1
|
Abbas H, Best N, Zerna G, Beddoe T. Development of LAMP assay for early detection of Yersinia ruckeri in aquaculture. PeerJ 2025; 13:e19015. [PMID: 40028206 PMCID: PMC11869897 DOI: 10.7717/peerj.19015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Accepted: 01/28/2025] [Indexed: 03/05/2025] Open
Abstract
Yersinia ruckeri is the causative agent of yersiniosis or enteric red mouth disease (ERM) that causes significant economic losses in the salmonid aquaculture industry. Due to an increasing number of outbreaks, lack of effective vaccines and the bacteria's ability to survive in the environment for long periods, there is a necessity for novel measures to control ERM. New techniques capable of rapidly detecting Y. ruckeri are critical to aid effective control programs. Molecular methods, like real-time polymerase chain reaction, can detect Y. ruckeri; however, that methodology is not field-deployable and cannot support local decision-making during an outbreak. We present a field-deployable molecular assay using loop mediated isothermal amplification (LAMP) and water filtering method for the detection of Y. ruckeri eDNA from water samples to improve current surveillance methods. The assay was optimised to amplify the glutamine synthetase gene (glnA) of Y. ruckeri in under 20 min. The assay demonstrated high specificity and sensitivity, as it did not amplify any non-target bacteria typically present in water sources. It achieved a limit of detection (LOD) of 0.5 × 10-7 ng/µl, significantly surpassing the LOD of 0.5 × 10-4 ng/µl obtained through conventional polymerase chain reaction (cPCR). When applied to environmental water samples spiked with transformed Escherichia coli containing the G-block of the Yersinia ruckeri (glnA) target gene, the Yr-LAMP method exhibited an analytical sensitivity of 0.08 cells/µl from the initial filtered water sample. Notably, the cumulative time for sample preparation and amplification was under 1 h. The simplicity of the developed field-deployable Yr-LAMP assay makes it suitable as a routine procedure to monitor fish for ERM infection. This will enable informed decision-making on mitigating pathogen prevalence in aquaculture farms.
Collapse
Affiliation(s)
- Hoda Abbas
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria, Australia
| | - Nickala Best
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria, Australia
| | - Gemma Zerna
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria, Australia
| | - Travis Beddoe
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria, Australia
| |
Collapse
|
2
|
Odiwuor N, Li J, He P, Wang N, Murtaza A, Jiang M, Yu J, Wei H. Facilitating self-testing with a fast, accurate, and simplified shelf-stable colorimetric LAMP system for Mpox and SARS-CoV-2 detection. Talanta 2025; 283:127119. [PMID: 39509899 DOI: 10.1016/j.talanta.2024.127119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/23/2024] [Accepted: 10/27/2024] [Indexed: 11/15/2024]
Abstract
The rapid and accurate detection of viral infections is essential for effective disease management and prevention. Quantitative polymerase chain reaction (qPCR) remains the gold standard for viral detection due to its high sensitivity and specificity. However, its limitations-including the need for specialized equipment, trained personnel, and longer processing times-make it impractical for at-home or rapid testing. Although numerous point-of-care assays based on isothermal nucleic acid amplification have been developed, they often lack the simplicity and adaptability required for self-testing in non-laboratory settings such as at home. To address this, we developed and validated the SCOLAR (Shelf-stable Colorimetric LAMP system for Rapid self-testing of viruses) system, a simplified, portable, and accurate diagnostic tool designed for self-testing of Mpox and SARS-CoV-2 infections. The SCOLAR system employs novel lyophilized colorimetric loop-mediated isothermal amplification (LAMP) beads, a customized sample lysis buffer, and smartphone-assisted RGB color analysis for interpreting results. Validation was conducted using 24 mock Mpox skin swabs, 32 wastewater samples, and 104 clinical SARS-CoV-2 nasopharyngeal swabs, with comparisons to an in-house qPCR assay. The SCOLAR system demonstrated an analytical sensitivity of below 10 copies/μL for all targets within 15 min. Diagnostic performance for mock Mpox samples exhibited 93.8 % sensitivity and 100 % specificity, while wastewater samples achieved 100 % sensitivity and specificity. SARS-CoV-2 swabs had 96 % sensitivity and 100 % specificity. The system also proved effective for self-testing by untrained individuals. SCOLAR offers a reliable, easy-to-use platform for rapid self-testing, with potential for broader applications in public health strategies to enhance pandemic preparedness and response.
Collapse
Affiliation(s)
- Nelson Odiwuor
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya
| | - Junhua Li
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Ping He
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nuo Wang
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Ali Murtaza
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengwei Jiang
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Junping Yu
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Hongping Wei
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya.
| |
Collapse
|
3
|
Liu X, Guo Z, Qiao Y, Zhang S, Han W, Li X, Gu J. Detection of Staphylococcus aureus via IgY-based immunomagnetic separation and a phage lysin LysGH15-based colloidal gold immunochromatographic assay. J Adv Res 2025:S2090-1232(25)00053-0. [PMID: 39892607 DOI: 10.1016/j.jare.2025.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 01/13/2025] [Accepted: 01/22/2025] [Indexed: 02/04/2025] Open
Abstract
INTRODUCTION Staphylococcus aureus (S. aureus) is an important human pathogen that frequently causes disease in hospital and community settings. Due to the pervasive emergence of virulent and multidrug-resistant methicillin-resistant S. aureus (MRSA) strains, S. aureus infections have become a leading cause of morbidity and mortality. OBJECTIVES We aimed to develop a reliable and effective detection method that can be used for preventing and managing infections caused by S. aureus. METHODS A novel S. aureus detection platform that combines immunomagnetic separation via immunomagnetic beads (IMBs) and the phage lysin LysGH15-based colloidal gold immunochromatographic assay (GICA) (named IMBs-GICA) was developed. IMBs-GICA was performed on 426 consecutive samples, including 185, 107, 74 and 60 samples from sputum, urine, bronchoalveolar lavage fluid (BALF) and serum samples, respectively. S. aureus culture and PCR assays were routinely conducted in parallel. RESULTS By targetingS. aureus, the IMBs-GICA platform could detect as little as 40 CFU/mL within 35 min. Among the clinical specimens, 38 samples were S. aureus culture positive, and 36 were IMBs-GICA positive, resulting in an IMBs-GICA sensitivity of 89.5 % (95 % confidence interval 74.3-96.6) and a specificity of 99.5 % (97.9-99.9). DISCUSSION IMBs-GICA can rapidly and sensitively detect for S. aureus, demonstrating the potential utility of this developed method in the field of testing.
Collapse
Affiliation(s)
- Xiao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062 China; School of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000 China
| | - Zhimin Guo
- Department of Laboratory Medicine, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun 130021 China
| | - Yinghan Qiao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062 China
| | - Shiyu Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062 China
| | - Wenyu Han
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062 China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009 China
| | - Xinwei Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062 China.
| | - Jingmin Gu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062 China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009 China.
| |
Collapse
|
4
|
Arevalo-Rodriguez I, Mateos-Haro M, Dinnes J, Ciapponi A, Davenport C, Buitrago-Garcia D, Bennouna-Dalero T, Roqué-Figuls M, Van den Bruel A, von Eije KJ, Emperador D, Hooft L, Spijker R, Leeflang MM, Takwoingi Y, Deeks JJ. Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2024; 10:CD015618. [PMID: 39400904 PMCID: PMC11472845 DOI: 10.1002/14651858.cd015618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
BACKGROUND Diagnosing people with a SARS-CoV-2 infection played a critical role in managing the COVID-19 pandemic and remains a priority for the transition to long-term management of COVID-19. Initial shortages of extraction and reverse transcription polymerase chain reaction (RT-PCR) reagents impaired the desired upscaling of testing in many countries, which led to the search for alternatives to RNA extraction/purification and RT-PCR testing. Reference standard methods for diagnosing the presence of SARS-CoV-2 infection rely primarily on real-time reverse transcription-polymerase chain reaction (RT-PCR). Alternatives to RT-PCR could, if sufficiently accurate, have a positive impact by expanding the range of diagnostic tools available for the timely identification of people infected by SARS-CoV-2, access to testing and the use of resources. OBJECTIVES To assess the diagnostic accuracy of alternative (to RT-PCR assays) laboratory-based molecular tests for diagnosing SARS-CoV-2 infection. SEARCH METHODS We searched the COVID-19 Open Access Project living evidence database from the University of Bern until 30 September 2020 and the WHO COVID-19 Research Database until 31 October 2022. We did not apply language restrictions. SELECTION CRITERIA We included studies of people with suspected or known SARS-CoV-2 infection, or where tests were used to screen for infection, and studies evaluating commercially developed laboratory-based molecular tests for the diagnosis of SARS-CoV-2 infection considered as alternatives to RT-PCR testing. We also included all reference standards to define the presence or absence of SARS-CoV-2, including RT-PCR tests and established clinical diagnostic criteria. DATA COLLECTION AND ANALYSIS Two authors independently screened studies and resolved disagreements by discussing them with a third author. Two authors independently extracted data and assessed the risk of bias and applicability of the studies using the QUADAS-2 tool. We presented sensitivity and specificity, with 95% confidence intervals (CIs), for each test using paired forest plots and summarised results using average sensitivity and specificity using a bivariate random-effects meta-analysis. We illustrated the findings per index test category and assay brand compared to the WHO's acceptable sensitivity and specificity threshold for diagnosing SARS-CoV-2 infection using nucleic acid tests. MAIN RESULTS We included data from 64 studies reporting 94 cohorts of participants and 105 index test evaluations, with 74,753 samples and 7517 confirmed SARS-CoV-2 cases. We did not identify any published or preprint reports of accuracy for a considerable number of commercially produced NAAT assays. Most cohorts were judged at unclear or high risk of bias in more than three QUADAS-2 domains. Around half of the cohorts were considered at high risk of selection bias because of recruitment based on COVID status. Three quarters of 94 cohorts were at high risk of bias in the reference standard domain because of reliance on a single RT-PCR result to determine the absence of SARS-CoV-2 infection or were at unclear risk of bias due to a lack of clarity about the time interval between the index test assessment and the reference standard, the number of missing results, or the absence of a participant flow diagram. For index tests categories with four or more evaluations and when summary estimations were possible, we found that: a) For RT-PCR assays designed to omit/adapt RNA extraction/purification, the average sensitivity was 95.1% (95% CI 91.1% to 97.3%), and the average specificity was 99.7% (95% CI 98.5% to 99.9%; based on 27 evaluations, 2834 samples and 1178 SARS-CoV-2 cases); b) For RT-LAMP assays, the average sensitivity was 88.4% (95% CI 83.1% to 92.2%), and the average specificity was 99.7% (95% CI 98.7% to 99.9%; 24 evaluations, 29,496 samples and 2255 SARS-CoV-2 cases); c) for TMA assays, the average sensitivity was 97.6% (95% CI 95.2% to 98.8%), and the average specificity was 99.4% (95% CI 94.9% to 99.9%; 14 evaluations, 2196 samples and 942 SARS-CoV-2 cases); d) for digital PCR assays, the average sensitivity was 98.5% (95% CI 95.2% to 99.5%), and the average specificity was 91.4% (95% CI 60.4% to 98.7%; five evaluations, 703 samples and 354 SARS-CoV-2 cases); e) for RT-LAMP assays omitting/adapting RNA extraction, the average sensitivity was 73.1% (95% CI 58.4% to 84%), and the average specificity was 100% (95% CI 98% to 100%; 24 evaluations, 14,342 samples and 1502 SARS-CoV-2 cases). Only two index test categories fulfil the WHO-acceptable sensitivity and specificity requirements for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. In addition, WHO-acceptable performance criteria were met for two assays out of 35 when tests were used according to manufacturer instructions. At 5% prevalence using a cohort of 1000 people suspected of SARS-CoV-2 infection, the positive predictive value of RT-PCR assays omitting/adapting RNA extraction/purification will be 94%, with three in 51 positive results being false positives, and around two missed cases. For TMA assays, the positive predictive value of RT-PCR assays will be 89%, with 6 in 55 positive results being false positives, and around one missed case. AUTHORS' CONCLUSIONS Alternative laboratory-based molecular tests aim to enhance testing capacity in different ways, such as reducing the time, steps and resources needed to obtain valid results. Several index test technologies with these potential advantages have not been evaluated or have been assessed by only a few studies of limited methodological quality, so the performance of these kits was undetermined. Only two index test categories with enough evaluations for meta-analysis fulfil the WHO set of acceptable accuracy standards for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. These assays might prove to be suitable alternatives to RT-PCR for identifying people infected by SARS-CoV-2, especially when the alternative would be not having access to testing. However, these findings need to be interpreted and used with caution because of several limitations in the evidence, including reliance on retrospective samples without information about the symptom status of participants and the timing of assessment. No extrapolation of found accuracy data for these two alternatives to any test brands using the same techniques can be made as, for both groups, one test brand with high accuracy was overrepresented with 21/26 and 12/14 included studies, respectively. Although we used a comprehensive search and had broad eligibility criteria to include a wide range of tests that could be alternatives to RT-PCR methods, further research is needed to assess the performance of alternative COVID-19 tests and their role in pandemic management.
Collapse
Affiliation(s)
- Ingrid Arevalo-Rodriguez
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS). CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Evidence Production & Methods Directorate, Cochrane, London, UK
| | - Miriam Mateos-Haro
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- Doctoral programme in Clinical Medicine and Public Health, Universidad de Granada, Granada, Spain
| | - Jacqueline Dinnes
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Agustín Ciapponi
- Argentine Cochrane Centre, Institute for Clinical Effectiveness and Health Policy (IECS-CONICET), Buenos Aires, Argentina
| | - Clare Davenport
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Diana Buitrago-Garcia
- Institute for Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Hospital Universitario Mayor - Méderi. Universidad del Rosario, Bogotá, Colombia
| | - Tayeb Bennouna-Dalero
- Preventive Medicine and Public Health Department, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Marta Roqué-Figuls
- Iberoamerican Cochrane Centre, Institut de Recerca Sant Pau (IR SANT PAU), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | | | - Karin J von Eije
- Department of Viroscience, ErasmusMC, University Medical Center, Rotterdam, Netherlands
| | | | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - René Spijker
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Yemisi Takwoingi
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| |
Collapse
|
5
|
Fry J, Lee JYH, McAuley JL, Porter JL, Monk IR, Martin ST, Collins DJ, Barbante GJ, Fitzgerald NJ, Stinear TP. Optimization of Reverse Transcription Loop-Mediated Isothermal Amplification for In Situ Detection of SARS-CoV-2 in a Micro-Air-Filtration Device Format. ACS OMEGA 2024; 9:40832-40840. [PMID: 39372017 PMCID: PMC11447726 DOI: 10.1021/acsomega.4c05784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 09/06/2024] [Accepted: 09/11/2024] [Indexed: 10/08/2024]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic has supercharged innovation in the field of molecular diagnostics and led to the exploration of systems that permit the autonomous identification of airborne infectious agents. Airborne virus detection is an emerging approach for determining exposure risk, although current methods limit intervention timeliness. Here, we explore reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for one-pot detection of Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) (SCV2) run on membrane filters suitable for micro-air-filtration of airborne viruses. We use a design of experiments statistical framework to establish the optimal additive composition for running RT-LAMP on membrane filters. Using SCV2 liquid spike-in experiments and fluorescence detection, we show that single-pot RT-LAMP on glass fiber filters reliably detected 0.10 50% tissue culture infectious dose (TCID50) SCV2 per reaction (3600 E-gene copies) and is an order of magnitude more sensitive than conventional RT-LAMP.
Collapse
Affiliation(s)
- Jacob Fry
- ARC
Centre of Excellence in Exciton Science, The School of Chemistry, The University of Melbourne, Masson Rd, Parkville, Victoria 3010, Australia
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Jean Y. H. Lee
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Julie L. McAuley
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Jessica L. Porter
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Ian R. Monk
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Samuel T. Martin
- Department
of Biomedical Engineering, The University
of Melbourne, Building
261/203 Bouverie St, Carlton, Victoria 3053, Australia
| | - David J. Collins
- Department
of Biomedical Engineering, The University
of Melbourne, Building
261/203 Bouverie St, Carlton, Victoria 3053, Australia
- Graeme
Clarke Institute, The University of Melbourne, Chemical Engineering 2 Building
167, Parkville, Victoria 3010, Australia
| | - Gregory J. Barbante
- Defence
Science and Technology Group, Australian
Department of Defence, 506 Lorimer Street, Fishermans Bend, Victoria 3207, Australia
| | - Nicholas J. Fitzgerald
- Defence
Science and Technology Group, Australian
Department of Defence, 506 Lorimer Street, Fishermans Bend, Victoria 3207, Australia
| | - Timothy P. Stinear
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| |
Collapse
|
6
|
Storms SM, Shisler J, Nguyen TH, Zuckermann FA, Lowe JF. Lateral flow paired with RT-LAMP: A speedy solution for Influenza A virus detection in swine. Vet Microbiol 2024; 296:110174. [PMID: 38981201 DOI: 10.1016/j.vetmic.2024.110174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/31/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024]
Abstract
Influenza A Virus in swine (IAV-S) is a zoonotic pathogen that is nearly ubiquitous in commercial swine in the USA. Swine possess sialic acid receptors that allow co-infection of human and avian viruses with the potential of pandemic reassortment. We aimed to develop a fast and robust testing method for IAV-S detection on swine farms. Two primers of the RT-LAMP assay were labeled for use in a lateral flow readout. A commercially available lateral flow kit was used to read the amplicon product. With a runtime of ∼ 45 minutes, the limit of detection for the assay is comparable with an RT-qPCR Cq less than 35, with a sensitivity of 83.5 % and a specificity of 89.6 %. This assay allows veterinarians and producers with limited access to diagnostic services to perform and detect Matrix gene amplification on-site with low equipment costs. The time from sample collection to detection is less than one hour, making this method an accessible, convenient, and affordable tool to prevent the spread of zoonotic disease.
Collapse
Affiliation(s)
- Suzanna M Storms
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, 2001 South Lincoln Ave, Urbana, IL 61802, USA.
| | - Joanna Shisler
- Department of Microbiology, University of Illinois at Urbana-Champaign. Chemical and Life Sciences Laboratory, B103 CLSL, MC-110, S Goodwin Ave, Urbana, IL 61801, USA.
| | - Thanh H Nguyen
- Department of Civil Engineering, University of Illinois at Urbana-Champaign, 205 N Mathews Ave, Urbana, IL 61801, USA.
| | - Federico A Zuckermann
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 South Lincoln Ave, Urbana, IL 61802, USA.
| | - James F Lowe
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, 2001 South Lincoln Ave, Urbana, IL 61802, USA.
| |
Collapse
|
7
|
Peng JM, Liu H, Ying ZM. Rapid one-pot isothermal amplification reassembled of fluorescent RNA aptamer for SARS-CoV-2 detection. Talanta 2024; 276:126264. [PMID: 38761661 DOI: 10.1016/j.talanta.2024.126264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
The outbreak of SARS-CoV-2 poses a serious threat to human life and health. A rapid nucleic acid tests can effectively curb the spread of the disease. With the advantages of fluorescent RNA aptamers, low background and high sensitivity. A variety of fluorescent RNA aptamer sensors have been developed for the detection of nucleic acid. Here, we report a hypersensitive detection platform in which SARS-CoV-2 initiates RTF-EXPAR to amplify trigger fragments. This activation leads to the reassembled of the SRB2 fluorescent RNA aptamer, restoring its secondary structure for SR-DN binding and turn-on fluorescence. The platform completes the assay in 30 min and all reactions occur in one tube. The detection limit is as low as 116 aM. Significantly, the platform's quantitative analyses were almost identical to qPCR results in simulated tests of positive samples. In conclusion, the platform is sensitive, accurate and provides a new protocol for point-of-care testing of viruses.
Collapse
Affiliation(s)
- Jia-Min Peng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Hao Liu
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Zhan-Ming Ying
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
| |
Collapse
|
8
|
Hanifehpour H, Ashrafi F, Siasi E, Fallahi S. Evaluation and comparison of one-step real-time PCR and one-step RT-LAMP methods for detection of SARS-CoV-2. BMC Infect Dis 2024; 24:679. [PMID: 38982392 PMCID: PMC11232332 DOI: 10.1186/s12879-024-09574-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 06/27/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND There is an increasing disease trend for SARS-COV-2, so need a quick and affordable diagnostic method. It should be highly accurate and save costs compared to other methods. The purpose of this research is to achieve these goals. METHODS This study analyzed 342 samples using TaqMan One-Step RT-qPCR and fast One-Step RT-LAMP (Reverse Transcriptase Loop-Mediated Isothermal Amplification). The One-Step LAMP assay was conducted to assess the sensitivity and specificity. RESULTS The research reported positive samples using two different methods. In the RT-LAMP method, saliva had 92 positive samples (26.9%) and 250 negative samples (73.09%) and nasopharynx had 94 positive samples (27.4%) and 248 negative samples (72.51%). In the RT-qPCR method, saliva had 86 positive samples (25.1%) and 256 negative samples (74.8%) and nasopharynx had 93 positive samples (27.1%) and 249 negative samples (72.8%). The agreement between the two tests in saliva and nasopharynx samples was 93% and 94% respectively, based on Cohen's kappa coefficient (κ) (P < 0.001). The rate of sensitivity in this technique was reported at a dilution of 1 × 101 and 100% specificity. CONCLUSIONS Based on the results of the study the One-Step LAMP assay has multiple advantages. These include simplicity, cost-effectiveness, high sensitivity, and specificity. The One-Step LAMP assay shows promise as a diagnostic tool. It can help manage disease outbreaks, ensure prompt treatment, and safeguard public health by providing rapid, easy-to-use testing.
Collapse
Affiliation(s)
- Hooman Hanifehpour
- Department of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Ashrafi
- Department of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Elham Siasi
- Department of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Shirzad Fallahi
- Hepatitis Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.
- Department of Parasitology and Mycology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| |
Collapse
|
9
|
Cai J, Zhu Q. New advances in signal amplification strategies for DNA methylation detection in vitro. Talanta 2024; 273:125895. [PMID: 38508130 DOI: 10.1016/j.talanta.2024.125895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.
Collapse
Affiliation(s)
- Jiajing Cai
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China
| |
Collapse
|
10
|
Kang S, Choi P, Maile-Moskowitz A, Brown CL, Gonzalez RA, Pruden A, Vikesland PJ. Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance. ACS ES&T WATER 2024; 4:1629-1636. [PMID: 38633369 PMCID: PMC11019537 DOI: 10.1021/acsestwater.3c00690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.
Collapse
Affiliation(s)
- Seju Kang
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Petra Choi
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Ayella Maile-Moskowitz
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Connor L. Brown
- Department
of Genetics, Bioinformatics, and Computational Biology, Blacksburg, Virginia 24061, United States
| | - Raul A. Gonzalez
- Hampton
Roads Sanitation District, Virginia Beach ,Virginia23455, United States
| | - Amy Pruden
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Peter J. Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| |
Collapse
|
11
|
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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [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.
Collapse
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
| |
Collapse
|
12
|
Bi H, You R, Bian X, Li P, Zhao X, You Z. A magnetic control enrichment technique combined with terahertz metamaterial biosensor for detecting SARS-CoV-2 spike protein. Biosens Bioelectron 2024; 243:115763. [PMID: 37890389 DOI: 10.1016/j.bios.2023.115763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023]
Abstract
The highly contagious SARS-CoV-2 virus, responsible for the COVID-19 pandemic continues to pose significant challenges to public health. Developing new methods for early detection and diagnosis is crucial in combatting the disease, mitigating its impact and be prepared for future challenges in pandemic diseases. In this study, we propose a terahertz (THz) biosensing technology that capitalizes on the properties of THz metamaterial in conjunction with magnetic nanoparticles. This approach can accurately identify the SARS-CoV-2 spike protein by pinpointing its location on the THz resonance sources grooved surface. The magnetic nanoparticles are employed to selectively bind with target molecules, and migrate towards the THz metamaterial unit cell when exposed to an applied magnetic field. The presence of target molecules in to the metamaterial variation in the frequency, amplitude, and phase of the resonance response, thus enabling swift, accurate and sensitive detection. To assess the effectiveness of the proposed technique, we have conducted a comparative analysis between real samples on platforms controlled by magnetic manipulation and those without the control. It was confirmed that the proposed THz sensing method demonstrated a linear detection range spanning from 0.005 ng mL-1 to 1000 ng mL-1 with a detection limit of 0.002 ng mL-1. Furthermore, it exhibited a frequency shift of 24 GHz and a stability index of 95%. The THz biosensing technique may pave a new avenue in identifying and preempting the spread of potential pandemic diseases.
Collapse
Affiliation(s)
- Hao Bi
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China
| | - Rui You
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China.
| | - Xiaomeng Bian
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China
| | - Peng Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China.
| | - Xiaoguang Zhao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China.
| | - Zheng You
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China
| |
Collapse
|
13
|
Momenifar N, Pirouzfar M, Hashemian Z, Daneshvar Amoli A. Development of an optimized RT-LAMP test for the detection of SARS-CoV-2. Biologicals 2023; 84:101716. [PMID: 37801803 DOI: 10.1016/j.biologicals.2023.101716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 06/17/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
SARS-COV-2 is the causative agent of an acute respiratory syndrome called Coronavirus disease 2019 (COVID-19) with a varying mortality rate from 2019 to 2022. There are several measures for control and prevention of Covid-19 including using mask, vaccine injections, as well as screening the potential cases. We aimed to design and develop a molecular method (RT-LAMP) for detecting coronavirus in biological samples that is cheaper, faster and easier than conventional molecular methods. In this study, various reaction components were explored to make the optimal combination of an RT-LAMP master mix composition. The results revealed the ability of this RT-LAMP test in specifically identifying 100 copies of mixture of N and E genes in just 30-45 min. This study demonstrated the reliable performance of the RT-LAMP method for the detection of SARS-COV-2 in biological samples. Given the significant advantages of this method compared to the gold standard qRT-PCR, it can be employed as a promising tool for the diagnosis of coronavirus as well as other pathogenic viruses.
Collapse
Affiliation(s)
- Navid Momenifar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Mohammad Pirouzfar
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Zohreh Hashemian
- Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | | |
Collapse
|
14
|
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] [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.
Collapse
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
| |
Collapse
|
15
|
Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
Collapse
Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| |
Collapse
|
16
|
Reyes-Morales R, Segundo-Ibañez P, Flores-de Los Ángeles C, Vizcarra-Ramos D, Ibañez-Galeana DI, Salas-Cuevas G, Olvera-Serrano Á, Pérez-Silva NB, Rocha-Rocha VM, El-Kassi EG, Escobedo-Straffon J, Contreras-Mioni L, Rosas-Díaz M, Lopez-Martinez KM, Arias-Matus CE, Bautista-Rodriguez E, Nolasco-Quiroga M. Reverse transcription loop‑mediated isothermal amplification has a high performance in the detection of SARS‑CoV‑2 in saliva samples and nasal swabs from asymptomatic and symptomatic individuals. Exp Ther Med 2023; 26:398. [PMID: 37522063 PMCID: PMC10375439 DOI: 10.3892/etm.2023.12097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/31/2023] [Indexed: 08/01/2023] Open
Abstract
The detection of coronavirus disease 2019 cases represents a significant challenge at the epidemiological level. Limitations exist in effectively detecting asymptomatic cases, achieving good follow-up in hospitals without the infrastructure for reverse transcription-quantitative PCR (RT-qPCR) or in difficult-to-access areas and developing methods with the need for less invasive sampling procedures. Therefore, the present study evaluated the performance of the direct reverse transcription loop-mediated isothermal amplification (RT-LAMP) test for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the saliva and nasal samples of asymptomatic individuals belonging to the university population. In addition, this test was also assessed for effectiveness in symptomatic individuals referred from a hospital with poor infrastructure in molecular biology and located outside the urban area. The RT-LAMP assay was compared with the results obtained from the RT-qPCR nasopharyngeal swab test, where the diagnosis was confirmed by lateral flow immunoassay test for rapid antigen detection. A total of 128 samples were analyzed, of which 43% were symptomatic positive individuals, 25% were asymptomatic positive individuals and 32% were SARS-CoV2-negative control individuals. Among positive individuals, no differences were found between the Cq values determined by RT-qPCR. A sensitivity of 96.5% and a specificity of 97.6% was reported for the detection of SARS-CoV-2 in symptomatic individuals by salivary and nasal RT-LAMP, as well as a sensitivity of 100% and a specificity of 97.6% for the detection of SARS-CoV-2 in asymptomatic individuals. These findings indicated that performance of the direct RT-LAMP test using saliva and nasal samples has high sensitivity and specificity, which in turn suggest that it is a viable and reliable alternative for use in epidemiological monitoring.
Collapse
Affiliation(s)
- Rodolfo Reyes-Morales
- Laboratory of Medical and Pharmaceutical Biotechnology, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Patricia Segundo-Ibañez
- Molecular Biology Laboratory, Biotechnology Department, Interamerican University, Puebla 72828, Mexico
| | - César Flores-de Los Ángeles
- Molecular Diagnostic Laboratory, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - David Vizcarra-Ramos
- Molecular Biology Laboratory, Biotechnology Department, Interamerican University, Puebla 72828, Mexico
| | | | - Gabriela Salas-Cuevas
- COVID Area of Hospital Clinic Huauchinango, Institute of Social Security and Services for State Workers, Huauchinango, Puebla 73160, Mexico
| | - Ángel Olvera-Serrano
- COVID Area of Hospital Clinic Huauchinango, Institute of Social Security and Services for State Workers, Huauchinango, Puebla 73160, Mexico
| | - Nancy Bibiana Pérez-Silva
- Molecular Diagnostic Laboratory, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Valeria Magali Rocha-Rocha
- Biological Science Department, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Elie Girgis El-Kassi
- Biological Science Department, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Jorge Escobedo-Straffon
- Biological Science Department, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Laura Contreras-Mioni
- Biological Science Department, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Marisol Rosas-Díaz
- Molecular Biology Laboratory, Multidisciplinary Academic Unit Reynosa-Aztlan Reynosa, Autonomous University of Tamaulipas, Tamaulipas 88740, Mexico
| | - Karla María Lopez-Martinez
- Laboratory of Medical and Pharmaceutical Biotechnology, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Carlos Eduardo Arias-Matus
- Laboratory of Medical and Pharmaceutical Biotechnology, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Elizabeth Bautista-Rodriguez
- Laboratory of Medical and Pharmaceutical Biotechnology, Biotechnology Faculty, Puebla State Popular Autonomous University, Puebla 72410, Mexico
| | - Manuel Nolasco-Quiroga
- COVID Area of Hospital Clinic Huauchinango, Institute of Social Security and Services for State Workers, Huauchinango, Puebla 73160, Mexico
| |
Collapse
|
17
|
García-Sorribes S, Lara-Hernández F, Manzano-Blasco I, Abadía-Otero J, Albert E, Mulet A, Briongos-Figuero LS, Gabella-Martín M, Torres I, Signes-Costa J, Navarro D, Martín-Escudero JC, García-García AB, Chaves FJ. Sample Treatment with Trypsin for RT-LAMP COVID-19 Diagnosis. BIOLOGY 2023; 12:900. [PMID: 37508333 PMCID: PMC10376771 DOI: 10.3390/biology12070900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023]
Abstract
The SARS-CoV-2 coronavirus is responsible for the COVID-19 pandemic resulting in a global health emergency. Given its rapid spread and high number of infected individuals, a diagnostic tool for a rapid, simple, and cost-effective detection was essential. In this work, we developed a COVID-19 diagnostic test, that incorporates a human internal control, based on the Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). When working with synthetic SARS-CoV-2 RNA, the optimized RT-LAMP assay has a sensitivity of 10 viral copies and can be detected by fluorescence in less than 15 min or by the naked eye in 25 min using colorimetric RT-LAMP. To avoid the RNA extraction step, a pre-treatment of the sample was optimized. Subsequently, a validation was performed on 268 trypsin treated samples (including nasopharyngeal, buccal, and nasal exudates) and amplified with colorimetric RT-LAMP to evaluate its sensitivity and specificity in comparison with RT-qPCR of extracted samples. The validation results showed a sensitivity and specificity of 100% for samples with Ct ≤ 30. The rapid, simple, and inexpensive RT-LAMP SARS-CoV-2 extraction-free procedure developed may be an alternative test that could be applied for the detection of SARS-CoV-2 or adapted to detect other viruses present in saliva or nasopharyngeal samples with higher sensitivity and specificity of the antibody test.
Collapse
Affiliation(s)
| | | | - Iris Manzano-Blasco
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Jessica Abadía-Otero
- Internal Medicine Service, Rio Hortega University Hospital, 47012 Valladolid, Spain
| | - Eliseo Albert
- Microbiology Service, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | - Alba Mulet
- Pulmonary Department, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | | | | | - Ignacio Torres
- Microbiology Service, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | - Jaime Signes-Costa
- Pulmonary Department, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | - David Navarro
- Microbiology Service, University Clinic Hospital, INCLIVA, 46010 Valencia, Spain
| | - Juan-Carlos Martín-Escudero
- Internal Medicine Service, Rio Hortega University Hospital, 47012 Valladolid, Spain
- Medicine Department, Valladolid University, 47002 Valladolid, Spain
| | - Ana-Bárbara García-García
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
- CIBERDEM, ISCIII, 28029 Madrid, Spain
| | - Felipe Javier Chaves
- Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
- CIBERDEM, ISCIII, 28029 Madrid, Spain
| |
Collapse
|
18
|
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. JOURNAL OF CLINICAL VIROLOGY 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] [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.
Collapse
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
| |
Collapse
|
19
|
Srivastava P, Prasad D. Isothermal nucleic acid amplification and its uses in modern diagnostic technologies. 3 Biotech 2023; 13:200. [PMID: 37215369 PMCID: PMC10193355 DOI: 10.1007/s13205-023-03628-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.
Collapse
Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| |
Collapse
|
20
|
Khanizadeh S, Malekshahi A, Hanifehpour H, Birjandi M, Fallahi S. Rapid, sensitive, and specific detection of SARS-CoV-2 in nasopharyngeal swab samples of suspected patients using a novel one-step loop-mediated isothermal amplification (one-step LAMP) technique. BMC Microbiol 2023; 23:63. [PMID: 36882699 PMCID: PMC9989590 DOI: 10.1186/s12866-023-02806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND In the absence of effective antiviral drugs or vaccines, early and accurate detection of SARS-CoV-2 infection is essential to the COVID-19 pandemic. This study developed and evaluated a novel rapid One-Step LAMP assay to directly detect the SARS-CoV-2 RNA from nasopharyngeal (NP) swab samples of patients with suspected SARS-CoV-2 infection living in deprived areas in comparison to One-Step Real-time PCR. METHODS Two hundred fifty-four NP swab samples from patients suspected of COVID-19 infection living in deprived western areas of Iran were tested by TaqMan One-Step RT-qPCR and fast One-Step LAMP assays. Tenfold serial dilutions of SARS-CoV-2 RNA standard strain where the viral copy number in each dilution was previously determined using the qPCR and various templates were used to investigate the analytical sensitivity and specificity of the One-Step LAMP assay in triplicate. Also, the efficacy and reliability of the method compared to TaqMan One-Step RT-qPCR were evaluated using SARS-CoV-2 positive and negative clinical samples. RESULTS The results of the One-Step RT-qPCR and One-Step LAMP tests were positive in 131 (51.6%) and 127 (50%) participants, respectively. Based on Cohen's kappa coefficient (κ), the agreement between the two tests was 97%, which was statistically significant (P < 0.001). The detection limit for the One-Step LAMP assay was 1 × 101 copies of standard SARS-CoV-2 RNA per reaction in less than an hour in triplicates. Negative results in all samples with non-SARS-CoV-2 templates represent 100% specificity. CONCLUSIONS The results showed that the One-Step LAMP assay is an efficient consistent technique for detecting SARS-CoV-2 among suspected individuals due to its simplicity, speed, low cost, sensitivity, and specificity. Therefore, it has great potential as a useful diagnostic tool for disease epidemic control, timely treatment, and public health protection, especially in poor and underdeveloped countries.
Collapse
Affiliation(s)
- Sayyad Khanizadeh
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.,Department of Virology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Asra Malekshahi
- Department of Virology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Hooman Hanifehpour
- Department of Microbiology, Cancer Biomedical Research Center (CBC), Tehran, Iran
| | - Mehdi Birjandi
- Department of Biostatistics and Epidemiology, School of Health and Nutrition, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Shirzad Fallahi
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran. .,Department of Parasitology and Mycology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| |
Collapse
|
21
|
Szobi A, Buranovská K, Vojtaššáková N, Lovíšek D, Özbaşak HÖ, Szeibeczederová S, Kapustian L, Hudáčová Z, Kováčová V, Drobná D, Putaj P, Bírová S, Čirková I, Čarnecký M, Kilián P, Jurkáček P, Čabanová V, Boršová K, Sláviková M, Vaňová V, Klempa B, Čekan P, Paul ED. Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system. Commun Biol 2023; 6:233. [PMID: 36864129 PMCID: PMC9979146 DOI: 10.1038/s42003-023-04612-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Sensitive and rapid point-of-care assays have been crucial in the global response to SARS-CoV-2. Loop-mediated isothermal amplification (LAMP) has emerged as an important diagnostic tool given its simplicity and minimal equipment requirements, although limitations exist regarding sensitivity and the methods used to detect reaction products. We describe the development of Vivid COVID-19 LAMP, which leverages a metallochromic detection system utilizing zinc ions and a zinc sensor, 5-Br-PAPS, to circumvent the limitations of classic detection systems dependent on pH indicators or magnesium chelators. We make important strides in improving RT-LAMP sensitivity by establishing principles for using LNA-modified LAMP primers, multiplexing, and conducting extensive optimizations of reaction parameters. To enable point-of-care testing, we introduce a rapid sample inactivation procedure without RNA extraction that is compatible with self-collected, non-invasive gargle samples. Our quadruplexed assay (targeting E, N, ORF1a, and RdRP) reliably detects 1 RNA copy/µl of sample (=8 copies/reaction) from extracted RNA and 2 RNA copies/µl of sample (=16 copies/reaction) directly from gargle samples, making it one of the most sensitive RT-LAMP tests and even comparable to RT-qPCR. Additionally, we demonstrate a self-contained, mobile version of our assay in a variety of high-throughput field testing scenarios on nearly 9,000 crude gargle samples. Vivid COVID-19 LAMP can be an important asset for the endemic phase of COVID-19 as well as preparing for future pandemics.
Collapse
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.
| |
Collapse
|
22
|
Moon SH, Kim SC, Kim BW, Park GJ, Chai HS, Kim YM, Kim HS, Park HS. SARS-CoV-2 molecular diagnostic point-of-care testing based on loop-mediated isothermal amplification: A prospective, single-center validation study. Heliyon 2023; 9:e14564. [PMID: 36942218 PMCID: PMC10014123 DOI: 10.1016/j.heliyon.2023.e14564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Objectives Rapid and accurate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests are crucial for controlling the spread of infections in emergency settings. This study evaluated the diagnostic accuracy of a point-of-care (POC) test based on loop-mediated isothermal amplification (LAMP) that produces rapid results within 30 min. Methods We prospectively included adult patients (age >19 years) who were diagnosed with SARS-CoV-2 infection within the last 3 days and symptomatic patients who had visited the emergency room. Posterior nasopharyngeal (PNP) swabs and throat swabs collected by physicians were used to test the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy, and Cohen's Kappa coefficient (k) of the POC index and reference reverse transcription quantitative polymerase chain reaction (RT-qPCR) test devices. Results Of the 352 participants, 102 (29.0%) tested positive via the RT-PCR-based reference test device; the RT-LAMP-based POC test had a sensitivity of 70.6% and specificity of 98.0%, with 93.5% PPV, 89.1% NPV, 35.5% PLR, and 3.4% NLR. Cohen's k correlation of results from the two devices was 0.74. The cycle threshold value between the positive and negative POC test results differed (17.6 vs. 24.6, p < 0.001). Conclusions The RT-LAMP POC test in the emergency medical setting has a fair predictive value in high viral load cases in terms of infectivity.
Collapse
Affiliation(s)
- Sung Hun Moon
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Sang-Chul Kim
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
- Department of Emergency Medicine, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowongu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Byung Woo Kim
- Department of Paramedic Science, Korea National University of Transportation, 61, Daehak-ro, Jeungpyeong-gun, Chungcheongbuk-do, 27909, Republic of Korea
| | - Gwan-Jin Park
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Hyun-Seok Chai
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Young Min Kim
- Department of Emergency Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Hee Sung Kim
- Department of Internal Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
- College of Medicine and Medical Research Institute, Chungbuk National University, 1 Chungdae-ro, Seowongu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| | - Hee Sue Park
- Department of Laboratory Medicine, Chungbuk National University Hospital, 776, 1st Sunhwan-ro, Seowon-gu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, Chungbuk National University, 1 Chungdae-ro, Seowongu, Cheongju-si, Chungcheongbuk-do 28646, Republic of Korea
| |
Collapse
|
23
|
Tavakoli-Koopaei R, Javadi-Zarnaghi F, Aboutalebian S, Mirhendi H. Malachite Green-Based Detection of SARS-CoV-2 by One-Step Reverse Transcription Loop-Mediated Isothermal Amplification. IRANIAN JOURNAL OF SCIENCE 2023. [PMCID: PMC9898859 DOI: 10.1007/s40995-022-01392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The pandemic of severe acute respiratory syndrome 2 (SARS-CoV-2) revealed the necessity of diagnosis of the infected people to prevent the prevalence infection cycle. Many commercial pathogen diagnosis methods are based on the detection of genomic materials. Isothermal amplification methods such as loop-mediated-isothermal amplification (LAMP) are the method of choice in these cases. Reverse transcription steps are efficiently coupled to LAMP for the detection of pathogens with genomic RNAs such as SARS-CoV-2. Many detection systems for LAMP include fluorescent readout systems. Although such systems result in desirable limits of detection, the need for special instrumentation is the main dispute of such systems to become real point of care assays. In contrast, colorimetric detection methods would reduce costs and improve the applicability of the system. In this study one-step reverse transcription-LAMP reaction was established that enables visual detection of the SARS-CoV-2 genome. Nasopharyngeal RNA samples were first validated by reverse transcription quantitative polymerase chain reaction and then subjected to RT-LAMP. To lower the cost associated with the readout system equipment, malachite green (MG) was used. The color change of MG to blue allowed visual detection of the virus. Firstly, experiments were set up as two-step RT-LAMP reaction to identify the best primer sets. In addition, MG concentration was optimized with the significant colorimetric signal for the positive samples. Next, a one-step colorimetric method was developed for the detection of SARS-CoV-2 based on MG color shift in 2 h.
Collapse
Affiliation(s)
- Reyhaneh Tavakoli-Koopaei
- grid.411750.60000 0001 0454 365XDepartment of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Fatemeh Javadi-Zarnaghi
- grid.411750.60000 0001 0454 365XDepartment of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Shima Aboutalebian
- grid.411036.10000 0001 1498 685XDepartment of Medical Parasitology and Mycology, School of Medicine, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- grid.411036.10000 0001 1498 685XDepartment of Medical Parasitology and Mycology, School of Medicine, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
24
|
Cao G, Lin K, Ai J, Cai J, Zhang H, Yu Y, Liu Q, Zhang X, Zhang Y, Fu Z, Song J, Wang H, Yuan G, Wang S, Guan M, Zhang W. A diagnostic accuracy study comparing RNA LAMP, direct LAMP, and rapid antigen testing from nasopharyngeal swabs. Front Microbiol 2022; 13:1063414. [PMID: 36620063 PMCID: PMC9813509 DOI: 10.3389/fmicb.2022.1063414] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction During the coronavirus disease 2019 (COVID-19) pandemic, the early detection and isolation of individuals infected with severe acute respiratory syndrome coronavirus disease 2 (SARS-CoV-2) through mass testing can effectively prevent disease transmission. SARS-CoV-2 nucleic acid rapid detection based on loop-mediated isothermal amplification (LAMP) may be appropriate to include in testing procedures. Methods We used 860 nasopharyngeal specimens from healthcare workers of Huashan Hospital and COVID-19 patients collected from April 7th to 21st, 2022, to assess the clinical diagnostic performance of the LAMP assay marketed by Shanghai GeneSc Biotech and compared it to the result of a rapid antigen test (RAT) head-to-head. Results Overall, the diagnostic performance of LAMP assay and RAT were as follows. The LAMP assay represented higher sensitivity and specificity than RAT, especially in the extracted RNA samples. The sensitivity was 70.92% and 92.91% for direct LAMP and RNA-LAMP assay, respectively, while the specificity was 99.86% and 98.33%. The LAMP assay had overall better diagnostic performance on the specimens with relatively lower C t values or collected in the early phase (≤7 days) of COVID-19. The combination of LAMP assay and RAT improved diagnostic efficiency, providing new strategies for rapidly detecting SARS-CoV-2. Conclusion The LAMP assay are suitable for mass screenings of SARS-CoV-2 infections in the general population.
Collapse
Affiliation(s)
- Guojun Cao
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ke Lin
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianpeng Cai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Yiqi Yu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Qihui Liu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinyun Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhangfan Fu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jieyu Song
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Hongyu Wang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Guanmin Yuan
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Sen Wang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,*Correspondence: Sen Wang,
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,Ming Guan,
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China,Wenhong Zhang,
| |
Collapse
|
25
|
Abe H, Ushijima Y, Bikangui R, Ondo GN, Moure A, Yali-Assy-Oyamli Y, Yoshikawa R, Lell B, Adegnika AA, Yasuda J. Long-term validation of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 from March 2020 to October 2021 in Central Africa, Gabon. PLoS Negl Trop Dis 2022; 16:e0010964. [PMID: 36455044 DOI: 10.1371/journal.pntd.0010964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/13/2022] [Accepted: 11/19/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Despite the development of several methods for diagnosing COVID-19, long-term validation of such methods remains limited. In the early phase of the COVID-19 pandemic, we developed a rapid and sensitive diagnostic method based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) methodology, which is suitable for point-of-care application or for use in resource-limited settings to detect SARS-CoV-2. To assess the applicability of the RT-LAMP assay technique to resource-limited regions, such as rural areas in Africa, and to verify the usability of the method against various SARS-CoV-2 variants, the method was validated using clinical samples collected longitudinally during the pandemic. METHODOLOGY/PRINCIPAL FINDINGS First, the sensitivity of the RT-LAMP assay for detecting 10 SARS-CoV-2 variants was evaluated using viral RNA samples extracted from cell culture with a portable battery-supported device, resulting in the successful detection of 20-50 copies of the viral genome within 15 min, regardless of the variant. COVID-19 positive samples collected in Gabon between March 2020 and October 2021 were used to evaluate the sensitivity of the assay and to calculate the copy number of the SARS-CoV-2 genome. More than 292 copies of the viral genome were detected with 100% probability within 15 min in almost all tests. CONCLUSIONS This long-term validation study clearly demonstrated the applicability of the RT-LAMP assay for the clinical diagnosis of COVID-19 in resource-limited settings of Africa, such as rural areas in Gabon. The results show the potential of the assay as a promising COVID-19 diagnostic method, especially in rural and remote regions located far from the official diagnosis facilities in urban or semi-urban areas.
Collapse
Affiliation(s)
- Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Yuri Ushijima
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | | | | | - Ayong Moure
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | | | - Rokusuke Yoshikawa
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Medical University of Vienna, Vienna, Austria
| | - Ayola A Adegnika
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research, Tübingen, Germany
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| |
Collapse
|
26
|
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: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/15/2021] [Accepted: 02/18/2022] [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.
Collapse
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
| | | | - 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
| |
Collapse
|
27
|
Allsopp RC, Cowley CM, Barber RC, Jones C, Holmes CW, Bird PW, Gohil SG, Blackmore C, Tobin MD, Brunskill N, Baker PN, Shaw JA. A rapid RT-LAMP SARS-CoV-2 screening assay for collapsing asymptomatic COVID-19 transmission. PLoS One 2022; 17:e0273912. [PMID: 36048856 PMCID: PMC9436079 DOI: 10.1371/journal.pone.0273912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To demonstrate the diagnostic performance of rapid SARS-CoV-2 RT-LAMP assays, comparing the performance of genomic versus sub-genomic sequence target with subsequent application in an asymptomatic screening population. METHODS RT-LAMP diagnostic specificity (DSe) and sensitivity (DSe) was determined using 114 RT-PCR clinically positive and 88 RT-PCR clinically negative swab samples processed through the diagnostic RT-PCR service within the University Hospitals of Leicester NHS Trust. A swab-based RT-LAMP SARS-CoV-2 screening programme was subsequently made available to all staff and students at the University of Leicester (Autumn 2020), implemented to ISO 15189:2012 standards using NHS IT infrastructure and supported by University Hospital Leicester via confirmatory NHS diagnostic laboratory testing of RT-LAMP 'positive' samples. RESULTS Validation samples reporting a Ct < 20 were detected at 100% DSe and DSp, reducing to 95% DSe (100% DSp) for all samples reporting a Ct < 30 (both genomic dual sub-genomic assays). Advisory screening identified nine positive cases in 1680 symptom free individuals (equivalent to 540 cases per 100,000) with results reported back to participants and feed into national statistics within 48 hours. CONCLUSION This work demonstrates the utility of a rapid RT-LAMP assay for collapsing transmission of SARS-CoV-2 in an asymptomatic screening population.
Collapse
Affiliation(s)
- Rebecca C. Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Caroline M. Cowley
- Leicester Molecular Diagnostics, Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Ruth C. Barber
- Leicester Precision Medicine Institute, University of Leicester, Leicester, United Kingdom
| | - Carolyn Jones
- Leicester Precision Medicine Institute, University of Leicester, Leicester, United Kingdom
| | - Christopher W. Holmes
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, United Kingdom
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Paul W. Bird
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, United Kingdom
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Shailesh G. Gohil
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Claire Blackmore
- Centre for Environmental Health and Sustainability, University of Leicester, Leicester, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - Nigel Brunskill
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
| | - Philip N. Baker
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
- College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Jacqui A. Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| |
Collapse
|
28
|
Suwarti S, Zanjabila S, Bonifacius, Da Costa Y, Bogh C, Subekti D, Jeny J, Dewi AM, Nuraeni N, Rahardjani M, Elyazar I, Nelwan EJ, Shankar AH, Baird JK, Hamers RL. Evaluating Saliva Sampling with Reverse Transcription Loop-mediated Isothermal Amplification to Improve Access to SARS-CoV-2 Diagnosis in Low-Resource Settings. Am J Trop Med Hyg 2022; 107:284-290. [PMID: 35895405 PMCID: PMC9393441 DOI: 10.4269/ajtmh.22-0230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 11/07/2022] Open
Abstract
Standard diagnosis of SARS-CoV-2 by nasopharyngeal swab (NPS) and real-time reverse transcriptase-polymerase chain reaction (PCR) requires a sophisticated laboratory, skilled staff, and expensive reagents that are difficult to establish and maintain in isolated, low-resource settings. In the remote setting of tropical Sumba Island, eastern Indonesia, we evaluated alternative sampling with fresh saliva (FS) and testing with colorimetric loop-medicated isothermal amplification (LAMP). Between August 2020 and May 2021, we enrolled 159 patients with suspected SARS-CoV-2 infection, of whom 75 (47%) had a positive PCR on NPS (median cycle threshold [Ct] value: 27.6, interquartile range: 12.5-37.6). PCR on FS had a sensitivity of 72.5% (50/69, 95% confidence interval [CI]: 60.4-82.5) and a specificity of 85.7% (66/77, 95% CI: 75.9-92.6), and positive (PPV) and negative (NPV) predictive values of 82.0% (95% CI: 0.0-90.6) and 77.6% (95% CI: 67.3-86.0), respectively. LAMP on NPS had a sensitivity of 68.0% (51/75, 95% CI: 56.2-78.3) and a specificity of 70.8% (63/84, 95% CI: 58.9-81.0), with PPV 70.8% (95% CI: 58.9-81.0) and NPV 72.4% (95% CI: 61.8-81.5%). LAMP on FS had a sensitivity of 62.3% (43/69, 95% CI: 49.8-73.7%) and a specificity of 72.7% (56/77, 95% CI: 61.4-82.3%), with PPV 67.2% (95% CI: 54.3-78.4) and NPV 68.3% (95% CI: 57.1-78.1%). LAMP sensitivity was higher for NPS and FS specimens with high viral loads (87.1% and 75.0% for Ct value < 26, respectively). Dried saliva on filter paper was stable for 4 days at room temperature. LAMP on either NPS or FS could offer an accessible alternative for SARS-CoV-2 diagnosis in low-resource settings, with potential for optimizing sample collection and processing, and selection of gene targets.
Collapse
Affiliation(s)
- Suwarti Suwarti
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | | | - Bonifacius
- Karitas Hospital, Sumba Barat Daya, Nusa Tenggara Timur, Indonesia
| | - Yacobus Da Costa
- Pratama Reda Bolo Hospital, Sumba Barat Daya, Sumba, East Nusa Tenggara, Indonesia
| | - Claus Bogh
- Sumba Foundation, Sumba Barat, Nusa Tenggara Timur, Indonesia
| | - Decy Subekti
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Jeny Jeny
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Ayu Madri Dewi
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Nunung Nuraeni
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Mutia Rahardjani
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Iqbal Elyazar
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
| | - Erni J. Nelwan
- Tropical Infection Division, Internal Medicine Department, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Anuraj H Shankar
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - J. Kevin Baird
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Raph L. Hamers
- Eijkman-Oxford Clinical Research Unit, Jakarta, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
29
|
Zahavi M, Rohana H, Azrad M, Shinberg B, Peretz A. Rapid SARS-CoV-2 Detection Using the Lucira™ Check It COVID-19 Test Kit. Diagnostics (Basel) 2022; 12:diagnostics12081877. [PMID: 36010227 PMCID: PMC9406928 DOI: 10.3390/diagnostics12081877] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
The need for the early identification of SARS-CoV-2 has let to a quest for reliable tests that meet the standards of polymerase chain reaction (PCR) tests, on the one hand, and are low-cost, easy-to-use, and fast, on the other hand. One such test is the Lucira™ Check It COVID-19 Test kit (“Lucira”) (Lucira Health, Inc., Emeryville, CA, USA), which utilizes real-time loop-mediated isothermal amplification technology, developed for at-home use. This study evaluated the clinical sensitivity and specificity of Lucira in identifying the virus in 190 nasopharyngeal samples collected between January and October 2021. Each sample was also subjected to RT-PCR. All negative RT-PCR results were paralleled by a negative Lucira result. Out of 90 participants who had a positive RT-PCR result, 82 (91.1%) tested positive by Lucira. Among the 72 symptomatic participants, 67 (93%) tested positive by Lucira. All samples with a positive RT-PCR result with a threshold cycle (Ct) > 36, yielded a negative Lucira result. In addition, a significant positive correlation was found between Ct and time-to-positivity with Lucira (R = 0.8612, p < 0.0001). The implementation of such a portable and affordable assay may aid in breaking the COVID-19 transmission chain.
Collapse
Affiliation(s)
- Maya Zahavi
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
- Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Hanan Rohana
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
| | - Maya Azrad
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
| | - Bracha Shinberg
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
| | - Avi Peretz
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
- Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
- Correspondence: ; Tel.: +972-4-665-2322
| |
Collapse
|
30
|
O'Hara RW, Brown B, Hughes A, McEwan A, Birtles A, Hawker A, Davies E, Farooq HZ, Tilston P, Haigh D, Hesketh L, Dodgson A, Dodgson K, Shazaad A, Guiver M, Machin N. Evaluation of the artus® Prep&Amp UM RT-PCR for detection of SARS-CoV-2 from nasopharyngeal swabs without prior nucleic acid eluate extraction. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100098. [PMID: 35874465 PMCID: PMC9287855 DOI: 10.1016/j.jcvp.2022.100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022] Open
Abstract
Here we describe a retrospective clinical evaluation of the QIAGEN artus® SARS-CoV-2 Prep&Amp UM RT-PCR assay that detects SARS-CoV-2 RNA without the need for a nucleic acid eluate extraction procedure. Using Roche SARS-CoV-2 RT-PCR on the cobas® 8800 platform as a reference standard, a total of 225 confirmed SARS-CoV-2 positive and 320 negative nasopharyngeal swabs in viral transport media, were used to evaluate the artus® assay. Using the RT-PCR cycle threshold as a semi-quantitative marker of viral load, an assessment of over 370,000 SARS-CoV-2 RT-PCR positive results was used in the design of the reference positive specimen cohort. The viral load of all reference positive specimens used in the evaluation was a unique and accurate representation of the range and levels of SARS-CoV-2 positivity observed over a 13-month period of the COVID-19 pandemic. The artus® RT-PCR detects the presence of SARS-CoV-2 RNA, an internal control, and the human RNase P gene to ensure specimen quality. The diagnostic sensitivity of artus® was 92.89% with a specificity of 100%. To assess the analytical sensitivity, a limit of detection was performed using the 1st WHO NIBSC SARS-CoV-2 international standard, recording a 95% LOD of 1.1 × 103 IU/ml. The total invalid rate of specimens was 7.34% due to a lack of detectable RNase P (Ct >35). The artus® SARS-CoV-2 Prep&Amp UM RT-PCR assay is a new rapid RT-PCR assay, which may be considered to produce acceptable levels of diagnostic sensitivity and specificity whilst potentially halving the laboratory processing time.
Collapse
Affiliation(s)
- Robert William O'Hara
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Benjamin Brown
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Angela Hughes
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ashley McEwan
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew Birtles
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Adam Hawker
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Emma Davies
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Hamzah Z Farooq
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Infectious Diseases & Tropical Medicine, North Manchester General Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Peter Tilston
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Dominic Haigh
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Louise Hesketh
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew Dodgson
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
- University of Manchester, Manchester, UK
| | - Kirsty Dodgson
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
- University of Manchester, Manchester, UK
| | - Ahmad Shazaad
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
- University of Manchester, Manchester, UK
| | - Malcolm Guiver
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
- University of Manchester, Manchester, UK
| | - Nicholas Machin
- Department of Virology, UK Health Security Agency Manchester, Oxford Road, Manchester M13 9WL, UK
- Department of Virology, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
- University of Manchester, Manchester, UK
| |
Collapse
|
31
|
A molecular beacon biosensor for viral RNA detection based on HyCaSD strategy. Anal Chim Acta 2022; 1221:340134. [DOI: 10.1016/j.aca.2022.340134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/26/2022] [Indexed: 11/24/2022]
|
32
|
Li Z, Bruce JL, Cohen B, Cunningham CV, Jack WE, Kunin K, Langhorst BW, Miller J, Moncion RA, Poole CB, Premsrirut PK, Ren G, Roberts RJ, Tanner NA, Zhang Y, Carlow CKS. Development and implementation of a simple and rapid extraction-free saliva SARS-CoV-2 RT-LAMP workflow for workplace surveillance. PLoS One 2022; 17:e0268692. [PMID: 35617204 PMCID: PMC9135294 DOI: 10.1371/journal.pone.0268692] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 01/12/2023] Open
Abstract
Effective management of the COVID-19 pandemic requires widespread and frequent testing of the population for SARS-CoV-2 infection. Saliva has emerged as an attractive alternative to nasopharyngeal samples for surveillance testing as it does not require specialized personnel or materials for its collection and can be easily provided by the patient. We have developed a simple, fast, and sensitive saliva-based testing workflow that requires minimal sample treatment and equipment. After sample inactivation, RNA is quickly released and stabilized in an optimized buffer, followed by reverse transcription loop-mediated isothermal amplification (RT-LAMP) and detection of positive samples using a colorimetric and/or fluorescent readout. The workflow was optimized using 1,670 negative samples collected from 172 different individuals over the course of 6 months. Each sample was spiked with 50 copies/μL of inactivated SARS-CoV-2 virus to monitor the efficiency of viral detection. Using pre-defined clinical samples, the test was determined to be 100% specific and 97% sensitive, with a limit of detection of 39 copies/mL. The method was successfully implemented in a CLIA laboratory setting for workplace surveillance and reporting. From April 2021-February 2022, more than 30,000 self-collected samples from 755 individuals were tested and 85 employees tested positive mainly during December and January, consistent with high infection rates in Massachusetts and nationwide.
Collapse
Affiliation(s)
- Zhiru Li
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Barry Cohen
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - William E. Jack
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Katell Kunin
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Jacob Miller
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Reynes A. Moncion
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | | | - Guoping Ren
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Nathan A. Tanner
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Yinhua Zhang
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | |
Collapse
|
33
|
Kontos E, Samimi A, Hakze-van der Honing RW, Priem J, Avarguès-Weber A, Haverkamp A, Dicke M, Gonzales JL, van der Poel WHM. Bees can be trained to identify SARS-CoV-2 infected samples. Biol Open 2022; 11:275246. [PMID: 35502829 PMCID: PMC9096705 DOI: 10.1242/bio.059111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/20/2022] [Indexed: 11/24/2022] Open
Abstract
The COVID-19 pandemic has illustrated the need for the development of fast and reliable testing methods for novel, zoonotic, viral diseases in both humans and animals. Pathologies lead to detectable changes in the volatile organic compound (VOC) profile of animals, which can be monitored, thus allowing the development of a rapid VOC-based test. In the current study, we successfully trained honeybees (Apis mellifera) to identify SARS-CoV-2 infected minks (Neovison vison) thanks to Pavlovian conditioning protocols. The bees can be quickly conditioned to respond specifically to infected mink's odours and could therefore be part of a wider SARS-CoV-2 diagnostic system. We tested two different training protocols to evaluate their performance in terms of learning rate, accuracy and memory retention. We designed a non-invasive rapid test in which multiple bees are tested in parallel on the same samples. This provided reliable results regarding a subject's health status. Using the data from the training experiments, we simulated a diagnostic evaluation trial to predict the potential efficacy of our diagnostic test, which yielded a diagnostic sensitivity of 92% and specificity of 86%. We suggest that a honeybee-based diagnostics can offer a reliable and rapid test that provides a readily available, low-input addition to the currently available testing methods. A honeybee-based diagnostic test might be particularly relevant for remote and developing communities that lack the resources and infrastructure required for mainstream testing methods. Summary: Honeybees can be quickly trained to identify SARS-CoV2 infected samples. SARS-CoV2 positive sample detection by bees reached a diagnostic sensitivity of 92% and a specificity of 86%. Honeybee-based diagnostics can offer a reliable and rapid test that provides a readily available, low-input addition to the currently available testing methods.
Collapse
Affiliation(s)
- Evangelos Kontos
- InsectSense, Plus Ultra-II Building, Bronland, 10, 6708 WH, Wageningen, The Netherlands.,Laboratory of Entomology, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Aria Samimi
- InsectSense, Plus Ultra-II Building, Bronland, 10, 6708 WH, Wageningen, The Netherlands
| | | | - Jan Priem
- Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB, Lelystad, The Netherlands
| | - Aurore Avarguès-Weber
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse; CNRS, UPS, 118 Route de Narbonne, 31062 Toulouse, France
| | | | - Marcel Dicke
- Laboratory of Entomology, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Jose L Gonzales
- Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB, Lelystad, The Netherlands
| | - Wim H M van der Poel
- Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB, Lelystad, The Netherlands
| |
Collapse
|
34
|
DeFina SM, Wang J, Yang L, Zhou H, Adams J, Cushing W, Tuohy B, Hui P, Liu C, Pham K. SaliVISION: a rapid saliva-based COVID-19 screening and diagnostic test with high sensitivity and specificity. Sci Rep 2022; 12:5729. [PMID: 35388102 PMCID: PMC8986854 DOI: 10.1038/s41598-022-09718-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic-caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)– has posed a global threat and presented with it a multitude of economic and public-health challenges. Establishing a reliable means of readily available, rapid diagnostic testing is of paramount importance in halting the spread of COVID-19, as governments continue to ease lockdown restrictions. The current standard for laboratory testing utilizes reverse transcription quantitative polymerase chain reaction (RT-qPCR); however, this method presents clear limitations in requiring a longer run-time as well as reduced on-site testing capability. Therefore, we investigated the feasibility of a reverse transcription looped-mediated isothermal amplification (RT-LAMP)-based model of rapid COVID-19 diagnostic testing which allows for less invasive sample collection, named SaliVISION. This novel, two-step, RT-LAMP assay utilizes a customized multiplex primer set specifically targeting SARS-CoV-2 and a visual report system that is ready to interpret within 40 min from the start of sample processing and does not require a BSL-2 level testing environment or special laboratory equipment. When compared to the SalivaDirect and Thermo Fisher Scientific TaqPath RT-qPCR testing platforms, the respective sensitivities of the SaliVISION assay are 94.29% and 98.28% while assay specificity was 100% when compared to either testing platform. Our data illustrate a robust, rapid diagnostic assay in our novel RT-LAMP test design, with potential for greater testing throughput than is currently available through laboratory testing and increased on-site testing capability.
Collapse
Affiliation(s)
- Samuel M DeFina
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jianhui Wang
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Lei Yang
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Han Zhou
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jennifer Adams
- Department of Laboratory Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - William Cushing
- Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA.,Yale New Haven Hospital, New Haven, CT, USA
| | - Beth Tuohy
- Yale University Health Services, Yale University, New Haven, CT, USA
| | - Pei Hui
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA.
| | - Kien Pham
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA.
| |
Collapse
|
35
|
Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, Snell G, Wise EL, Goring A, Vincent-Mistiaen Z, Grippon S, Sawyer J, Cassar C, Cross D, Lewis T, Reid SM, Rivers S, James J, Skinner P, Banyard A, Davies K, Ptasinska A, Whalley C, Ferguson J, Bryer C, Poxon C, Bosworth A, Kidd M, Richter A, Burton J, Love H, Fouch S, Tillyer C, Sowood A, Patrick H, Moore N, Andreou M, Morant N, Houghton R, Parker J, Slater-Jefferies J, Brown I, Gretton C, Deans Z, Porter D, Cortes NJ, Douglas A, Hill SL, Godfrey KM, Fowler VL. Reverse-Transcription Loop-Mediated Isothermal Amplification Has High Accuracy for Detecting Severe Acute Respiratory Syndrome Coronavirus 2 in Saliva and Nasopharyngeal/Oropharyngeal Swabs from Asymptomatic and Symptomatic Individuals. J Mol Diagn 2022; 24:320-336. [PMID: 35121140 PMCID: PMC8806713 DOI: 10.1016/j.jmoldx.2021.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/02/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Previous studies have described reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal/oropharyngeal swab and saliva samples. This multisite clinical evaluation describes the validation of an improved sample preparation method for extraction-free RT-LAMP and reports clinical performance of four RT-LAMP assay formats for SARS-CoV-2 detection. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples from asymptomatic and symptomatic individuals across health care and community settings. For direct RT-LAMP, overall diagnostic sensitivity (DSe) was 70.35% (95% CI, 63.48%-76.60%) on swabs and 84.62% (95% CI, 79.50%-88.88%) on saliva, with diagnostic specificity of 100% (95% CI, 98.98%-100.00%) on swabs and 100% (95% CI, 99.72%-100.00%) on saliva, compared with quantitative RT-PCR (RT-qPCR); analyzing samples with RT-qPCR ORF1ab CT values of ≤25 and ≤33, DSe values were 100% (95% CI, 96.34%-100%) and 77.78% (95% CI, 70.99%-83.62%) for swabs, and 99.01% (95% CI, 94.61%-99.97%) and 87.61% (95% CI, 82.69%-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and diagnostic specificity were 96.06% (95% CI, 92.88%-98.12%) and 99.99% (95% CI, 99.95%-100%) for swabs, and 80.65% (95% CI, 73.54%-86.54%) and 99.99% (95% CI, 99.95%-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use cases, including frequent, interval-based direct RT-LAMP of saliva from asymptomatic individuals who may otherwise be missed using symptomatic testing alone.
Collapse
Affiliation(s)
- Stephen P Kidd
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Daniel Burns
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; School of Electronics and Computer Science, University of Southampton, Southampton, United Kingdom
| | - Bryony Armson
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom; vHive, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Andrew D Beggs
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | | | - Anthony Williams
- University of Southampton and Division of Specialist Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gemma Snell
- University of Southampton and Division of Specialist Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Emma L Wise
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Alice Goring
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | | | - Seden Grippon
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Jason Sawyer
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Claire Cassar
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - David Cross
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Thomas Lewis
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Scott M Reid
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Samantha Rivers
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Joe James
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Paul Skinner
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Ashley Banyard
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | - Anetta Ptasinska
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Celina Whalley
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Jack Ferguson
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Claire Bryer
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Charlie Poxon
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Andrew Bosworth
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Michael Kidd
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Public Health West Midlands Laboratory, Birmingham, United Kingdom
| | - Alex Richter
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jane Burton
- High Containment Microbiology, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Hannah Love
- High Containment Microbiology, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Sarah Fouch
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Claire Tillyer
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Amy Sowood
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Helen Patrick
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Nathan Moore
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, United Kingdom
| | - Rebecca Houghton
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Joe Parker
- National Biofilms Innovation Centre, University of Southampton, Southampton, United Kingdom
| | | | - Ian Brown
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Cosima Gretton
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Zandra Deans
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Deborah Porter
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Nicholas J Cortes
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; Gibraltar Health Authority, Gibraltar, United Kingdom
| | - Angela Douglas
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Sue L Hill
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Keith M Godfrey
- National Institute for Health Research Southampton Biomedical Research Centre, University of Southampton and University Hospital, Southampton, United Kingdom; MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, United Kingdom.
| | - Veronica L Fowler
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| |
Collapse
|
36
|
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: 1.7] [Reference Citation Analysis] [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.
Collapse
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.)
| |
Collapse
|
37
|
Dong Y, Zhao Y, Li S, Wan Z, Lu R, Yang X, Yu G, Reboud J, Cooper JM, Tian Z, Zhang C. Multiplex, Real-Time, Point-of-care RT-LAMP for SARS-CoV-2 Detection Using the HFman Probe. ACS Sens 2022; 7:730-739. [PMID: 35192340 PMCID: PMC8887655 DOI: 10.1021/acssensors.1c02079] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/08/2022] [Indexed: 12/11/2022]
Abstract
Viral evolution impacts diagnostic test performance through the emergence of variants with sequences affecting the efficiency of primer binding. Such variants that evade detection by nucleic acid-based tests are subject to selective pressure, enabling them to spread more efficiently. Here, we report a variant-tolerant diagnostic test for SARS-CoV-2 using a loop-mediated isothermal nucleic acid-based amplification (LAMP) assay containing high-fidelity DNA polymerase and a high-fidelity DNA polymerase-medicated probe (HFman probe). In addition to demonstrating a high tolerance to variable SARS-CoV-2 viral sequences, the mechanism also overcomes frequently observed limitations of LAMP assays arising from non-specific amplification within multiplexed reactions performed in a single "pot". Results showed excellent clinical performance (sensitivity 94.5%, specificity 100%, n = 190) when compared directly to a commercial gold standard reverse transcription quantitative polymerase chain reaction assay for the extracted RNA from nasopharyngeal samples and the capability of detecting a wide range of sequences containing at least alpha and delta variants. To further validate the test with no sample processing, directly from nasopharyngeal swabs, we also detected SARS-CoV-2 in positive clinical samples (n = 49), opening up the possibility for the assay's use in decentralized testing.
Collapse
Affiliation(s)
- Yajuan Dong
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjuan Zhao
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Shenwei Li
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Zhenzhou Wan
- Medical
Laboratory of Taizhou Fourth People’s Hospital, Taizhou 225300, China
| | - Renfei Lu
- Clinical
Laboratory, Nantong Third Hospital Affiliated
to Nantong University, Nantong 226006, China
| | - Xianguang Yang
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Guoying Yu
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Julien Reboud
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Jonathan M. Cooper
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Zhengan Tian
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Chiyu Zhang
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| |
Collapse
|
38
|
Evaluation of a Novel Direct RT-LAMP Assay for the Detection of SARS Cov-2 from Saliva Samples in Asymptomatic Individuals. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100074. [PMID: 35345440 PMCID: PMC8942569 DOI: 10.1016/j.jcvp.2022.100074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [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.
Collapse
|
39
|
Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
Collapse
Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| |
Collapse
|
40
|
Papadakis G, Pantazis AK, Fikas N, Chatziioannidou S, Tsiakalou V, Michaelidou K, Pogka V, Megariti M, Vardaki M, Giarentis K, Heaney J, Nastouli E, Karamitros T, Mentis A, Zafiropoulos A, Sourvinos G, Agelaki S, Gizeli E. Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples. Sci Rep 2022; 12:3775. [PMID: 35260588 PMCID: PMC8904468 DOI: 10.1038/s41598-022-06632-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/27/2022] [Indexed: 02/08/2023] Open
Abstract
Loop-mediated isothermal amplification is known for its high sensitivity, specificity and tolerance to inhibiting-substances. In this work, we developed a device for performing real-time colorimetric LAMP combining the accuracy of lab-based quantitative analysis with the simplicity of point-of-care testing. The device innovation lies on the use of a plastic tube anchored vertically on a hot surface while the side walls are exposed to a mini camera able to take snapshots of the colour change in real time during LAMP amplification. Competitive features are the rapid analysis (< 30 min), quantification over 9 log-units, crude sample-compatibility (saliva, tissue, swabs), low detection limit (< 5 copies/reaction), smartphone-operation, fast prototyping (3D-printing) and ability to select the dye of interest (Phenol red, HNB). The device’s clinical utility is demonstrated in cancer mutations-analysis during the detection of 0.01% of BRAF-V600E-to-wild-type molecules from tissue samples and COVID-19 testing with 97% (Ct < 36.8) and 98% (Ct < 30) sensitivity when using extracted RNA and nasopharyngeal-swabs, respectively. The device high technology-readiness-level makes it a suitable platform for performing any colorimetric LAMP assay; moreover, its simple and inexpensive fabrication holds promise for fast deployment and application in global diagnostics.
Collapse
Affiliation(s)
- G Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece. .,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece.
| | - A K Pantazis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - N Fikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - S Chatziioannidou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece.,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - V Tsiakalou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - K Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - V Pogka
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - M Megariti
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - M Vardaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - K Giarentis
- Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - J Heaney
- Advanced Pathogens Diagnostics Unit, University College London Hospitals NHS Trust, London, WC1H 9AX, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - E Nastouli
- Advanced Pathogens Diagnostics Unit, University College London Hospitals NHS Trust, London, WC1H 9AX, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - T Karamitros
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - A Mentis
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - A Zafiropoulos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - G Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - S Agelaki
- Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece.,Department of Medical Oncology, University General Hospital, 71110, Heraklion, Greece
| | - E Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece. .,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece.
| |
Collapse
|
41
|
Advances in nucleic acid amplification techniques (NAATs): COVID-19 point-of-care diagnostics as an example. Biosens Bioelectron 2022; 206:114109. [PMID: 35245867 DOI: 10.1016/j.bios.2022.114109] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/24/2022] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Achieving superhigh sensitivity is the ultimate goal for bio-detection in modern analytical science and life science. Among variable signal amplification strategies, nucleic acid amplification technologies are revolutionizing the field of bio-detection, providing greater possibilities in novel diagnosis achieving high efficiency, specificity, and cost-effectiveness. Nucleic acid amplification techniques (NAATs), such as Polymerase Chain Reaction (PCR), Rolling Circle Amplification (RCA), Loop-Mediated Isothermal Amplification (LAMP), Recombinase Polymerase Amplification (RPA), CRISPR-related amplification, and others are dominating methods employed in research and clinical settings. They each provide distinctively unique features that can offer desirable performance in terms of sensitivity, specificity, simplicity, stability, and cost. NAATs are in unmet demand in molecular diagnosis, especially in point-of-care scenario. This review will discuss the principles and recent advancements of each NAAT, respectively, revealing their strengths and challenges in achieving rapid and accurate bio-detection with a focus on point-of-care diagnosis. Furthermore, this review will explore the application of each of the technologies through the contemporary COVID-19 pandemic, analyzing their ability in point-of-care diagnosis of the COVID-19 with high sensitivity to emphasize significance of developing NAATs based methods in battling COVID-19. Finally, advantages and potentials of each NAAT in enhancements of sensitivity and specificity in bio-detection from bench side to the bedside will be discussed, aiming for full exploitation of capability of each NAAT. This review will provide novel aspects in the selection and combination of usages of various NAATs based on their distinctive characteristics and limitations. A possible advancing direction of future accurate POCT is also proposed.
Collapse
|
42
|
Lasserre P, Balansethupathy B, Vezza VJ, Butterworth A, Macdonald A, Blair EO, McAteer L, Hannah S, Ward AC, Hoskisson PA, Longmuir A, Setford S, Farmer ECW, Murphy ME, Flynn H, Corrigan DK. SARS-CoV-2 Aptasensors Based on Electrochemical Impedance Spectroscopy and Low-Cost Gold Electrode Substrates. Anal Chem 2022; 94:2126-2133. [PMID: 35043638 PMCID: PMC8790822 DOI: 10.1021/acs.analchem.1c04456] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/24/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 diagnostic practices broadly involve either quantitative polymerase chain reaction (qPCR)-based nucleic amplification of viral sequences or antigen-based tests such as lateral flow assays (LFAs). Reverse transcriptase-qPCR can detect viral RNA and is the gold standard for sensitivity. However, the technique is time-consuming and requires expensive laboratory infrastructure and trained staff. LFAs are lower in cost and near real time, and because they are antigen-based, they have the potential to provide a more accurate indication of a disease state. However, LFAs are reported to have low real-world sensitivity and in most cases are only qualitative. Here, an antigen-based electrochemical aptamer sensor is presented, which has the potential to address some of these shortfalls. An aptamer, raised to the SARS-CoV-2 spike protein, was immobilized on a low-cost gold-coated polyester substrate adapted from the blood glucose testing industry. Clinically relevant detection levels for SARS-CoV-2 are achieved in a simple, label-free measurement format using sample incubation times as short as 15 min on nasopharyngeal swab samples. This assay can readily be optimized for mass manufacture and is compatible with a low-cost meter.
Collapse
Affiliation(s)
- Perrine Lasserre
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | | | - Vincent J. Vezza
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Adrian Butterworth
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Alexander Macdonald
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Ewen O. Blair
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Liam McAteer
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Stuart Hannah
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Andrew C. Ward
- Department
of Civil and Environmental Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, U.K.
| | - Paul A. Hoskisson
- Strathclyde
Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, U.K.
| | - Alistair Longmuir
- LifeScan
Scotland Ltd, Beechwood Park North, Inverness IV2 3ED, U.K.
| | - Steven Setford
- LifeScan
Scotland Ltd, Beechwood Park North, Inverness IV2 3ED, U.K.
| | - Eoghan C. W. Farmer
- NHS GGC,
Department of Microbiology, Glasgow Royal
Infirmary, NEW Lister Building, Glasgow G31 2ER, United Kingdom
| | - Michael E. Murphy
- NHS GGC,
Department of Microbiology, Glasgow Royal
Infirmary, NEW Lister Building, Glasgow G31 2ER, United Kingdom
- School
of Medicine, Dentistry & Nursing, College of Medical Veterinary
& Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Harriet Flynn
- Aptamer
Group, Suite 2.78−2.91,
Bio Centre, Innovation Way, Heslington, York YO10 5NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, United Kingdom
| | - Damion K. Corrigan
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| |
Collapse
|
43
|
Lai MY, Suppiah J, Thayan R, Ismail I, Mustapa NI, Soh TST, Hassan AH, Peariasamy KM, Lee YL, Lau YL. RNA purification-free detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP). Trop Med Health 2022; 50:2. [PMID: 34980275 PMCID: PMC8723997 DOI: 10.1186/s41182-021-00396-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current diagnosis of SARS-CoV-2 infection relies on RNA purification prior to amplification. Typical extraction methods limit the processing speed and turnaround time for SARS-CoV-2 diagnostic testing. METHODS Here, we applied reverse transcription loop-mediated isothermal amplification directly onto human clinical swabs samples to amplify the RNA from SARS-CoV-2 swab samples after processing with chelating resin. RESULTS By testing our method on 64 samples, we managed to develop an RT-LAMP assay with 95.9% sensitivity (95% CI 86 to 99.5%) and 100% specificity (95% CI 78.2-100%). CONCLUSION The entire process including sample processing can be completed in approximately 50 min. This method has promising potential to be applied as a fast, simple and inexpensive diagnostic tool for the detection of SARS-CoV-2.
Collapse
Affiliation(s)
- Meng Yee Lai
- Department of Parasitology, Faculty of Medicine, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jeyanthi Suppiah
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Ravindran Thayan
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Ilyiana Ismail
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Sungai Buloh, Selangor, Malaysia
| | - Nur Izati Mustapa
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Sungai Buloh, Selangor, Malaysia
| | - Tuan Suhaila Tuan Soh
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Sungai Buloh, Selangor, Malaysia
| | - Afifah Haji Hassan
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Sungai Buloh, Selangor, Malaysia
| | - Kalaiarasu M Peariasamy
- Institute for Clinical Research, National Institutes of Health, Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Yee Leng Lee
- Clinical Research Centre, Hospital Sungai Buloh, Ministry of Health, Sungai Buloh, Selangor, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, University Malaya, 50603, Kuala Lumpur, Malaysia.
| |
Collapse
|
44
|
Coltella L, Ranno S, Piccioni L, Linardos G, Colagrossi L, Agosta M, Russo C, Concato C, Campana A, Muda AO, Villani A, Perno CF. Quantitative SARS-CoV-2 antigen test as a tool able to predict the stage of the infection. J Infect 2021; 84:418-467. [PMID: 34953907 PMCID: PMC9428766 DOI: 10.1016/j.jinf.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/02/2021] [Accepted: 12/15/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Luana Coltella
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Stefania Ranno
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy.
| | - Livia Piccioni
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Giulia Linardos
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Luna Colagrossi
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Marilena Agosta
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Cristina Russo
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Carlo Concato
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Andrea Campana
- Department of Emergency, Acceptance and General Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Andrea Onetti Muda
- Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Alberto Villani
- Department of Emergency, Acceptance and General Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| | - Carlo Federico Perno
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children Hospital IRCCS, Piazza Sant'Onofrio, 4 00165 Rome, Italy
| |
Collapse
|
45
|
Au WY, Cheung PPH. Diagnostic performances of common nucleic acid tests for SARS-CoV-2 in hospitals and clinics: a systematic review and meta-analysis. THE LANCET. MICROBE 2021; 2:e704-e714. [PMID: 34661181 PMCID: PMC8510644 DOI: 10.1016/s2666-5247(21)00214-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND An optimised standard experimental setup across different hospitals is urgently needed to ensure consistency in nucleic acid test results for SARS-CoV-2 detection. A standard comparison across different nucleic acid tests and their optimal experimental setups is not present. We assessed the performance of three common nucleic acid tests, namely digital PCR (dPCR), quantitative PCR (qPCR), and loop-mediated isothermal amplification (LAMP), to detect SARS-CoV-2 in clinical settings. METHODS In this systematic review and meta-analysis we compared sensitivity and specificity of qPCR, dPCR, and LAMP and their performances when different experimental setups (namely specimen type used, use of RNA extraction, primer-probe sets, and RNA extraction methods) are applied. We searched PubMed, BioRxiv, MedRxiv, SciFinder, and ScienceDirect for studies and preprints published between Feb 29 and Dec 15, 2020. Included dPCR, qPCR, and LAMP studies using any type of human specimens should report the number of true-positive, true-negative, false-positive, and false-negative cases with Emergency Use Authorization (EUA)-approved PCR assays as the comparator. Studies with a sample size of less than ten, descriptive studies, case studies, reviews, and duplicated studies were excluded. Pooled sensitivity and specificity were computed from the true and false positive and negative cases using Reitsma's bivariate random-effects and bivariate latent class models. Test performance reported in area under the curve (AUC) of the three nucleic acid tests was further compared by pooling studies with similar experimental setups (eg, tests that used RNA extracted pharyngeal swabs but with either the open reading frame 1ab or the N primer). Heterogeneity was assessed and reported in I 2 and τ2. FINDINGS Our search identified 1277 studies of which we included 66 studies (11 dPCR, 32 qPCR, and 23 LAMP) with 15 017 clinical samples in total in our systematic review and 52 studies in our meta-analysis. dPCR had the highest pooled diagnostic sensitivity (94·1%, 95% CI 88·9-96·6, by Reitsma's model and 95·8%, 54·9-100·0, by latent class model), followed by qPCR (92·7%, 88·3-95·6, and 93·4%, 60·9-99·9) and LAMP (83·3%, 76·9-88·2, and 86·2%, 20·7-99·9), using EUA-approved PCR kits as the reference standard. LAMP was the most specific with a pooled estimate of 96·3% (93·8-97·8) by Reitsma's model and 94·3% (49·1-100·0) by latent class model, followed by qPCR (92·9%, 87·2-96·2, and 93·1%, 47·1-100·0) and dPCR (78·5%, 57·4-90·8, and 73·8%, 0·9-100·0). The overall heterogeneity was I 2 0·5% (τ2 2·79) for dPCR studies, 0% (4·60) for qPCR studies, and 0% (3·96) for LAMP studies. AUCs of the three nucleic acid tests were the highest and differed the least between tests (ie, AUC>0·98 for all tests) when performed with RNA extracted pharyngeal swabs using SARS-CoV-2 open reading frame 1ab primer. INTERPRETATION All three nucleic acid tests consistently perform better with pharyngeal swabs using SARS-CoV-2 open reading frame 1ab primer with RNA extraction. dPCR was shown to be the most sensitive, followed by qPCR and LAMP. However, their accuracy does not differ significantly. Instead, accuracy depends on specific experimental conditions, implying that more efforts should be directed to optimising the experimental setups for the nucleic acid tests. Hence, our results could be a reference for optimising and establishing a standard nucleic acid test protocol that is applicable in laboratories worldwide. FUNDING University Grants Committee and The Chinese University of Hong Kong.
Collapse
Affiliation(s)
- Wing Ying Au
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
| | - Peter Pak Hang Cheung
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
| |
Collapse
|
46
|
Alves PA, de Oliveira EG, Franco-Luiz APM, Almeida LT, Gonçalves AB, Borges IA, Rocha FDS, Rocha RP, Bezerra MF, Miranda P, Capanema FD, Martins HR, Weber G, Teixeira SMR, Wallau GL, do Monte-Neto RL. Optimization and Clinical Validation of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification, a Fast, Highly Sensitive and Specific COVID-19 Molecular Diagnostic Tool That Is Robust to Detect SARS-CoV-2 Variants of Concern. Front Microbiol 2021; 12:713713. [PMID: 34867841 PMCID: PMC8637279 DOI: 10.3389/fmicb.2021.713713] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/28/2021] [Indexed: 12/23/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic unfolded due to the widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission reinforced the urgent need for affordable molecular diagnostic alternative methods for massive testing screening. We present the clinical validation of a pH-dependent colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) for SARS-CoV-2 detection. The method revealed a limit of detection of 19.3 ± 2.7 viral genomic copies/μL when using RNA extracted samples obtained from nasopharyngeal swabs collected in guanidine-containing viral transport medium. Typical RT-LAMP reactions were performed at 65°C for 30 min. When compared to reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), up to cycle-threshold (Ct) value 32, RT-LAMP presented 98% [95% confidence interval (CI) = 95.3-99.5%] sensitivity and 100% (95% CI = 94.5-100%) specificity for SARS-CoV-2 RNA detection targeting E and N genes. No cross-reactivity was detected when testing other non-SARS-CoV virus, confirming high specificity. The test is compatible with primary RNA extraction-free samples. We also demonstrated that colorimetric RT-LAMP can detect SARS-CoV-2 variants of concern and variants of interest, such as variants occurring in Brazil named gamma (P.1), zeta (P.2), delta (B.1.617.2), B.1.1.374, and B.1.1.371. The method meets point-of-care requirements and can be deployed in the field for high-throughput COVID-19 testing campaigns, especially in countries where COVID-19 testing efforts are far from ideal to tackle the pandemics. Although RT-qPCR is considered the gold standard for SARS-CoV-2 RNA detection, it requires expensive equipment, infrastructure, and highly trained personnel. In contrast, RT-LAMP emerges as an affordable, inexpensive, and simple alternative for SARS-CoV-2 molecular detection that can be applied to massive COVID-19 testing campaigns and save lives.
Collapse
Affiliation(s)
- Pedro A. Alves
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
- Centro de Tecnologia em Vacinas, UFMG/Fiocruz, Belo Horizonte, Brazil
| | | | | | | | | | - Iara A. Borges
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | | | - Raissa P. Rocha
- Centro de Tecnologia em Vacinas, UFMG/Fiocruz, Belo Horizonte, Brazil
| | - Matheus F. Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
| | - Pâmella Miranda
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávio D. Capanema
- Núcleo de Inovação Tecnológica, Fundação Hospitalar do Estado de Minas Gerais, Belo Horizonte, Brazil
| | - Henrique R. Martins
- Visuri Equipamentos e Serviços, Belo Horizonte, Brazil
- Departamento de Engenharia Elétrica, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Gabriel Luz Wallau
- Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
| | | |
Collapse
|
47
|
Saki EF, Setiawan SA, Wicaksono DHB. Portable Tools for COVID-19 Point-of-Care Detection: A Review. IEEE SENSORS JOURNAL 2021; 21:23737-23750. [PMID: 35582343 PMCID: PMC8864949 DOI: 10.1109/jsen.2021.3110857] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 06/12/2023]
Abstract
Recently, several methods for SARS-CoV-2 detection have been developed to obtain rapid, portable, cheap, and easy-to-use diagnostic tools. This review paper summarizes and discusses studies on the development of point-of-care devices for SARS-CoV-2 diagnosis with comparisons between them from several aspects. Various detection methods of the recently developed portable COVID-19 biosensor will be presented in this review. The discussion is divided into four major classifications based on the target biomarkers of SARS-CoV-2, such as antibodies, nucleic acids, antigens, and metabolic products. An overview of the potential development for future study is also provided. Moreover, basic knowledge of biosensors is also explained for tutoring the implementation of theory into the research of COVID-19 biosensors. This review paper is aimed to provide a tutorial by collecting the information on the development of a point-of-care device for SARS-CoV-2 detection to provide information for further research and propose the new COVID-19 portable diagnostic tool.
Collapse
Affiliation(s)
- Elga F. Saki
- Department of Biomedical EngineeringFaculty of Life Sciences and TechnologySwiss German University (SGU)Tangerang15143Indonesia
| | | | - Dedy H. B. Wicaksono
- Department of Biomedical EngineeringFaculty of Life Sciences and TechnologySwiss German University (SGU)Tangerang15143Indonesia
| |
Collapse
|
48
|
Development of a Novel Loop Mediated Isothermal Amplification Assay (LAMP) for the Rapid Detection of Epizootic Haemorrhagic Disease Virus. Viruses 2021; 13:v13112187. [PMID: 34834993 PMCID: PMC8621080 DOI: 10.3390/v13112187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Epizootic haemorragic disease (EHD) is an important disease of white-tailed deer and can cause a bluetongue-like illness in cattle. A definitive diagnosis of EHD relies on molecular assays such as real-time RT-qPCR or conventional PCR. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a cost-effective, specific, and sensitive technique that provides an alternative to RT-qPCR. We designed two sets of specific primers targeting segment-9 of the EHD virus genome to enable the detection of western and eastern topotypes, and evaluated their performance in singleplex and multiplex formats using cell culture isolates (n = 43), field specimens (n = 20), and a proficiency panel (n = 10). The limit of detection of the eastern and western RT-LAMP assays was estimated as ~24.36 CT and as ~29.37 CT in relation to real-time RT-qPCR, respectively, indicating a greater sensitivity of the western topotype singleplex RT-LAMP. The sensitivity of the western topotype RT-LAMP assay, relative to the RT-qPCR assay, was 72.2%, indicating that it could be theoretically used to detect viraemic cervines and bovines. For the first time, an RT-LAMP assay was developed for the rapid detection of the EHD virus that could be used as either a field test or high throughput screening tool in established laboratories to control the spread of EHD.
Collapse
|
49
|
Development, evaluation of the PNA RT-LAMP assay for rapid molecular detection of SARS-CoV-2. Sci Rep 2021; 11:20471. [PMID: 34650067 PMCID: PMC8516927 DOI: 10.1038/s41598-021-00041-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022] Open
Abstract
Dual-labeled PNA probe used RT-LAMP molecular rapid assay targeting SARS-CoV-2 ORF1ab and N genes was developed, and the analytical, clinical performances for detection of SARS-CoV-2 RNA extracted from clinical nasopharyngeal swab specimens were evaluated in this study. Data showed that this assay is highly specific for SARS-CoV-2, and the absolute detection limit is 1 genomic copy per microliter of viral RNA which can be considered to be comparable to gold-standard molecular diagnostic method real-time reverse transcriptase PCR. Both clinical sensitivity and specificity against a commercial real-time RT-PCR assay were determined as identical. In conclusion, the PNA RT-LAMP assay showed high analytical and clinical accuracy which are identical to real-time RT-PCR which has been routinely used for the detection of SARS-CoV-2.
Collapse
|
50
|
Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
Collapse
Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|