recently, rapid isothermal nucleic acid amplification technology has emerged as an alternative for rapid diagnosis. Here, we developed a rapid SARS-CoV-2 reverse transcription loop-mediated isothermal amplification (RT-LAMP)-lateral flow assay (LFA) kit. This kit includes a Chelex-100/boiling nucleic acid extraction device and a one-step amplification detection apparatus capable of performing the entire process, from RNA extraction to detection, and diagnosing SARS-CoV-2 infection within 40 min without contamination. The detection limits of the rapid SARS-CoV-2 RT-LAMP-LFA kit were 100 plaque-forming units (PFUs) mL-1 and 10-1 PFU mL-1 for RNA samples extracted using the Chelex-100/boiling nucleic acid extraction device and commercial AdvansureTM E3 system, respectively. The sensitivity and specificity of the rapid SARS-CoV-2 RT-LAMP-LFA kit were 97.8% and 100%, respectively. Our SARS-CoV-2 RT-LAMP-LFA kit exhibited high sensitivity and specificity within 40 min without requiring laboratory instruments, suggesting that the kit could be used as a rapid POC molecular diagnostic test for SARS-CoV-2.
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Affiliation(s)
- Hyunseul Jee
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea; (H.J.); (M.C.); (I.S.P.); (J.L.)
| | - Minkyeong Choi
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea; (H.J.); (M.C.); (I.S.P.); (J.L.)
| | - In Su Park
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea; (H.J.); (M.C.); (I.S.P.); (J.L.)
| | - Junmin Lee
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea; (H.J.); (M.C.); (I.S.P.); (J.L.)
| | - Woong Sik Jang
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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13
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Singh M, Misra CS, Bindal G, Rangu SS, Rath D. CRISPR-Cas12a assisted specific detection of mpox virus. J Med Virol 2023; 95:e28974. [PMID: 37515526 DOI: 10.1002/jmv.28974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023]
Abstract
Mpox virus, a member of genus Orthopoxvirus, causes rash and flu-like symptoms in humans. In the recent global outbreak, it was reported from several geographical areas that have not historically reported mpox. Point of care, sensitive and specific mpox diagnostic assays are critical in checking the spread of the disease. We have developed a clustered regularly interspaced short palindromic repeats associated Cas12a nuclease-based assay for detecting mpox virus. Mpox specific conserved sequences were identified in polA (E9L) gene which differ by a single nucleotide polymorphism (SNP) from all the viruses present in the genus Orthopoxvirus. This SNP was exploited in our assay to specifically distinguish mpox virus from other related orthopox viruses with a limit of detection of 1 copy/μl in 30 min. The assay exhibits a sensitive and specific detection of mpox virus which can prove to be of practical value for its surveillance in areas infected with multiple orthopox viruses, especially in hotspots of mpox virus infections.
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Affiliation(s)
- Mandeep Singh
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, India
| | | | - Gargi Bindal
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | | | - Devashish Rath
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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14
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Cabral KMDS, Baptista RCG, Castineiras TMPP, Tanuri A, Carneiro FA, Almeida MDS, Montero-Lomeli M. Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assay. Braz J Infect Dis 2023; 27:102790. [PMID: 37478898 PMCID: PMC10391658 DOI: 10.1016/j.bjid.2023.102790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/02/2023] [Accepted: 07/04/2023] [Indexed: 07/23/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic demanded rapid diagnosis to isolate new COVID-19 cases and prevent disease transmission. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) rapidly became the gold standard for diagnosis. However, due to the high cost and delay of the results, other types of diagnosis were implemented, such as COVID-19 Ag Rapid Tests and Reverse Transcription Technique followed by Loop-Mediated isothermal Amplification (RT-LAMP). In this work, we validated the use of RT-LAMP in saliva samples rather than nasopharyngeal swabs, as the collection is more comfortable. First, we selected 5 primer sets based on the limit of detection for SARS-CoV-2 RNA, then validated their sensitivity and specificity in patient samples. A total of 117 samples were analyzed by fluorometric RT-LAMP and compared with qRT-PCR results. Our results show that the use of a high-sensitive primer ORF1-a, together with a low-sensitive primer set Gene E (time to threshold of 22.9 and 36.4 minutes, respectively, using 200 copies of viral RNA), achieved sensitivity in purified RNA from saliva samples of 95.2% (95% CI 76.1‒99.8) with 90.5% specificity (95% CI 69.6‒98.8) (n = 42).As RNA purification increases the turnaround time, we tested the outcome of RT-LAMP utilizing raw saliva samples without purification. The test achieved a sensitivity of 81.8% (95% CI 59.7‒94.8) and a specificity of 90.9% (95% CI 70.8‒98.8). As a result, the accuracy of 92.9% (95% CI 80.5‒98.5) in purified RNA-saliva samples was lowered to an acceptable level of 86.4% (95% CI 72.6‒94.8) in raw saliva. Although mass vaccination has been implemented, new strains and low vaccination progress helped to spread COVID-19. This study shows that it is feasible to track new COVID-19 cases in a large population with the use of raw saliva as sample in RT-LAMP assay which yields accurate results and offers a less invasive test.
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Affiliation(s)
- Kátia Maria Dos Santos Cabral
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Bioquímica Médica-Leopoldo de Meis, Rio de Janeiro, RJ, Brazil; Centro Nacional de Biologia Estrutural e Bioimagem, Plataforma Avançada de Biomoléculas, Rio de Janeiro, RJ, Brazil
| | - Ramon Cid Gismonti Baptista
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Bioquímica Médica-Leopoldo de Meis, Rio de Janeiro, RJ, Brazil
| | | | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia, Departamento de Genética, Rio de Janeiro, RJ, Brazil
| | - Fabiana Avila Carneiro
- Centro de Pesquisa de Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brazil; Núcleo de Pesquisa (Numpex-Bio), Campus Duque de Caxias Professor Geraldo Cidade, Duque de Caxias, RJ, Brazil
| | - Marcius da Silva Almeida
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Bioquímica Médica-Leopoldo de Meis, Rio de Janeiro, RJ, Brazil; Centro Nacional de Biologia Estrutural e Bioimagem, Plataforma Avançada de Biomoléculas, Rio de Janeiro, RJ, Brazil
| | - Monica Montero-Lomeli
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Bioquímica Médica-Leopoldo de Meis, Rio de Janeiro, RJ, Brazil.
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15
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Tomichan R, Sharma A, Akash K, Siddiqui AA, Dubey A, Upadhyay TK, Kumar D, Pandey S, Nagraik R. Insight of smart biosensors for COVID-19: A review. LUMINESCENCE 2023; 38:1102-1110. [PMID: 36577837 PMCID: PMC9880657 DOI: 10.1002/bio.4430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
The review discusses the diagnostic application of biosensors as point-of-care devices in the COVID-19 pandemic. Biosensors are important analytical tools that can be used for the robust and effective detection of infectious diseases in real-time. In this current scenario, the utilization of smart, efficient biosensors for COVID-19 detection is increasing and we have included a few smart biosensors such as smart and intelligent based biosensors, plasmonic biosensors, field effect transistor (FET) biosensors, smart optical biosensors, surface enhanced Raman scattering (SERS) biosensor, screen printed electrode (SPE)-based biosensor, molecular imprinted polymer (MIP)-based biosensor, MXene-based biosensor and metal-organic frame smart sensor. Their significance as well as the benefits and drawbacks of each kind of smart sensor are mentioned in depth. Furthermore, we have compiled a list of various biosensors which have been developed across the globe for COVID-19 and have shown promise as commercial detection devices. Significant challenges in the development of effective diagnostic methods are discussed and recommendations have been made for better diagnostic outcomes to manage the ongoing pandemic effectively.
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Affiliation(s)
- Rosemary Tomichan
- Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
| | - Avinash Sharma
- Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
| | - K. Akash
- Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
| | - Adeeb Ahmad Siddiqui
- Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
| | - Amit Dubey
- Computational Chemistry and Drug Discovery DivisionQuanta Calculus Pvt. LtdKushinagarUttar PradeshIndia
- Department of Pharmacology, Saveetha Dental College and HospitalSaveetha Institute of Medical and Technical SciencesChennaiTamil NaduIndia
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences, Animal Cell Culture and Immunobiochemistry LabParul UniversityVadodaraGujaratIndia
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical SciencesShoolini UniversitySolanHimachal PradeshIndia
| | - Sadanand Pandey
- Department of Chemistry, College of Natural SciencesYeungnam UniversityGyeongsanGyeongbukSouth Korea
| | - Rupak Nagraik
- Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
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16
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Bahlmann NA, Mautner L, Hoyos M, Sallard E, Berger C, Dangel A, Jönsson F, Fischer JC, Kreppel F, Zhang W, Esposito I, Bölke E, Baiker A, Ehrhardt A. In Vitro Analysis of the Effect of SARS-CoV-2 Non-VOC and four Variants of Concern on MHC-Class-I Expression on Calu-3 and Caco-2 Cells. Genes (Basel) 2023; 14:1348. [PMID: 37510253 PMCID: PMC10378856 DOI: 10.3390/genes14071348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
As the MHC-I-pathway is key to antigen presentation to cytotoxic T-cells and, therefore, recognition by the host adaptive immune system, we hypothesized that SARS-CoV-2 including its Variants of Concern (VOCs), influences MHC-I expression on epithelial cell surfaces as an immune evasion strategy. We conducted an in vitro time course experiment with the human airway epithelial cell line Calu-3 and the human colorectal adenocarcinoma cell line Caco-2. Cells were infected with SARS-CoV-2 strains non-VOC/B.1.1, Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, and Delta/B.1.617.2. At 2, 24, 48 and 72 h post-infection we performed RT-qPCR to track viral replication. Simultaneously, we performed intracellular staining with a serum of a double-vaccinated healthy adult containing a high amount of spike protein antibody. In flow cytometry experiments, we differentiated between infected (spike protein positive) and bystander (spike protein negative) cells. To compare their HLA expression levels, cells were stained extracellularly with anti-HLA-A-IgG and anti-HLA-B,C-IgG. While HLA-A expression was stable on infected Calu-3 cells for all variants, it increased to different degrees on bystander cells in samples infected with VOCs Beta, Gamma, Delta, or non-VOC over the time course analyzed. In contrast, HLA-A levels were stable in bystander Calu-3 cells in samples infected with the Alpha variant. The upregulation of MHC-I on spike protein negative bystander cells in Calu-3 cell cultures infected with Beta, Gamma, Delta, and partly non-VOC might suggest that infected cells are still capable of secreting inflammatory cytokines like type-I interferons stimulating the MHC-I expression on bystander cells. In comparison, there was no distinct effect on HLA expression level on Caco-2 cells of any of the VOCs or non-VOC. Further investigations of the full range of immune evasion strategies of SARS-CoV-2 variants are warranted.
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Affiliation(s)
- Nora A Bahlmann
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Lena Mautner
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Mona Hoyos
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Erwan Sallard
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Carola Berger
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Alexandra Dangel
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Franziska Jönsson
- Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Johannes C Fischer
- Institute for Transplant Diagnostics and Cell Therapeutics, Heinrich-Heine-University, 40204 Duesseldorf, Germany
| | - Florian Kreppel
- Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Wenli Zhang
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Irene Esposito
- Institute of Pathology, Heinrich Heine University and University Hospital, 40204 Duesseldorf, Germany
| | - Edwin Bölke
- Department of Radiation Oncology, Heinrich-Heine-University, 40204 Duesseldorf, Germany
| | - Armin Baiker
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Anja Ehrhardt
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
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17
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Barboza VDS, Domingues WB, de Souza TT, Collares TV, Seixas FK, Pacheco BS, Sousa FSS, Oliveira TL, de Lima M, de Pereira CMP, Spilki FR, Giongo JL, Vaucher RDA. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay as a rapid molecular diagnostic tool for COVID-19 in healthcare workers. J Clin Virol Plus 2023; 3:100134. [PMID: 36742065 PMCID: PMC9891106 DOI: 10.1016/j.jcvp.2023.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/19/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023] Open
Abstract
In December 2019, the Chinese Center for Disease Control (CDC of China) reported an outbreak of pneumonia in the city of Wuhan (Hubei province, China) that haunted the world, resulting in a global pandemic. This outbreak was caused by a betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several of these cases have been observed in healthcare professionals working in hospitals and providing care on the pandemic's frontline. In the present study, nasopharyngeal swab samples of healthcare workers were used to assess the performance of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay and subsequently compared with the real-time reverse-transcription quantitative PCR (RT-qPCR) method. Thus, in this study, we validated a method for detecting SARS-CoV-2 based on RT-LAMP that can be used to diagnose these workers. The methodology used was based on analyzing the sensitivity, specificity, evaluation of the detection limit, and cross-reaction with other respiratory viruses. The agreement was estimated using a dispersion diagram designed using the Bland-Altman method. A total of 100 clinical specimens of nasopharyngeal swabs were collected from symptomatic and asymptomatic healthcare workers in Pelotas, Brazil, during the SARS-CoV-2 outbreak. RT-LAMP assay, it was possible to detect SARS-CoV-2 in 96.7% of the healthcare professionals tested using the E gene and N gene primers approximately and 100% for the gene of human β-actin. The observed agreement was considered excellent for the primer set of the E and N genes (k = 0.957 and k = 0.896), respectively. The sensitivity of the RT-LAMP assay was positive for the primer set of the E gene, detected to approximately 2 copies per reaction. For the primer set of the N gene, the assay was possible to verify an LoD of approximately 253 copies per reaction. After executing the RT-LAMP assay, no positive reactions were observed for any of the virus respiratory tested. Therefore, we conclude that RT-LAMP is effective for rapid molecular diagnosis during the COVID-19 outbreak period in healthcare professionals.
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Affiliation(s)
- Victor dos Santos Barboza
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-organismos, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - William Borges Domingues
- Laboratório de Genômica Estrutural, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Thobias Toniolo de Souza
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-organismos, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tiago Veiras Collares
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fabiana Kommling Seixas
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Bruna Silveira Pacheco
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fernanda Severo Sabedra Sousa
- Laboratório de Biotecnologia do Câncer, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Thaís Larré Oliveira
- Laboratório de Vacinologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Marcelo de Lima
- Laboratório de Virologia e Imunologia, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | | | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Janice Luehring Giongo
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-organismos, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Rodrigo de Almeida Vaucher
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-organismos, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil,Corresponding author
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Zhang Y, Clarke SP, Wu H, Li W, Zhou C, Lin K, Wang J, Wang J, Liang Y, Wang X, Wang L. A comprehensive overview on the transmission, pathogenesis, diagnosis, treatment, and prevention of SARS-CoV-2. J Med Virol 2023; 95:e28776. [PMID: 37212261 DOI: 10.1002/jmv.28776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) is a single positive-strand RNA virus that is responsible for the current pandemic that the world has been facing since 2019. The primary route of transmission of SARS-CoV-2 is through respiratory tract transmission. However, other transmission routes such as fecal-oral, vertical transmission, and aerosol-eye also exist. In addition, it has been found that the pathogenesis of this virus involves the binding of the virus's S protein to its host cell surface receptor angiotensin-converting enzyme 2, which results in the subsequent membrane fusion that is required for SARS-CoV-2 to replicate and complete its entire life. The clinical symptoms of patients infected with SARS-CoV-2 can range from asymptomatic to severe. The most common symptoms seen include fever, dry cough, and fatigue. Once these symptoms are observed, a nucleic acid test is done using reverse transcription-polymerase chain reaction. This currently serves as the main confirmatory tool for COVID-19. Despite the fact that no cure has been found for SARS-CoV-2, prevention methods such as vaccines, specific facial mask, and social distancing have proven to be quite effective. It is imperative to have a complete understanding of the transmission and pathogenesis of this virus. To effectively develop new drugs as well as diagnostic tools, more knowledge about this virus would be needed.
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Affiliation(s)
- Yiting Zhang
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | | | - Huanwu Wu
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Wenli Li
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Chang Zhou
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Kang Lin
- Department of Basic Medical Sciences, Morphological Experimental Center, Anhui Medical University, Hefei, Anhui, China
| | - Jiawen Wang
- Department of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Jinzhi Wang
- Department of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Ying Liang
- Department of The Second Clinical School of Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Xin Wang
- Department of Chemistry, Anhui Medical University, Hefei, Anhui, China
| | - Linding Wang
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
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20
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Kim HN, Lee J, Yoon SY, Jang WS, Lim CS. Rapid Detection of Mycobacterium Tuberculosis Using a Novel Point-of-Care BZ TB/NTM NALF Assay: Integrating LAMP and LFIA Technologies. Diagnostics (Basel) 2023; 13:diagnostics13081497. [PMID: 37189598 DOI: 10.3390/diagnostics13081497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Tuberculosis (TB) is one of the leading causes of infectious mortality from a single infectious agent, Mycobacterium tuberculosis (MTB). This study evaluated the performance of the newly developed BZ TB/NTM NALF assay, which integrated loop-mediated isothermal amplification and lateral flow immunochromatographic assay technologies, for the detection of MTB. A total of 80 MTB-positive samples and 115 MTB-negative samples were collected, all of which were confirmed by TB real-time PCR (RT-PCR) using either AdvanSureTM TB/NTM RT-PCR Kit or Xpert® MTB/RIF Assay. The performance of the BZ TB/NTM NALF assay was evaluated by calculating its sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) in comparison to those of the RT-PCR methods. Compared to the RT-PCR, the sensitivity, specificity, PPV, and NPV of BZ TB/NTM NALF assay were 98.7%, 99.1%, 98.7%, and 99.1%, respectively. The concordance rate between BZ TB/NTM NALF and RT-PCR was 99.0%. Rapid and simple detection of MTB is essential for global case detection and further elimination of TB. The performance of the BZ TB/NTM NALF Assay is acceptable with a high concordance with RT-PCR, indicating that it is reliable for use in a low-resource environment.
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Affiliation(s)
- Ha Nui Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Junmin Lee
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Soo-Young Yoon
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Woong Sik Jang
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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21
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Jee H, Park S, Lee J, Lim CS, Jang WS. Comparative Clinical Evaluation of a Novel FluA/FluB/SARS-CoV-2 Multiplex LAMP and Commercial FluA/FluB/SARS-CoV-2/RSV RT-qPCR Assays. Diagnostics (Basel) 2023; 13:diagnostics13081432. [PMID: 37189533 DOI: 10.3390/diagnostics13081432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/04/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023] Open
Abstract
Influenza and coronaviruses cause highly contagious respiratory diseases that cause millions of deaths worldwide. Public health measures implemented during the current coronavirus disease (COVID-19) pandemic have gradually reduced influenza circulation worldwide. As COVID-19 measures have relaxed, it is necessary to monitor and control seasonal influenza during this COVID-19 pandemic. In particular, the development of rapid and accurate diagnostic methods for influenza and COVID-19 is of paramount importance because both diseases have significant public health and economic impacts. To address this, we developed a multi-loop-mediated isothermal amplification (LAMP) kit capable of simultaneously detecting influenza A/B and SARS-CoV-2. The kit was optimized by testing various ratios of primer sets for influenza A/B (FluA/FluB) and SARS-CoV-2 and internal control (IC). The FluA/FluB/SARS-CoV-2 multiplex LAMP assay showed 100% specificity for uninfected clinical samples and sensitivities of 90.6%, 86.89%, and 98.96% for LAMP kits against influenza A, influenza B, and SARS-CoV-2 clinical samples, respectively. Finally, the attribute agreement analysis for clinical tests indicated substantial agreement between the multiplex FluA/FluB/SARS-CoV-2/IC LAMP and commercial AllplexTM SARS-CoV-2/FluA/FluB/RSV assays.
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Affiliation(s)
- Hyunseul Jee
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Seoyeon Park
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Junmin Lee
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Woong Sik Jang
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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22
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Ganesh S, Dhinakaran AK, Premnath P, Venkatakrishnan K, Tan B. Label-Free Saliva Test for Rapid Detection of Coronavirus Using Nanosensor-Enabled SERS. Bioengineering (Basel) 2023; 10:bioengineering10030391. [PMID: 36978782 PMCID: PMC10045265 DOI: 10.3390/bioengineering10030391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/14/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
The recent COVID-19 pandemic has highlighted the inadequacies of existing diagnostic techniques and the need for rapid and accurate diagnostic systems. Although molecular tests such as RT-PCR are the gold standard, they cannot be employed as point-of-care testing systems. Hence, a rapid, noninvasive diagnostic technique such as Surface-enhanced Raman scattering (SERS) is a promising analytical technique for rapid molecular or viral diagnosis. Here, we have designed a SERS- based test to rapidly diagnose SARS-CoV-2 from saliva. Physical methods synthesized the nanostructured sensor. It significantly increased the detection specificity and sensitivity by ~ten copies/mL of viral RNA (~femtomolar concentration of nucleic acids). Our technique combines the multiplexing capability of SERS with the sensitivity of novel nanostructures to detect whole virus particles and infection-associated antibodies. We have demonstrated the feasibility of the test with saliva samples from individuals who tested positive for SARS-CoV-2 with a specificity of 95%. The SERS-based test provides a promising breakthrough in detecting potential mutations that may come up with time while also preparing the world to deal with other pandemics in the future with rapid response and very accurate results.
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Affiliation(s)
- Swarna Ganesh
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Ashok Kumar Dhinakaran
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Priyatha Premnath
- Department of biomedical engineering, College of Engineering and Applied Sciences, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Nanocharacterization Laboratory, Department of Aerospace Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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24
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Song M, Hong S, Lee LP. Multiplexed Ultrasensitive Sample-to-Answer RT-LAMP Chip for the Identification of SARS-CoV-2 and Influenza Viruses. Adv Mater 2023; 35:e2207138. [PMID: 36398425 DOI: 10.1002/adma.202207138] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Prompt on-site diagnosis of SARS-CoV-2 with other respiratory infections will have minimized the global impact of the COVID-19 pandemic through rapid, effective management. However, no such multiplex point-of-care (POC) chip has satisfied a suitable sensitivity of gold-standard nucleic acid amplification tests (NAATs). Here, a rapid multiplexed ultrasensitive sample-to-answer loop-mediated isothermal amplification (MUSAL) chip operated by simple LED-driven photothermal amplification to detect six targets from single-swab sampling is presented. First, the MUSAL chip allows ultrafast on-chip sample preparation with ≈500-fold preconcentration at a rate of 1.2 mL min-1 . Second, the chip enables contamination-free amplification using autonomous target elution into on-chip reagents by photothermal activation. Finally, the chip accomplishes multiplexed on-chip diagnostics of SARS-CoV-2 and influenza viruses with a limit of detection (LoD) of 0.5 copies µL-1 . The rapid, ultrasensitive, cost-effective sample-to-answer chip with a multiplex capability will allow timely management of various pandemics situations that may be faced shortly.
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Affiliation(s)
- Minsun Song
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - SoonGweon Hong
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, Gyeonggi-do, 16419, Republic of Korea
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25
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Weber L, Mautner L, Hoyos M, Ehrhardt A, Baiker A, Bachmann HS. Effect of farnesyltransferase inhibitors on SARS-CoV-2. J Glob Antimicrob Resist 2023; 32:164-166. [PMID: 36462736 PMCID: PMC9711904 DOI: 10.1016/j.jgar.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/06/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
OBJECTIVES The emergence of SARS-CoV-2 in 2019 led to a severe pandemic situation. Treatment options are limited, and the efficacy of vaccines decreases due to mutations in SARS-CoV-2 strains. Therefore, new treatment options are urgently needed, and computational compound screenings are used to predict drugs quickly. One of these screenings revealed farnesyltransferase inhibitors (FTIs) as potential candidates. METHODS SARS-CoV-2 infected Calu-3 cells were treated with lonafarnib and tipifarnib and fold change viral replication of SARS-CoV-2 was measured using RT-qPCR. Furthermore, morphological changes, like CPE formation, were evaluated. Effects on Calu-3 cells were analyzed using MTT assay. RESULTS We demonstrated that the FTIs lonafarnib and tipifarnib have an effect on SARS-CoV-2 Wildtype and the Delta variant. Both FTIs dose-dependently reduced morphological changes and the formation of cytopathic effects in SARS-CoV-2 infected Calu-3 cells. The effect of the FTIs on Omicron needs to be further elucidated because of inefficient viral replication. CONCLUSIONS The FTI lonafarnib and tipifarnib might be effective drugs against different SARS-CoV-2 strains.
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Affiliation(s)
- Lea Weber
- Institute of Pharmacology and Toxicology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Lena Mautner
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Oberschleißheim, Germany
| | - Mona Hoyos
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Oberschleißheim, Germany
| | - Anja Ehrhardt
- Virology and Microbiology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Armin Baiker
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Oberschleißheim, Germany
| | - Hagen Sjard Bachmann
- Institute of Pharmacology and Toxicology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany.
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26
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Tarim EA, Oksuz C, Karakuzu B, Appak O, Sayiner AA, Tekin HC. Electromechanical RT-LAMP device for portable SARS-CoV-2 detection. Talanta 2023; 254:124190. [PMID: 36521325 PMCID: PMC9733968 DOI: 10.1016/j.talanta.2022.124190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Rapid point-of-care tests for infectious diseases are essential, especially in pandemic conditions. We have developed a point-of-care electromechanical device to detect SARS-CoV-2 viral RNA using the reverse-transcription loop-mediated isothermal amplification (RT-LAMP) principle. The developed device can detect SARS-CoV-2 viral RNA down to 103 copies/mL and from a low amount of sample volumes (2 μL) in less than an hour of standalone operation without the need for professional labor and equipment. Integrated Peltier elements in the device keep the sample at a constant temperature, and an integrated camera allows automated monitoring of LAMP reaction in a stirring sample by using colorimetric analysis of unfocused sample images in the hue/saturation/value color space. This palm-fitting, portable and low-cost device does not require a fully focused sample image for analysis, and the operation could be stopped automatically through image analysis when the positive test results are obtained. Hence, viral infections can be detected with the portable device produced without the need for long, expensive, and labor-intensive tests and equipment, which can make the viral tests disseminated at the point-of-care.
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Affiliation(s)
- E. Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
| | - Cemre Oksuz
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
| | - Betul Karakuzu
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
| | - Ozgur Appak
- Department of Medical Microbiology, Dokuz Eylul University, Faculty of Medicine, Izmir 35330, Turkey
| | - Ayca Arzu Sayiner
- Department of Medical Microbiology, Dokuz Eylul University, Faculty of Medicine, Izmir 35330, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey,METU MEMS Center, Ankara 06520, Turkey,Corresponding author. Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
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Chavda VP, Valu DD, Parikh PK, Tiwari N, Chhipa AS, Shukla S, Patel SS, Balar PC, Paiva-Santos AC, Patravale V. Conventional and Novel Diagnostic Tools for the Diagnosis of Emerging SARS-CoV-2 Variants. Vaccines (Basel) 2023; 11:vaccines11020374. [PMID: 36851252 PMCID: PMC9960989 DOI: 10.3390/vaccines11020374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Accurate identification at an early stage of infection is critical for effective care of any infectious disease. The "coronavirus disease 2019 (COVID-19)" outbreak, caused by the virus "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)", corresponds to the current and global pandemic, characterized by several developing variants, many of which are classified as variants of concern (VOCs) by the "World Health Organization (WHO, Geneva, Switzerland)". The primary diagnosis of infection is made using either the molecular technique of RT-PCR, which detects parts of the viral genome's RNA, or immunodiagnostic procedures, which identify viral proteins or antibodies generated by the host. As the demand for the RT-PCR test grew fast, several inexperienced producers joined the market with innovative kits, and an increasing number of laboratories joined the diagnostic field, rendering the test results increasingly prone to mistakes. It is difficult to determine how the outcomes of one unnoticed result could influence decisions about patient quarantine and social isolation, particularly when the patients themselves are health care providers. The development of point-of-care testing helps in the rapid in-field diagnosis of the disease, and such testing can also be used as a bedside monitor for mapping the progression of the disease in critical patients. In this review, we have provided the readers with available molecular diagnostic techniques and their pitfalls in detecting emerging VOCs of SARS-CoV-2, and lastly, we have discussed AI-ML- and nanotechnology-based smart diagnostic techniques for SARS-CoV-2 detection.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
- Correspondence: (V.P.C.); or (V.P.)
| | - Disha D. Valu
- Formulation and Drug Product Development, Biopharma Division, Intas Pharmaceutical Ltd., 3000-548 Moraiya, Ahmedabad 380054, Gujarat, India
| | - Palak K. Parikh
- Department of Pharmaceutical Chemistry and Quality Assurance, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Nikita Tiwari
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
| | - Abu Sufiyan Chhipa
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India
| | - Somanshi Shukla
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
| | - Snehal S. Patel
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India
| | - Pankti C. Balar
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548 Coimbra, Portugal
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
- Correspondence: (V.P.C.); or (V.P.)
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28
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Li S, Guo W, Xiao M, Chen Y, Luo X, Xu W, Zhou J, Wang J. Rapid and Sensitive Diagnosis of COVID-19 Using an Electricity-Free Self-Testing System. Biosensors (Basel) 2023; 13:180. [PMID: 36831946 PMCID: PMC9953845 DOI: 10.3390/bios13020180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Rapid and sensitive detection of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for early diagnosis and effective treatment. Nucleic acid testing has been considered the gold standard method for the diagnosis of COVID-19 for its high sensitivity and specificity. However, the polymerase chain reaction (PCR)-based method in the central lab requires expensive equipment and well-trained personnel, which makes it difficult to be used in resource-limited settings. It highlights the need for a sensitive and simple assay that allows potential patients to detect SARS-CoV-2 by themselves. Here, we developed an electricity-free self-testing system based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) that allows for rapid and accurate detection of SARS-CoV-2. Our system employs a heating bag as the heat source, and a 3D-printed box filled with phase change material (PCM) that successfully regulates the temperature for the RT-LAMP. The colorimetric method could be completed in 40 min and the results could be read out by the naked eye. A ratiometric measurement for exact readout was also incorporated to improve the detection accuracy of the system. This self-testing system is a promising tool for point-of-care testing (POCT) that enables rapid and sensitive diagnosis of SARS-CoV-2 in the real world and will improve the current COVID-19 screening efforts for control and mitigation of the pandemic.
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Affiliation(s)
- Sheng Li
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Wenlong Guo
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Minmin Xiao
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yulin Chen
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xinyi Luo
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Wenfei Xu
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Jianhua Zhou
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiasi Wang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
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29
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Marchini A, Petrillo M, Parrish A, Buttinger G, Tavazzi S, Querci M, Betsou F, Elsinga G, Medema G, Abdelrahman T, Gawlik B, Corbisier P. New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants. Viruses 2023; 15:206. [PMID: 36680246 PMCID: PMC9863853 DOI: 10.3390/v15010206] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/05/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets of genetic changes that confer to the virus higher transmissibility and ability to evade existing immunity. The continuous evolution of SARS-CoV-2 may pose challenges for current treatment options and diagnostic tools. In this study, we have first evaluated the performance of the 14 WHO-recommended real-time reverse transcription (RT)-PCR assays currently in use for the detection of SARS-CoV-2 and found that only one assay has reduced performance against Omicron. We then developed a new duplex real-time RT-PCR assay based on the amplification of two ultra-conserved elements present within the SARS-CoV-2 genome. The new duplex assay successfully detects all of the tested SARS-CoV-2 variants of concern (including Omicron sub-lineages BA.4 and BA.5) from both clinical and wastewater samples with high sensitivity and specificity. The assay also functions as a one-step droplet digital RT-PCR assay. This new assay, in addition to clinical testing, could be adopted in surveillance programs for the routine monitoring of SARS-CoV-2's presence in a population in wastewater samples. Positive results with our assay in conjunction with negative results from an Omicron-specific assay may provide timely indication of the emergence of a novel SARS-CoV-2 variant in a certain community and thereby aid public health interventions.
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Affiliation(s)
- Antonio Marchini
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium
| | | | - Amy Parrish
- Department of Microbiology, Laboratoire National de Santé, 3583 Dudelange, Luxembourg
| | - Gerhard Buttinger
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium
| | - Simona Tavazzi
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy
| | - Maddalena Querci
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy
| | - Fay Betsou
- Department of Microbiology, Laboratoire National de Santé, 3583 Dudelange, Luxembourg
- Biological Resource Center of Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Goffe Elsinga
- KWR Water Research Institute, 3433 PE Nieuwegein, The Netherlands
| | - Gertjan Medema
- KWR Water Research Institute, 3433 PE Nieuwegein, The Netherlands
| | - Tamir Abdelrahman
- Department of Microbiology, Laboratoire National de Santé, 3583 Dudelange, Luxembourg
| | - Bernd Gawlik
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy
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30
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Maryam S, Ul Haq I, Yahya G, Ul Haq M, Algammal AM, Saber S, Cavalu S. COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2. Front Cell Infect Microbiol 2023; 12:978643. [PMID: 36683701 PMCID: PMC9854263 DOI: 10.3389/fcimb.2022.978643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
- Department of Physical Chemistry and Polymers Technology, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mehboob Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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31
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Tripathy S, Agarkar T, Talukdar A, Sengupta M, Kumar A, Ghosh S. Evaluation of indirect sequence-specific magneto-extraction-aided LAMP for fluorescence and electrochemical SARS-CoV-2 nucleic acid detection. Talanta 2023; 252:123809. [PMID: 35985192 PMCID: PMC9373715 DOI: 10.1016/j.talanta.2022.123809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 12/17/2022]
Abstract
Nucleic acid amplification tests (NAATs) such as quantitative real-time reverse transcriptase PCR (qRT-PCR) or isothermal NAATs (iNAATs) such as loop-mediated isothermal amplification (LAMP) require pure nucleic acid free of any polymerase inhibitors as its substrate. This in turn, warrants the use of spin-column mediated extraction with centralized high-speed centrifuges. Additionally, the utilization of centralized real-time fluorescence readout and TaqMan-like molecular probes in qRT-PCR and real-time LAMP add cost and restrict their deployment. To circumvent these disadvantages, we report a novel sample-to-answer workflow comprising an indirect sequence-specific magneto-extraction (also referred to as magnetocapture, magneto-preconcentration, or magneto-enrichment) for detecting SARS-CoV-2 nucleic acid. It was followed by in situ fluorescence or electrochemical LAMP. After in silico validation of the approach's sequence selectivity against SARS-CoV-2 variants of concern, the comparative performance of indirect and direct magnetocapture in detecting SARS-CoV-2 nucleic acid in the presence of excess host nucleic acid or serum was probed. After proven superior, the sensitivity of the indirect sequence-specific magnetocapture in conjunction with electrochemical LAMP was investigated. In each case, its sensitivity was assessed through the detection of clinically relevant 102 and 103 copies of target nucleic acid. Overall, a highly specific nucleic acid detection method was established that can be accommodated for either centralized real-time SYBR-based fluorescence LAMP or portable electrochemical LAMP.
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32
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Li Y, Kim H, Ju Y, Park Y, Kang T, Yong D, Park HG. Ultrasensitive Isothermal Detection of SARS-CoV-2 Based on Self-Priming Hairpin-Utilized Amplification of the G-Rich Sequence. Anal Chem 2022; 94:17448-17455. [PMID: 36480911 PMCID: PMC9743493 DOI: 10.1021/acs.analchem.2c03442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
The outbreak of the novel coronavirus disease 2019 (COVID-19) pandemic induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of fatalities all over the world. Unquestionably, the effective and timely testing for infected individuals is the most imperative for the prevention of the ongoing pandemic. Herein, a new method was established for detecting SARS-CoV-2 based on the self-priming hairpin-utilized isothermal amplification of the G-rich sequence (SHIAG). In this strategy, the target RNA binding to the hairpin probe (HP) was uniquely devised to lead to the self-priming-mediated extension followed by the continuously repeated nicking and extension reactions, consequently generating abundant G-rich sequences from the intended reaction capable of producing fluorescence signals upon specifically interacting with thioflavin T (ThT). Based on the unique isothermal design concept, we successfully identified SARS-CoV-2 genomic RNA (gRNA) as low as 0.19 fM with excellent selectivity by applying only a single HP and further verified its practical diagnostic capability by reliably testing a total of 100 clinical specimens for COVID-19 with 100% clinical sensitivity and specificity. This study would provide notable insights into the design and evolution of new isothermal strategies for the sensitive and facile detection of SARS-CoV-2 under resource constraints.
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Affiliation(s)
- Yan Li
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Hansol Kim
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Yong Ju
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Yeonkyung Park
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea
Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu,
Daejeon34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan
University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do16419,
Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and
Research Institute of Bacterial Resistance, Yonsei University College of
Medicine, Seoul03722, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
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34
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Fernandes Q, Inchakalody VP, Merhi M, Mestiri S, Taib N, Moustafa Abo El-Ella D, Bedhiafi T, Raza A, Al-Zaidan L, Mohsen MO, Yousuf Al-Nesf MA, Hssain AA, Yassine HM, Bachmann MF, Uddin S, Dermime S. Emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis, therapeutics and vaccines. Ann Med 2022; 54:524-540. [PMID: 35132910 PMCID: PMC8843115 DOI: 10.1080/07853890.2022.2031274] [Citation(s) in RCA: 188] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The emergence of novel and evolving variants of SARS-CoV-2 has fostered the need for change in the form of newer and more adaptive diagnostic methods for the detection of SARS-CoV-2 infections. On the other hand, developing rapid and sensitive diagnostic technologies is now more challenging due to emerging variants and varying symptoms exhibited among the infected individuals. In addition to this, vaccines remain the major mainstay of prevention and protection against infection. Novel vaccines and drugs are constantly being developed to unleash an immune response for the robust targeting of SARS-CoV-2 and its associated variants. In this review, we provide an updated perspective on the current challenges posed by the emergence of novel SARS-CoV-2 mutants/variants and the evolution of diagnostic techniques to enable their detection. In addition, we also discuss the development, formulation, working mechanisms, advantages, and drawbacks of some of the most used vaccines/therapeutic drugs and their subsequent immunological impact.Key messageThe emergence of novel variants of the SARS-CoV-2 in the past couple of months, highlights one of the primary challenges in the diagnostics, treatment, as well as vaccine development against the virus.Advancements in SARS-CoV-2 detection include nucleic acid based, antigen and immuno- assay-based and antibody-based detection methodologies for efficient, robust, and quick testing; while advancements in COVID-19 preventive and therapeutic strategies include novel antiviral and immunomodulatory drugs and SARS-CoV-2 targeted vaccines.The varied COVID-19 vaccine platforms and the immune responses induced by each one of them as well as their ability to battle post-vaccination infections have all been discussed in this review.
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Affiliation(s)
- Queenie Fernandes
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,College of Medicine, Qatar University, Doha, Qatar
| | - Varghese Philipose Inchakalody
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Dina Moustafa Abo El-Ella
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Takwa Bedhiafi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Lobna Al-Zaidan
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Mona O Mohsen
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Department of Biomedical Research, Immunology RIA, University of Bern, Bern, Switzerland
| | | | - Ali Ait Hssain
- Medical Intensive Care Unit, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | | | - Martin F Bachmann
- Department of Biomedical Research, Immunology RIA, University of Bern, Bern, Switzerland.,Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
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Mary Vermi Aizza Corpuz, Antonio Buonerba, Tiziano Zarra, Shadi W. Hasan, Gregory V. Korshin, Vincenzo Belgiorno, Vincenzo Naddeo. Advances in virus detection methods for wastewater-based epidemiological applications. Case Studies in Chemical and Environmental Engineering 2022; 6. [PMID: 37520925 PMCID: PMC9339091 DOI: 10.1016/j.cscee.2022.100238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 06/08/2023]
Abstract
Wastewater-based epidemiology (WBE) is a powerful tool that has the potential to reveal the extent of an ongoing disease outbreak or to predict an emerging one. Recent studies have shown that SARS-CoV-2 concentration in wastewater may be correlated with the number of COVID-19 cases in the corresponding population. Most of the recent studies and applications of wastewater-based surveillance of SARS-CoV-2 applied the “gold standard” real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) detection method. However, this method also has its limitations. The paper aimed to present recent improvements and applications of the PCR-based methods for SARS-CoV-2 monitoring in wastewater. Furthermore, it aimed to review alternative methods utilized and/or proposed for the detection of the virus in wastewater matrices. From the review, it was found that several studies have investigated the use of reverse-transcription digital polymerase reaction (RT-dPCR), which was generally shown to have a lower limit of detection (LOD) over the RT-qPCR. Aside from this, non-PCR-based and non-RNA based methods have also been explored for the detection of SARS-CoV-2 in wastewater, with detailed attention given to the detection of SARS-CoV-2 proteins. The potential methods for protein detection include mass spectrometry, the use of immunosensors, and nanotechnological applications. In addition, the review of recent studies also revealed two types of emerging methods related to the detection of SARS-CoV-2 in wastewater: i) capsid-integrity assays to infer about the infectivity of SARS-CoV-2 present in wastewater, and ii) alternative methods for detection of SARS-CoV-2 variants of concern (VOCs) in wastewater. The recent studies on proposed methods of SARS-CoV-2 detection in wastewater have considered improving this approach in one or more of the following aspects: rapidity, simplicity, cost, sensitivity, and specificity. However, further studies are needed in order to realize the full application of these methods for WBE in the field.
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Donia A, Furqan Shahid M, Hassan SU, Shahid R, Ahmad A, Javed A, Nawaz M, Yaqub T, Bokhari H. Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform. Food Environ Virol 2022; 14:364-373. [PMID: 35508752 PMCID: PMC9067896 DOI: 10.1007/s12560-022-09522-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/04/2022] [Indexed: 05/21/2023]
Abstract
Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.
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Affiliation(s)
- Ahmed Donia
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Furqan Shahid
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sammer-ul Hassan
- Department of Mechanical Engineering, University of Hong Kong, Pok Fu Lam, Hong Kong, Hong Kong
| | - Ramla Shahid
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aneela Javed
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habib Bokhari
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
- Kohsar University Murree, Murree, Pakistan
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Ngay Lukusa I, Van Reet N, Mumba Ngoyi D, Mwamba Miaka E, Masumu J, Patient Pyana P, Mutombo W, Ngolo D, Kobo V, Akwaso F, Ilunga M, Kaninda L, Mutanda S, Mpoyi Muamba D, Valverde Mordt O, Tarral A, Rembry S, Büscher P, Lejon V. Trypanosome spliced leader RNA for diagnosis of acoziborole treatment outcome in gambiense human African trypanosomiasis: A longitudinal follow-up study. EBioMedicine 2022; 86:104376. [PMID: 36436279 PMCID: PMC9700268 DOI: 10.1016/j.ebiom.2022.104376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Detection of spliced leader (SL)-RNA allows sensitive diagnosis of gambiense human African trypanosomiasis (HAT). We investigated its diagnostic performance for treatment outcome assessment. METHODS Blood and cerebrospinal fluid (CSF) from a consecutive series of 97 HAT patients, originating from the Democratic Republic of the Congo, were prospectively collected before treatment with acoziborole, and during 18 months of longitudinal follow-up after treatment. For treatment outcome assessment, SL-RNA detection was compared with microscopic trypanosome detection and CSF white blood cell count. The trial was registered under NCT03112655 in clinicaltrials.gov. FINDINGS Before treatment, respectively 94.9% (92/97; CI 88.5-97.8%) and 67.7% (65/96; CI 57.8-76.2%) HAT patients were SL-RNA positive in blood or CSF. During follow-up, one patient relapsed with trypanosomes observed at 18 months, and was SL-RNA positive in blood and CSF at 12 months, and CSF positive at 18 months. Among cured patients, one individual tested SL-RNA positive in blood at month 12 (Specificity 98.9%; 90/91; CI 94.0-99.8%) and 18 (Specificity 98.9%; 88/89; CI 93.9-99.8%). INTERPRETATION SL-RNA detection for HAT treatment outcome assessment shows ≥98.9% specificity in blood and 100% in CSF, and may detect relapses without lumbar puncture. FUNDING The DiTECT-HAT project is part of the EDCTP2 programme, supported by Horizon 2020, the European Union Funding for Research and Innovation (grant number DRIA-2014-306-DiTECT-HAT).
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Affiliation(s)
- Ipos Ngay Lukusa
- Department of Parasitology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Nick Van Reet
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dieudonné Mumba Ngoyi
- Department of Parasitology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Erick Mwamba Miaka
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Justin Masumu
- Department of Parasitology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Pati Patient Pyana
- Department of Parasitology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Wilfried Mutombo
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Digas Ngolo
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Vincent Kobo
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Felix Akwaso
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Médard Ilunga
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Lewis Kaninda
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Sylvain Mutanda
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Dieudonné Mpoyi Muamba
- Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA), Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | | | - Antoine Tarral
- Drugs for Neglected Diseases Initiative, Geneva, Switzerland
| | - Sandra Rembry
- Drugs for Neglected Diseases Initiative, Geneva, Switzerland
| | - Philippe Büscher
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Veerle Lejon
- Mixed Research Unit 177 Intertryp, Institut de Recherche pour le Développement, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, University of Montpellier, Montpellier, France.
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Baldanti F, Ganguly NK, Wang G, Möckel M, O’Neill LA, Renz H, dos Santos Ferreira CE, Tateda K, Van Der Pol B. Choice of SARS-CoV-2 diagnostic test: challenges and key considerations for the future. Crit Rev Clin Lab Sci 2022; 59:445-459. [PMID: 35289222 PMCID: PMC8935452 DOI: 10.1080/10408363.2022.2045250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A plethora of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests are available, each with different performance specifications, detection methods, and targets. This narrative review aims to summarize the diagnostic technologies available and how they are best selected to tackle SARS-CoV-2 infection as the pandemic evolves. Seven key settings have been identified where diagnostic tests are being deployed: symptomatic individuals presenting for diagnostic testing and/or treatment of COVID-19 symptoms; asymptomatic individuals accessing healthcare for planned non-COVID-19-related reasons; patients needing to access emergency care (symptom status unknown); patients being discharged from healthcare following hospitalization for COVID-19; healthy individuals in both single event settings (e.g. airports, restaurants, hotels, concerts, and sporting events) and repeat access settings (e.g. workplaces, schools, and universities); and vaccinated individuals. While molecular diagnostics remain central to SARS-CoV-2 testing strategies, we have offered some discussion on the considerations for when other tools and technologies may be useful, when centralized/point-of-care testing is appropriate, and how the various additional diagnostics can be deployed in differently resourced settings. As the pandemic evolves, molecular testing remains important for definitive diagnosis, but increasingly widespread point-of-care testing is essential to the re-opening of society.
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Affiliation(s)
- Fausto Baldanti
- Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | | | - Guiqiang Wang
- The Center for Liver Diseases, Peking University First Hospital, Beijing, China
| | - Martin Möckel
- Charité – Universitätsmedizin, Berlin, Germany,CONTACT Martin Möckel Departments of Emergency Medicine and Chest Pain Units CVK/CCM, Charité – Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Luke A. O’Neill
- Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, University Hospital Giessen and Marburg GmbH, Giessen, Germany,Department of Clinical Immunology and Allergology, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Barbara Van Der Pol
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
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Chatterjee S, Mukhopadhyay S. Recent advances of lateral flow immunoassay components as “point of need”. J Immunoassay Immunochem 2022; 43:579-604. [DOI: 10.1080/15321819.2022.2122063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Susraba Chatterjee
- Department of Laboratory Medicine, School of Tropical Medicine, 108, C.R.Avenue, Kolkata 700073, West Bengal
| | - Sumi Mukhopadhyay
- Department of Laboratory Medicine, School of Tropical Medicine, 108, C.R.Avenue, Kolkata 700073, West Bengal
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Fernandes RS, de Oliveira Silva J, Gomes KB, Azevedo RB, Townsend DM, de Paula Sabino A, Branco de Barros AL. Recent advances in point of care testing for COVID-19 detection. Biomed Pharmacother 2022; 153:113538. [PMID: 36076617 PMCID: PMC9371983 DOI: 10.1016/j.biopha.2022.113538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 12/23/2022] Open
Abstract
The World Health Organizations declaration of the COVID-19 pandemic was a milestone for the scientific community. The high transmission rate and the huge number of deaths, along with the lack of knowledge about the virus and the evolution of the disease, stimulated a relentless search for diagnostic tests, treatments, and vaccines. The main challenges were the differential diagnosis of COVID-19 and the development of specific, rapid, and sensitive tests that could reach all people. RT-PCR remains the gold standard for diagnosing COVID-19. However, new methods, such as other molecular techniques and immunoassays emerged. Also, the need for accessible tests with quick results boosted the development of point of care tests (POCT) that are fast, and automated, with high precision and accuracy. This assay reduces the dependence on laboratory conditions and mass testing of the population, dispersing the pressure regarding screening and detection. This review summarizes the advances in the diagnostic field since the pandemic started, emphasizing various laboratory techniques for detecting COVID-19. We reviewed the main existing diagnostic methods, as well as POCT under development, starting with RT-PCR detection, but also exploring other nucleic acid techniques, such as digital PCR, loop-mediated isothermal amplification-based assay (RT-LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and next-generation sequencing (NGS), and immunoassay tests, and nanoparticle-based biosensors, developed as portable instruments for the rapid standard diagnosis of COVID-19.
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Tripathy SP, Ponnapati M, Bhat S, Jacobson J, Chatterjee P. Femtomolar detection of SARS-CoV-2 via peptide beacons integrated on a miniaturized TIRF microscope. Sci Adv 2022; 8:eabn2378. [PMID: 36001655 PMCID: PMC9401610 DOI: 10.1126/sciadv.abn2378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 07/13/2022] [Indexed: 05/29/2023]
Abstract
The novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) continues to pose a substantial global health threat. Along with vaccines and targeted therapeutics, there is a critical need for rapid diagnostic solutions. In this work, we use computational protein modeling tools to suggest molecular beacon architectures that function as conformational switches for high-sensitivity detection of the SARS-CoV-2 spike protein receptor binding domain (S-RBD). Integrating these beacons on a miniaturized total internal reflection fluorescence (mini-TIRF) microscope, we detect the S-RBD and pseudotyped SARS-CoV-2 with limits of detection in the femtomolar range. We envision that our designed mini-TIRF platform will serve as a robust platform for point-of-care diagnostics for SARS-CoV-2 and future emergent viral threats.
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Affiliation(s)
- Soumya P. Tripathy
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manvitha Ponnapati
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Suhaas Bhat
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Joseph Jacobson
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pranam Chatterjee
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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Zhang Z, Li D, Wang X, Wang Y, Lin J, Jiang S, Wu Z, He Y, Gao X, Zhu Z, Xiao Y, Qu Z, Li Y. Rapid detection of viruses: Based on silver nanoparticles modified with bromine ions and acetonitrile. Chem Eng J 2022; 438:135589. [PMID: 35261557 PMCID: PMC8890791 DOI: 10.1016/j.cej.2022.135589] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 05/02/2023]
Abstract
Nearly 200 million people have been diagnosed with COVID-19 since the outbreak in 2019, and this disease has claimed more than 5 million lives worldwide. Currently, researchers are focusing on vaccine development and the search for an effective strategy to control the infection source. This work designed a detection platform based on Surface-Enhanced Raman Spectroscopy (SERS) by introducing acetonitrile and calcium ions into the silver nanoparticle reinforced substrate system to realize the rapid detection of novel coronavirus. Acetonitrile may amplify the calcium-induced hot spots of silver nanoparticles and significantly enhanced the stability of silver nanoparticles. It also elicited highly sensitive SERS signals of the virus. This approach allowed us to capture the characteristic SERS signals of SARS-CoV-2, Human Adenovirus 3, and H1N1 influenza virus molecules at a concentration of 100 copies/test (PFU/test) with upstanding reproduction and signal-to-noise ratio. Machine learning recognition technology was employed to qualitatively distinguish the three virus molecules with 1000 groups of spectra of each virus. Acetonitrile is a potent internal marker in regulating the signal intensity of virus molecules in saliva and serum. Thus, we used the SERS peak intensity to quantify the virus content in saliva and serum. The results demonstrated a satisfactory linear relationship between peak intensity and protein concentration. Collectively, this rapid detection method has a broad application prospect in clinical diagnosis of viruses, management of emergent viral infectious diseases, and exploration of the interaction between viruses and host cells.
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Affiliation(s)
- Zhe Zhang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Dan Li
- Institute of Physics, Guizhou University, Guiyang City, Guizhou Province 550025, PR China
| | - Xiaotong Wang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Yunpeng Wang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Jingyi Lin
- The Fourth Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
| | - Shen Jiang
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Zheng Wu
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Yingying He
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
| | - Xin Gao
- Institute of Physics, Guizhou University, Guiyang City, Guizhou Province 550025, PR China
| | - Zhuo Zhu
- The Second Hospital of Jilin University, Jilin University, Changchun City, Jilin Province 130041, PR China
| | - Yanlong Xiao
- The Second Hospital of Jilin University, Jilin University, Changchun City, Jilin Province 130041, PR China
| | - Zhangyi Qu
- College of Public Health, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
| | - Yang Li
- College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, PR China
- Research Center for Innovative Technology of Pharmaceutical Analysis, Baojian Road No. 157, Harbin, Heilongjiang Province, 150081, China
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Asghar R, Rasheed M, ul Hassan J, Rafique M, Khan M, Deng Y. Advancements in Testing Strategies for COVID-19. Biosensors (Basel) 2022; 12:410. [PMID: 35735558 PMCID: PMC9220779 DOI: 10.3390/bios12060410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 coronavirus, also known as the disease-causing agent for COVID-19, is a virulent pathogen that may infect people and certain animals. The global spread of COVID-19 and its emerging variation necessitates the development of rapid, reliable, simple, and low-cost diagnostic tools. Many methodologies and devices have been developed for the highly sensitive, selective, cost-effective, and rapid diagnosis of COVID-19. This review organizes the diagnosis platforms into four groups: imaging, molecular-based detection, serological testing, and biosensors. Each platform's principle, advancement, utilization, and challenges for monitoring SARS-CoV-2 are discussed in detail. In addition, an overview of the impact of variants on detection, commercially available kits, and readout signal analysis has been presented. This review will expand our understanding of developing advanced diagnostic approaches to evolve into susceptible, precise, and reproducible technologies to combat any future outbreak.
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Affiliation(s)
- Rabia Asghar
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Madiha Rasheed
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Jalees ul Hassan
- Department of Wildlife and Ecology, Faculty of Fisheries and Wildlife, University of Veterinary and Animal Sciences-UVAS, Lahore 54000, Pakistan;
| | - Mohsin Rafique
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China;
| | - Mashooq Khan
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China;
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
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Luz MS, da Silva Júnior RT, Santos de Santana GA, Rodrigues GS, Crivellaro HDL, Calmon MS, dos Santos CFSM, Silva LGDO, Ferreira QR, Mota GR, Heim H, Silva FAFD, de Brito BB, de Melo FF. Molecular and serology methods in the diagnosis of COVID-19: An overview. World J Methodol 2022; 12:83-91. [PMID: 35721247 PMCID: PMC9157626 DOI: 10.5662/wjm.v12.i3.83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/31/2021] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) has become a pandemic, being a global health concern since December 2019 when the first cases were reported. Severe acute respiratory syndrome coronavirus 2, the COVID-19 causal agent, is a β-coronavirus that has on its surface the spike protein, which helps in its virulence and pathogenicity towards the host. Thus, effective and applicable diagnostic methods to this disease come as an important tool for the management of the patients. The use of the molecular technique PCR, which allows the detection of the viral RNA through nasopharyngeal swabs, is considered the gold standard test for the diagnosis of COVID-19. Moreover, serological methods, such as enzyme-linked immunosorbent assays and rapid tests, are able to detect severe acute respiratory syndrome coronavirus 2-specific immunoglobulin A, immunoglobulin M, and immunoglobulin G in positive patients, being important alternative techniques for the diagnostic establishment and epidemiological surveillance. On the other hand, reverse transcription loop-mediated isothermal amplification also proved to be a useful diagnostic method for the infection, mainly because it does not require a sophisticated laboratory apparatus and has similar specificity and sensitivity to PCR. Complementarily, imaging exams provide findings of typical pneumonia, such as the ground-glass opacity radiological pattern on chest computed tomography scanning, which along with laboratory tests assist in the diagnosis of COVID-19.
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Affiliation(s)
- Marcel Silva Luz
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | | | | | - Gabriela Santos Rodrigues
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Henrique de Lima Crivellaro
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Mariana Santos Calmon
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | | | | | - Qesya Rodrigues Ferreira
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Guilherme Rabelo Mota
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Heloísa Heim
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | | | - Breno Bittencourt de Brito
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45002175, Bahia, Brazil
| | - Fabrício Freire de Melo
- Instituto Multidisciplinar em Saúde , Universidade Federal da Bahia, Vitória da Conquista 45029-094, Bahia, Brazil
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Gärtner K, Meleke H, Kamdolozi M, Chaima D, Samikwa L, Paynter M, Nyirenda Nyang’Wa M, Cloutman-Green E, Nastouli E, Klein N, Nyirenda T, Msefula C, Alber DG. A fast extraction-free isothermal LAMP assay for detection of SARS-CoV-2 with potential use in resource-limited settings. Virol J 2022; 19:77. [PMID: 35501862 PMCID: PMC9059459 DOI: 10.1186/s12985-022-01800-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022] Open
Abstract
Background To retain the spread of SARS-CoV-2, fast, sensitive and cost-effective testing is essential, particularly in resource limited settings (RLS). Current standard nucleic acid-based RT-PCR assays, although highly sensitive and specific, require transportation of samples to specialised laboratories, trained staff and expensive reagents. The latter are often not readily available in low- and middle-income countries and this may significantly impact on the successful disease management in these settings. Various studies have suggested a SARS-CoV-2 loop mediated isothermal amplification (LAMP) assay as an alternative method to RT-PCR. Methods Four previously published primer pairs were used for detection of SARS-CoV-2 in the LAMP assay. To determine optimal conditions, different temperatures, sample input and incubation times were tested. Ninety-three extracted RNA samples from St. George's Hospital, London, 10 non-extracted nasopharyngeal swab samples from Great Ormond Street Hospital for Children, London, and 92 non-extracted samples from Queen Elisabeth Central Hospital (QECH), Malawi, which have previously been tested for SARS-Cov-2 by quantitative reverse-transcription RealTime PCR (qRT-PCR), were analysed in the LAMP assay. Results In this study we report the optimisation of an extraction-free colourimetric SARS-CoV-2 LAMP assay and demonstrated that a lower limit of detection (LOD) between 10 and 100 copies/µL of SARS-CoV-2 could be readily detected by a colour change of the reaction within as little as 30 min. We further show that this assay could be quickly established in Malawi, as no expensive equipment is necessary. We tested 92 clinical samples from QECH and showed the sensitivity and specificity of the assay to be 86.7% and 98.4%, respectively. Some viral transport media, used routinely to stabilise RNA in clinical samples during transportation, caused a non-specific colour-change in the LAMP reaction and therefore we suggest collecting samples in phosphate buffered saline (which did not affect the colour) as the assay allows immediate sample analysis on-site. Conclusion SARS-CoV-2 LAMP is a cheap and reliable assay that can be readily employed in RLS to improve disease monitoring and management. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01800-7.
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Jang M, Kim S, Song J, Kim S. Rapid and simple detection of influenza virus via isothermal amplification lateral flow assay. Anal Bioanal Chem 2022; 414:4685-4696. [PMID: 35501506 PMCID: PMC9060413 DOI: 10.1007/s00216-022-04090-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022]
Abstract
Respiratory illness caused by influenza virus is a serious public health problem worldwide. As the symptoms of influenza virus infection are similar to those of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, it is essential to distinguish these two viruses. Therefore, to properly respond to a pathogen, a detection method that is capable of rapid and accurate diagnosis in a hospital or at home is required. To satisfy this need, we applied loop-mediated isothermal amplification (LAMP) and an isothermal nucleic acid amplification technique, along with a system to analyze the results without specialized equipment, a lateral flow assay (LFA). Using the platform developed in this study, all processes, from sample preparation to detection, can be performed without special equipment. Unlike existing PCR methods, the nucleic acid amplification can be performed in the field because hot packs do not require electricity. Thus, the designed platform can provide rapid results without the need to transport the samples to a laboratory or hospital. These advantages are not limited to operations in developing countries with poor access to medical systems. In conclusion, the developed technology is a promising tool for infectious disease management that allows for rapid identification of infectious diseases and appropriate treatment of patients.
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Affiliation(s)
- Minju Jang
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea
| | - SeJin Kim
- 33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea
| | - Junkyu Song
- 33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea
| | - Sanghyo Kim
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea. .,33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea.
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Mautner L, Hoyos M, Dangel A, Berger C, Ehrhardt A, Baiker A. Replication kinetics and infectivity of SARS-CoV-2 variants of concern in common cell culture models. Virol J 2022; 19:76. [PMID: 35473640 PMCID: PMC9038516 DOI: 10.1186/s12985-022-01802-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/13/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND During the ongoing Covid-19 pandemic caused by the emerging virus SARS-CoV-2, research in the field of coronaviruses has expanded tremendously. The genome of SARS-CoV-2 has rapidly acquired numerous mutations, giving rise to several Variants of Concern (VOCs) with altered epidemiological, immunological, and pathogenic properties. METHODS As cell culture models are important tools to study viruses, we investigated replication kinetics and infectivity of SARS-CoV-2 in the African Green Monkey-derived Vero E6 kidney cell line and the two human cell lines Caco-2, a colon epithelial carcinoma cell line, and the airway epithelial carcinoma cell line Calu-3. We assessed viral RNA copy numbers and infectivity of viral particles in cell culture supernatants at different time points ranging from 2 to 96 h post-infection. RESULTS We here describe a systematic comparison of growth kinetics of the five SARS-CoV-2 VOCs Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2, and Omicron/B.1.1.529 and a non-VOC/B.1.1 strain on three different cell lines to provide profound information on the differential behaviour of VOCs in different cell lines for researchers worldwide. We show distinct differences in viral replication kinetics of the SARS-CoV-2 non-VOC and five VOCs on the three cell culture models Vero E6, Caco-2, and Calu-3. CONCLUSION This is the first systematic comparison of all SARS-CoV-2 VOCs on three different cell culture models. This data provides support for researchers worldwide in their experimental design for work on SARS-CoV-2. It is recommended to perform virus isolation and propagation on Vero E6 while infection studies or drug screening and antibody-based assays should rather be conducted on the human cell lines Caco-2 and Calu-3.
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Affiliation(s)
- Lena Mautner
- Unit of Molecular Biologic Analytics and Biogenetics, Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Mona Hoyos
- Unit of Molecular Biologic Analytics and Biogenetics, Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Alexandra Dangel
- Public Health Microbiology Unit, Bavarian Health and Food Safety Authority, 85764, Oberschleißheim, Germany
| | - Carola Berger
- Public Health Microbiology Unit, Bavarian Health and Food Safety Authority, 85764, Oberschleißheim, Germany
| | - Anja Ehrhardt
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453, Witten, Germany
| | - Armin Baiker
- Unit of Molecular Biologic Analytics and Biogenetics, Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany. .,Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453, Witten, Germany.
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Odiwuor N, Xiong J, Ogolla F, Hong W, Li X, Khan FM, Wang N, Yu J, Wei H. A point-of-care SARS-CoV-2 test based on reverse transcription loop-mediated isothermal amplification without RNA extraction with diagnostic performance same as RT-PCR. Anal Chim Acta 2022; 1200:339590. [PMID: 35256137 PMCID: PMC8844505 DOI: 10.1016/j.aca.2022.339590] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/04/2022]
Abstract
The global public health crisis and economic losses resulting from the current novel coronavirus disease (COVID-19) pandemic have been dire. The most used real-time reverse transcription polymerase chain reaction (RT-PCR) method needs expensive equipment, technical expertise, and a long turnaround time. Therefore, there is a need for a rapid, accurate, and alternative technique of diagnosis that is deployable at resource-poor settings like point-of-care. This study combines heat deactivation and a novel mechanical lysis method by bead beating for quick and simple sample preparation. Then, using an optimized reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to target genes encoding the open reading frame 8 (ORF8), spike and nucleocapsid proteins of the novel coronavirus, SARS-CoV-2. The test results can be read simultaneously in fluorometric and colorimetric readouts within 40 min from sample collection. We also calibrated a template transfer tool to simplify sample addition into LAMP reactions when pipetting skills are needed. Most importantly, validation of the direct RT-LAMP system based on multiplexing primers S1:ORF8 in a ratio (1:0.8) using 143 patients’ nasopharyngeal swab samples showed a diagnostic performance of 99.30% accuracy, with 98.81% sensitivity and 100% selectivity, compared to commercial RT-PCR kits. Since our workflow does not rely on RNA extraction and purification, the time-to-result is two times faster than other workflows with FDA emergency use authorization. Considering all its strengths: speed, simplicity, accuracy and extraction-free, the system can be useful for optimal point-of-care testing of COVID-19.
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Londono-Avendano MA, Libreros G, Osorio L, Parra B. A Rapid RT-LAMP Assay for SARS-CoV-2 with Colorimetric Detection Assisted by a Mobile Application. Diagnostics (Basel) 2022; 12:diagnostics12040848. [PMID: 35453896 PMCID: PMC9032071 DOI: 10.3390/diagnostics12040848] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Loop-mediated amplification has been promoted for SARS-CoV-2 screening, however, antigen tests are preferred in low-income countries and remote zones. Poor training in molecular biology, plus the need for RNA purification or reading instruments to overcome issues of sensitivity in colorimetric detection, are some of the reasons limiting the use of this technique. In this study, nasopharyngeal swabs, aspirates and saliva were amplified in an in-house LAMP assay and subject to colorimetric detection, achieved by the naked eye and by image analysis with a mobile application. Accuracy of detection by the naked eye ranged from 61–74% but improved to 75–86% when using the application. Sensitivity of the digital approach was 81% and specificity 83%, with poor positive predictive value, and acceptable negative predictive value. Additionally to the reported effect of some transport media’s pH, the presence of mucus and warming up of reagents while setting up the reaction critically affected performance. Accuracy per type of sample was 55, 70 and 80%, for swabs, aspirates and saliva, respectively, suggesting potential to improve the test in saliva. This assay, carried out in a closed tube, reduces contamination, has few pipetting steps and requires minimal equipment. Strategies to improve performance and implications of the use this sort of colorimetric LAMP for massive testing are discussed.
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Affiliation(s)
- María Aurora Londono-Avendano
- Departamento de Microbiología, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Calle 4B # 36-00, edificio 120, oficina 223/229, Cali 760043, Colombia; (G.L.); (B.P.)
- Correspondence: ; Tel.: +573-3212100 (ext. 5205)
| | - Gerardo Libreros
- Departamento de Microbiología, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Calle 4B # 36-00, edificio 120, oficina 223/229, Cali 760043, Colombia; (G.L.); (B.P.)
| | - Lyda Osorio
- Escuela de Salud Pública, Facultad de Salud, Universidad del Valle, Calle 4B # 36-00, edificio 120, oficina 223/229, Cali 760043, Colombia;
| | - Beatriz Parra
- Departamento de Microbiología, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Calle 4B # 36-00, edificio 120, oficina 223/229, Cali 760043, Colombia; (G.L.); (B.P.)
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Brown B, O'Hara RW, Guiver M, Davies E, Birtles A, Farooq H, Verma A, Guo H, Hayden K, Machin N. Evaluation of a Novel Direct RT-LAMP Assay for the Detection of SARS Cov-2 from Saliva Samples in Asymptomatic Individuals. J Clin Virol Plus 2022;:100074. [PMID: 35345440 DOI: 10.1016/j.jcvp.2022.100074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 01/31/2023] Open
Abstract
Large scale screening of health care workers and the general population for asymptomatic COVID-19 infection requires modalities that are amenable to testing at scale while retaining acceptable levels of sensitivity and specificity. This study evaluated a novel COVID-19 Direct-RT LAMP assay using saliva samples in asymptomatic individuals by comparison to RT-PCR. Additional studies were performed using VTM collected from routine diagnostic testing. Analytical sensitivity was determined for Direct RT-LAMP assay using the WHO International Standard. Finally, quantified results from RT-PCR testing of 9177 nose and throat swabs obtained from routine diagnostic testing were used to estimate the sensitivity of Direct RT-LAMP using the limit of detection curve obtained from the analytical sensitivity data. Results from saliva testing demonstrated a sensitivity of 40.91% and a specificity of 100% for Direct RT-LAMP. The sensitivity and specificity for nose and throat swabs were 44.85% and 100% respectively. The 95% limit of detection (LOD) for Direct RT-LAMP was log 7.13 IU/ml (95% 6.9–7.5). The estimated sensitivity for Direct-RT LAMP based on the results of 9117 nose and throat swabs was 34% and 45% for saliva and VTM respectively. The overall diagnostic sensitivity of Direct RT-LAMP was low compared to RT-PCR. Testing of nose and throat swabs and estimating the sensitivity based on a large cohort of clinical samples demonstrated similar results. This study highlights the importance of utilising the prospective collection of samples from the intended target population in the assessment of diagnostic sensitivity.
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