1
|
Boza JM, Amirali A, Williams SL, Currall BB, Grills GS, Mason CE, Solo-Gabriele HM, Erickson DC. Evaluation of a field deployable, high-throughput RT-LAMP device as an early warning system for COVID-19 through SARS-CoV-2 measurements in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173744. [PMID: 38844223 DOI: 10.1016/j.scitotenv.2024.173744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/02/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024]
Abstract
Quantification of SARS-CoV-2 RNA copies in wastewater can be used to estimate COVID-19 prevalence in communities. While such results are important for mitigating disease spread, SARS-CoV-2 measurements require sophisticated equipment and trained personnel, for which a centralized laboratory is necessary. This significantly impacts the time to result, defeating its purpose as an early warning detection tool. The objective of this study was to evaluate a field portable device (called MINI) for detecting SARS-CoV-2 viral loads in wastewater using real-time reverse transcriptase loop-mediated isothermal amplification (real-time RT-LAMP). The device was tested using wastewater samples collected from buildings (with 430 to 1430 inhabitants) that had known COVID-19-positive cases. Results show comparable performance of RT-LAMP against reverse transcriptase polymerase chain reaction (RT-qPCR) when detecting SARS-CoV-2 copies in wastewater. Both RT-LAMP and RT-qPCR detected SARS-CoV-2 in wastewater from buildings with at least three positive individuals within a 6-day time frame prior to diagnosis. The large 96-well throughput provided by MINI provided scalability to multi-building detection. The portability of the MINI device enabled decentralized on-site detection, significantly reducing the time to result. The overall findings support the use of RT-LAMP within the MINI configuration as an early detection system for COVID-19 infection using wastewater collected at the building scale.
Collapse
Affiliation(s)
- J M Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - A Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - S L Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - B B Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - G S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - C E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - H M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - D C Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA; Division of Nutritional Science, Cornell University, Ithaca, NY 14850, USA.
| |
Collapse
|
2
|
Santos DJAD, Oliveira TRD, Araújo GMD, Pott-Junior H, Melendez ME, Sabino EC, Leite OD, Faria RC. An electrochemical genomagnetic assay for detection of SARS-CoV-2 and Influenza A viruses in saliva. Biosens Bioelectron 2024; 255:116210. [PMID: 38537427 DOI: 10.1016/j.bios.2024.116210] [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: 12/31/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 04/15/2024]
Abstract
Viral respiratory infections represent a major threat to the population's health globally. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease and in some cases the symptoms can be confused with Influenza disease caused by the Influenza A viruses. A simple, fast, and selective assay capable of identifying the etiological agent and differentiating the diseases is essential to provide the correct clinical management to the patient. Herein, we described the development of a genomagnetic assay for the selective capture of viral RNA from SARS-CoV-2 and Influenza A viruses in saliva samples and employing a simple disposable electrochemical device for gene detection and quantification. The proposed method showed excellent performance detecting RNA of SARS-CoV-2 and Influenza A viruses, with a limit of detection (LoD) and limit of quantification (LoQ) of 5.0 fmol L-1 and 8.6 fmol L-1 for SARS-CoV-2, and 1.0 fmol L-1 and 108.9 fmol L-1 for Influenza, respectively. The genomagnetic assay was employed to evaluate the presence of the viruses in 36 saliva samples and the results presented similar responses to those obtained by the real-time reverse transcription-polymerase chain reaction (RT-PCR), demonstrating the reliability and capability of a method as an alternative for the diagnosis of COVID-19 and Influenza with point-of-care capabilities.
Collapse
Affiliation(s)
| | | | | | - Henrique Pott-Junior
- Department of Medicine, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | | | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Oldair Donizeti Leite
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil; Federal Technological University of Paraná, Campus Medianeira, Medianeira, PR, 85884-000, Brazil.
| | - Ronaldo Censi Faria
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil.
| |
Collapse
|
3
|
Whang K, Min J, Shin Y, Hwang I, Lee H, Kwak T, La JA, Kim S, Kim D, Lee LP, Kang T. Capillarity-Driven Enrichment and Hydrodynamic Trapping of Trace Nucleic Acids by Plasmonic Cavity Membrane for Rapid and Sensitive Detections. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2403896. [PMID: 38663435 DOI: 10.1002/adma.202403896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Small-reactor-based polymerase chain reaction (PCR) has attracted considerable attention. A significant number of tiny reactors must be prepared in parallel to capture, amplify, and accurately quantify few target genes in clinically relevant large volume, which, however, requires sophisticated microfabrication and longer sample-to-answer time. Here, single plasmonic cavity membrane is reported that not only enriches and captures few nucleic acids by taking advantage of both capillarity and hydrodynamic trapping but also quickly amplifies them for sensitive plasmonic detection. The plasmonic cavity membrane with few nanoliters in a void volume is fabricated by self-assembling gold nanorods with SiO2 tips. Simulations reveal that hydrodynamic stagnation between the SiO2 tips is mainly responsible for the trapping of the nucleic acid in the membrane. Finally, it is shown that the plasmonic cavity membrane is capable of enriching severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes up to 20 000-fold within 1 min, amplifying within 3 min, and detecting the trace genes as low as a single copy µL-1. It is anticipated that this work not only expands the utility of PCR but also provides an innovative way of the enrichment and detection of trace biomolecules in a variety of point-of-care testing applications.
Collapse
Affiliation(s)
- Keumrai Whang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Junwon Min
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Yonghee Shin
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Inhyeok Hwang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Hyunjoo Lee
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Taejin Kwak
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Ju A La
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Sungbong Kim
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
- Department of Chemistry, Military Academy, Seoul, 01805, South Korea
| | - Dongchoul Kim
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Luke P Lee
- Harvard Institute of Medicine, Harvard Medical School, Brigham and Women's Hospital, Harvard University, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwonsi, Gyeonggi-do, 16419, South Korea
| | - Taewook Kang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| |
Collapse
|
4
|
D'Aoust PM, Hegazy N, Ramsay NT, Yang MI, Dhiyebi HA, Edwards E, Servos MR, Ybazeta G, Habash M, Goodridge L, Poon A, Arts E, Brown RS, Payne SJ, Kirkwood A, Simmons D, Desaulniers JP, Ormeci B, Kyle C, Bulir D, Charles T, McKay RM, Gilbride K, Oswald C, Peng H, Pileggi V, Wang ML, Tong A, Orellano D, DeGroot CT, Delatolla R. SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic. Sci Data 2024; 11:656. [PMID: 38906875 PMCID: PMC11192951 DOI: 10.1038/s41597-024-03414-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024] Open
Abstract
During the COVID-19 pandemic, the Province of Ontario, Canada, launched a wastewater surveillance program to monitor SARS-CoV-2, inspired by the early work and successful forecasts of COVID-19 waves in the city of Ottawa, Ontario. This manuscript presents a dataset from January 1, 2021, to March 31, 2023, with RT-qPCR results for SARS-CoV-2 genes and PMMoV from 107 sites across all 34 public health units in Ontario, covering 72% of the province's and 26.2% of Canada's population. Sampling occurred 2-7 times weekly, including geographical coordinates, serviced populations, physico-chemical water characteristics, and flowrates. In doing so, this manuscript ensures data availability and metadata preservation to support future research and epidemic preparedness through detailed analyses and modeling. The dataset has been crucial for public health in tracking disease locally, especially with the rise of the Omicron variant and the decline in clinical testing, highlighting wastewater-based surveillance's role in estimating disease incidence in Ontario.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Gustavo Ybazeta
- Health Sciences North Research Institute, Sudbury, ON, Canada
| | | | | | - Art Poon
- Western University, London, ON, Canada
| | - Eric Arts
- Western University, London, ON, Canada
| | | | | | | | | | | | | | | | | | | | | | | | - Claire Oswald
- Toronto Metropolitan University, Toronto, ON, Canada
| | - Hui Peng
- University of Toronto, Toronto, ON, Canada
| | - Vince Pileggi
- Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON, Canada
| | - Menglu L Wang
- Toronto Metropolitan University, Toronto, ON, Canada
| | - Arthur Tong
- Toronto Metropolitan University, Toronto, ON, Canada
| | | | | | | |
Collapse
|
5
|
Weishaar H, Pozo-Martin F, Geurts B, Lopez de Abechuco E, Montt-Maray E, Cristea F, Abrokwa SK, Bahr T, Al-Awlaqi S, El Bcheraoui C. Capacity-building during public health emergencies: perceived usefulness and cost savings of an online training on SARS-CoV-2 real-time polymerase chain reaction (qPCR) diagnostics in low- and middle-income settings during the COVID-19 pandemic. Front Public Health 2024; 12:1197729. [PMID: 38912269 PMCID: PMC11192048 DOI: 10.3389/fpubh.2024.1197729] [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: 03/31/2023] [Accepted: 05/27/2024] [Indexed: 06/25/2024] Open
Abstract
Introduction Upon the onset of the COVID-19 pandemic, the Public Health Laboratory Support Unit (ZIG4) at the Robert Koch Institute (RKI), the German National Public Health Institute, developed and delivered an online training on SARS-CoV-2 qPCR diagnostics to 17 partner countries in low- and middle-income countries (LMIC). This article analyses the usefulness and cost savings of this training. Methods The authors performed a concurrent mixed-methodology study based on key informant interviews, interviewer-administered questionnaires, and document reviews. Economic costs were estimated from the perspective of RKI. Results Responding participants indicated that the course provided good and comprehensive information on up-to-date scientific knowledge and laboratory practice in PCR diagnostics. Respondents appreciated how the technical content of the training enhanced their ability to apply diagnostic methods in their daily work. Interviewees highlighted that the fast implementation and the low threshold of attending an online training had allowed them to quickly build skills that were crucial during, and beyond, the COVID-19 crisis. The total estimated cost of the online SARS-CoV-2 qPCR training was 61,644 euros. The total estimated cost of the equivalent face-to-face training was estimated at 267,592 euros. Programme weaknesses identified included the top-down approaches taken, lack of interactive components and opportunities to directly engage with other course participants and with teachers. Conclusions An online training was developed and implemented to support RKI partner countries in SARS-CoV-2 qPCR diagnostics during the COVID-19 pandemic, thereby strengthening pandemic response and health system resilience. The training incurred in important cost savings compared to the equivalent face-to-face training. Post-pandemic studies could usefully build on these research findings and explore ways to enhance end user involvement and improve interactive features to build stronger communities of learners and facilitate exchange of information and mutual learning.
Collapse
|
6
|
Angela S, Fadhilah G, Hsiao WWW, Lin HY, Ko J, Lu SCW, Lee CC, Chang YS, Lin CY, Chang HC, Chiang WH. Nanomaterials in the treatment and diagnosis of rheumatoid arthritis: Advanced approaches. SLAS Technol 2024; 29:100146. [PMID: 38844139 DOI: 10.1016/j.slast.2024.100146] [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: 10/02/2023] [Revised: 04/06/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024]
Abstract
Rheumatoid arthritis (RA), a chronic inflammatory condition that affects persons between the ages of 20 and 40, causes synovium inflammation, cartilage loss, and joint discomfort as some of its symptoms. Diagnostic techniques for RA have traditionally been split into two main categories: imaging and serological tests. However, significant issues are associated with both of these methods. Imaging methods are costly and only helpful in people with obvious symptoms, while serological assays are time-consuming and require specialist knowledge. The drawbacks of these traditional techniques have led to the development of novel diagnostic approaches. The unique properties of nanomaterials make them well-suited as biosensors. Their compact dimensions are frequently cited for their outstanding performance, and their positive impact on the signal-to-noise ratio accounts for their capacity to detect biomarkers at low detection limits, with excellent repeatability and a robust dynamic range. In this review, we discuss the use of nanomaterials in RA theranostics. Scientists have recently synthesized, characterized, and modified nanomaterials and biomarkers commonly used to enhance RA diagnosis and therapy capabilities. We hope to provide scientists with the promising potential that nanomaterials hold for future theranostics and offer suggestions on further improving nanomaterials as biosensors, particularly for detecting autoimmune disorders.
Collapse
Affiliation(s)
- Stefanny Angela
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Gianna Fadhilah
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Wesley Wei-Wen Hsiao
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Hsuan-Yi Lin
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Joshua Ko
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Steven Che-Wei Lu
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Cheng-Chung Lee
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yu-Sheng Chang
- Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, Shuang Ho Hospital, New Taipei City, Taiwan; Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ching-Yu Lin
- The Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Huan-Cheng Chang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan; Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Wei-Hung Chiang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan; Sustainable Electrochemical Energy Development (SEED) Center, National Taiwan University of Science and Technology, Taipei, Taiwan; Advanced Manufacturing Research Center, National Taiwan University of Science and Technology, Taipei, Taiwan.
| |
Collapse
|
7
|
Sepahi N, Samsami S, Mansoori Y, Chenari M, Namavari N, Yazdanpanah A, Ghasemian A, Montaseri Z, Sharifzadeh M, Ranjbar R, Namavari S, Ghanbariasad A. Development of a novel Colorimetric Assay for the rapid diagnosis of Coronavirus disease 2019 from nasopharyngeal samples. Sci Rep 2024; 14:12125. [PMID: 38802360 PMCID: PMC11130264 DOI: 10.1038/s41598-024-53747-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/04/2024] [Indexed: 05/29/2024] Open
Abstract
Emergence of Coronavirus disease 2019 (COVID-19) pandemic has posed a huge threat to public health. Rapid and reliable test to diagnose infected subjects is crucial for disease spread control. We developed a colorimetric test for COVID-19 detection using a Colorimetric Assay based on thiol-linked RNA modified gold nanoparticles (AuNPs) and oligonucleotide probes. This method was conducted on RNA from 200 pharyngeal swab samples initially tested by Real-Time polymerase chain reaction (RT-PCR) as gold standard. A specific oligonucleotide probe designed based on ORF1ab of COVID-19 was functionalized with AuNPs-probe conjugate. The exposure of AuNP-probe to isolated RNA samples was tested using hybridization. In this comparative study, the colorimetric functionalized AuNPs assay exhibited a detection limit of 25 copies/µL. It was higher in comparison to the RT-PCR method, which could only detect 15 copies/µL. The results demonstrated 100% specificity and 96% sensitivity for the developed method. Herein, we developed an incredibly rapid, simple and cost-effective Colorimetric Assay lasting approximately 30 min which could process considerably higher number of COVID-19 samples compared to the RT-PCR. This AuNP-probe conjugate colorimetric method could be considered the optimum alternatives for conventional diagnostic tools especially in over-populated and/or low-income countries.
Collapse
Affiliation(s)
- Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Sahar Samsami
- Student Research Committee, Fasa University of Medical Sciences, Fasa, Iran
| | - Yaser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Maryam Chenari
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Negin Namavari
- School of Medicine Grenada, St. George's University, St. George's, West Indies, Grenada
| | - Ava Yazdanpanah
- Student Research Committee, Fasa University of Medical Sciences, Fasa, Iran
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Zahra Montaseri
- Department of Infectious Diseases, School of Medicine, Fasa University of Medical Science, Fasa, Iran
| | - Mahboobeh Sharifzadeh
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Razie Ranjbar
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Sahar Namavari
- Department of Medical Biotechnologies, School of Advanced Technologies, Fasa University of Medical Sciences, Avicenna Square, Fasa, Fars, Islamic Republic of Iran
| | - Ali Ghanbariasad
- Department of Medical Biotechnologies, School of Advanced Technologies, Fasa University of Medical Sciences, Avicenna Square, Fasa, Fars, Islamic Republic of Iran.
| |
Collapse
|
8
|
Fokam J, Takou D, Semengue ENJ, Molimbou E, Chenwi Ambe C, Durand Nka A, Ndjeyep SD, Beloumou GA, Ka'e CA, Gouissi Anguechia DH, Mundo Nayang AR, Moko Fotso LG, Kengni Ngueko AM, Etame NK, Tueguem PP, Tommo Tchouaket CM, Fainguem N, Abega Abega C, Abba A, Tambe Ayuk Ngwese D, Djubgang Djoukwe R, Akenji B, Okomo Assoumou MC, Mandeng N, Esso L, Cappelli G, Shang J, Ndongmo C, Etoundi Mballa GA, Ndembi N, Colizzi V, Perno CF, Ndjolo A. Performance characteristics of INDICAID antigen rapid diagnostic test on SARS-CoV-2 samples during the omicron wave in Cameroon. Heliyon 2024; 10:e29937. [PMID: 38694118 PMCID: PMC11058880 DOI: 10.1016/j.heliyon.2024.e29937] [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: 01/24/2024] [Revised: 02/20/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
Background WHO recommends the use of COVID-19 antigen rapid diagnostic tests (Ag-RDT) with at least 80 % sensitivity and 97 % specificity. In the era of Omicron variants, we sought to ascertain the performance of the INDICAID™ Ag-RDT compared to real-time PCR (RT-PCR) as the gold standard. Methods A laboratory-based study was conducted among consenting individuals tested for COVID-19 at the virology laboratory of the Chantal BIYA International Reference Centre, Yaoundé-Cameron. The samples were processed by INDICAID™ Ag-RDT and DaAn Gene real-time PCR according to the manufacturer's instructions, and PCR-results were interpreted as per cycle thresholds (CT). The sensitivity, specificity, positive and negative predictive values (PPV and NVP) of INDICAID™ Ag-RDT were evaluated according to PCR CT-values. Results A total of 565 nasopharyngeal swabs were collected from participants (median age [IQR]: 40 [31-75]; M/F sex-ratio was 1.2 and 380 were vaccinated). Following PCR, overall COVID-19 positivity was 5.66 %. For CT < 37, INDICAID™ Ag-RDT sensitivity was 21.9 % (95%CI: [8.3-39.9]), specificity 100 % (95%CI: [99.3-100]); PPV 100 % (95%CI: [59.0-100]), NPV 95.5 % (95%CI: [93.4-97.1]) and kappa = 0.34 (95%CI: [0.19-0.35]). For CT < 25, sensitivity was 100 % (95%CI: [47.8-100.0]), specificity 99.6 % (95%CI: [98.7-99.9]); PPV 94.4 % (95%CI: [51.7-100]), NPV 100 % (95%CI: [99.3-100]) and kappa = 0.83 (95%CI: [0.6-1.0]). COVID-19 sequences generated were all Omicron BA.1 subvariants. Conclusion For patients infected with high viral loads (CT < 25), INDICAID™ Ag-RDT has high intrinsic (sensitivity and specificity) and extrinsic (predictive values) performances for COVID-19 diagnosis. Due to its simplicity and short turnaround time, INDICAID™ Ag-RDT is, therefore a reliable tool to prevent the spread of COVID-19 at community level in the current era of Omicron subvariants.
Collapse
Affiliation(s)
- Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
- National Public Health Emergency Operations Coordination Centre, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Désiré Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | | | - Evariste Molimbou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
- Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Collins Chenwi Ambe
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Alex Durand Nka
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Sandrine Djupsa Ndjeyep
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Grace Angong Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Christelle Aude Ka'e
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Davy-Hyacinthe Gouissi Anguechia
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Audrey Rachel Mundo Nayang
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Larissa Gaëlle Moko Fotso
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Aurelie Minelle Kengni Ngueko
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Naomi-Karell Etame
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Pamela Patricia Tueguem
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Carlos Michel Tommo Tchouaket
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- School of Health Sciences, Catholic University of Central Africa, Yaoundé, Cameroon
| | - Nadine Fainguem
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Cyrille Abega Abega
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Aissatou Abba
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Laboratory Department, Garoua Regional Health Centre, Garoua, Cameroon
| | - Derrick Tambe Ayuk Ngwese
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Rina Djubgang Djoukwe
- Directorate for Pharmacy, Drug and Laboratory, Ministry of Public Health, Yaounde, Cameroon
| | - Blaise Akenji
- National Public Health Laboratory, Yaoundé, Cameroon
| | - Marie-Claire Okomo Assoumou
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
- National Public Health Laboratory, Yaoundé, Cameroon
| | - Nadia Mandeng
- National Public Health Emergency Operations Coordination Centre, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Health Sciences, University of Bamenda, Bamenda, Cameroon
- Department of Disease, Epidemic and Pandemic Control, Ministry of Public Health, Yaounde, Cameroon
| | - Linda Esso
- National Public Health Emergency Operations Coordination Centre, Ministry of Public Health, Yaoundé, Cameroon
- Department of Disease, Epidemic and Pandemic Control, Ministry of Public Health, Yaounde, Cameroon
| | - Giulia Cappelli
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- National Research Council, Rome, Italy
| | - Judith Shang
- United States Centres for Disease Control and Prevention, Country Office, Yaoundé, Cameroon
| | - Clement Ndongmo
- United States Centres for Disease Control and Prevention, Country Office, Yaoundé, Cameroon
| | - Georges Alain Etoundi Mballa
- National Public Health Emergency Operations Coordination Centre, Ministry of Public Health, Yaoundé, Cameroon
- Department of Disease, Epidemic and Pandemic Control, Ministry of Public Health, Yaounde, Cameroon
| | - Nicaise Ndembi
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
- Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
| | | | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| |
Collapse
|
9
|
Juchem CF, Corbellini VA, Horst A, Heidrich D. Infrared spectroscopy combined with chemometrics in transflectance mode: An alternative approach in the photodiagnosis of COVID-19 using saliva. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 312:124066. [PMID: 38428213 DOI: 10.1016/j.saa.2024.124066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has required the search for sensitive, rapid, specific, and lower-cost diagnostic methods to meet the high demand. The gold standard method of laboratory diagnosis is real-time reverse transcription polymerase chain reaction (RT-PCR). However, this method is costly and results can take time. In the literature, several studies have already described the potential of Fourier transform infrared spectroscopy (FTIR) as a tool in the biomedical field, including the diagnosis of viral infections, while being fast and inexpensive. In view of this, the objective of this study was to develop an FTIR model for the diagnosis of COVID-19. For this analysis, all private clients who had performed a face-to-face collection at the Univates Clinical Analysis Laboratory (LAC Univates) within a period of six months were invited to participate. Data from clients who agreed to participate in the study were collected, as well as nasopharyngeal secretions and a saliva sample. For the development of models, the RT-PCR result of nasopharyngeal secretions was used as a reference method. Absorptions with high discrimination (p < 0.001) between GI (28 patients, RT-PCR test positive to SARS-CoV-2 virus) and GII (173 patients who did not have the virus detected in the test) were most relevant at 3512 cm-1, 3385 cm-1 and 1321 cm-1 after 2nd derivative data transformation. To carry out the diagnostic modeling, chemometrics via FTIR and Discriminant Analysis of Orthogonal Partial Least Squares (OPLS-DA) by salivary transflectance mode with one latent variable and one orthogonal signal correction component were used. The model generated predictions with 100 % sensitivity, specificity and accuracy. With the proposed model, in a single application of an individual's saliva in the FTIR equipment, results related to the detection of SARS-CoV-2 can be obtained in a few minutes of spectral evaluation.
Collapse
Affiliation(s)
- Calebe Fernando Juchem
- Postgraduate Program in Medical Sciences, Universidade do Vale do Taquari - Univates, Lajeado, RS, Brazil
| | - Valeriano Antonio Corbellini
- Postgraduate Program in Health Promotion, Postgraduate Program in Environmental Technology, Universidade de Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Andréa Horst
- Life Sciences Center, Universidade do Vale do Taquari - Univates, Lajeado, RS, Brazil
| | - Daiane Heidrich
- Postgraduate Program in Medical Sciences, Universidade do Vale do Taquari - Univates, Lajeado, RS, Brazil; Postgraduate Program in Biotechnology, Universidade do Vale do Taquari - Univates, Lajeado, RS, Brazil.
| |
Collapse
|
10
|
Fernández-Sánchez F, Martín-Bautista E, Rivas-Ruiz F, Wu W, García-Aranda M. Evaluation of the EasyNAT SARS-CoV-2 assay PCR test for the diagnosis of SARS-CoV-2 infection. J Virol Methods 2024; 326:114908. [PMID: 38423363 DOI: 10.1016/j.jviromet.2024.114908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Reverse transcription polymerase chain reaction (RT-PCR) tests are commonly utilized in commercial settings but pose challenges due to labor-intensive procedures and extended response times during peak demand. In contrast, real-time fluorescence and isothermal amplification assays using Crossing Priming Amplification (CPA) offer faster genetic material analysis, eliminate subjectivity, and require less manipulation and personnel training. This study aimed to validate the EasyNAT SARS-CoV-2 Assay, a diagnostic kit based on CPA, using oral and nasopharyngeal samples. The EasyNAT kit was compared to the Xpert Xpress SARS-CoV-2 kit, evaluating 873 samples obtained during routine analysis at the Microbiology Laboratory of the Hospital Costa del Sol (Marbella, Spain). The overall sensitivity and specificity for the EasyNAT SARS-CoV-2 Assay were 79.1% (95%CI 74.5-83.7) and 99.5% (95%CI 98.7-100), respectively; with, validity index of 91.9%, positive predictive value of 98.9%, negative predictive value of 88.9%, positive likelihood ratio of 144.5, negative likelihood ratio of 0.21 and a total Youden Index of 0.79. Notably, sensitivity improved in fresh samples (91.4%), along with a high Youden Index (0.91). The EasyNAT SARS-CoV-2 Assay achieved a higher percentage of concordance in positive samples with Xpert Xpress SARS-CoV-2 when analyzing cycle threshold (Ct) intervals below 30 compared to intervals equal or greater than 30, and demons. In conclusion, the EasyNAT SARS-CoV-2 Assay demonstrated high sensitivity and agreement with Xpert Xpress SARS-CoV-2, particularly in fresh samples or when the signal was detected at Ct intervals below 30, indicating higher viral loads. This makes it suitable for rapid screening in various settings, including those with limited access to conventional molecular laboratory setting.
Collapse
Affiliation(s)
- Fernando Fernández-Sánchez
- Microbiology Unit. Hospital Universitario Costa del Sol, Autovía A-7, km 187, Málaga, Marbella 29603, Spain.
| | - Elena Martín-Bautista
- Research and Innovation Unit. Hospital Universitario Costa del Sol, Autovía A-7, km 187, Málaga, Marbella 29603, Spain
| | - Francisco Rivas-Ruiz
- Research and Innovation Unit. Hospital Universitario Costa del Sol, Autovía A-7, km 187, Málaga, Marbella 29603, Spain
| | - Winnie Wu
- GeneFirst, Abingdon Science Park, Abingdon Oxfordshire, United Kingdom
| | - Marilina García-Aranda
- Research and Innovation Unit. Hospital Universitario Costa del Sol, Autovía A-7, km 187, Málaga, Marbella 29603, Spain; Department of Surgical Specialties, Biochemistry and Immunology, Faculty of Medicine, University of Málaga. Málaga, Spain
| |
Collapse
|
11
|
Diforti JF, Cunningham T, Piccinini E, Marmisollé WA, Piccinini JM, Azzaroni O. Noninvasive and Multiplex Self-Test of Kidney Disease Biomarkers with Graphene-Based Lab-on-a-Chip (G-LOC): Toward Digital Diagnostics in the Hands of Patients. Anal Chem 2024; 96:5832-5842. [PMID: 38573917 DOI: 10.1021/acs.analchem.3c05148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Chronic kidney disease is one of the major health issues worldwide. However, diagnosis is now highly centralized in large laboratories, resulting in low access to patient monitoring and poor personalized treatments. This work reports the development of a graphene-based lab-on-a-chip (G-LOC) for the digital testing of renal function biomarkers in serum and saliva samples. G-LOC integrates multiple bioelectronic sensors with a microfluidic system that enables multiplex self-testing of urea, potassium, sodium, and chloride. The linearity, limit of detection (LOD), accuracy, and coefficient of variability (CV) were studied. Accuracy values higher than 95.5% and CV lower than 9% were obtained for all of the biomarkers. The analytical performance was compared against three reference lab benchtop analyzers by measuring healthy- and renal-failure-level samples of serum. From receiver operating characteristic (ROC) plots, sensitivities (%) of 99.7, 97.6, 99.1, and 89.0 were obtained for urea, potassium, sodium, and chloride, respectively. Then, the test was evaluated in noninvasive saliva samples and compared against reference methods. Correlation and Bland-Altman plots showed good correlation and agreement of the G-LOC with the reference methods. It is noteworthy that the precision of G-LOC was similar to better than benchtop lab analyzers, with the advantage of being highly portable. Finally, a user testing study was conducted. The analytical performance obtained with untrained volunteers was similar to that obtained with trained chemists. Additionally, based on a user experience survey, G-LOC was found to have very simple usability and would be suitable for at-home diagnostics.
Collapse
Affiliation(s)
- Joaquin F Diforti
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA)-Departamento de Química-Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET. 64 and 113, 1900 Buenos Aires, Argentina
- Department of Bioelectronic, GISENS BIOTECH, 2150 Shattuck Ave PH, Berkeley, California 94704, United States
| | - Thomas Cunningham
- Department of Bioelectronic, GISENS BIOTECH, 2150 Shattuck Ave PH, Berkeley, California 94704, United States
| | - Esteban Piccinini
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA)-Departamento de Química-Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET. 64 and 113, 1900 Buenos Aires, Argentina
| | - Waldemar A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA)-Departamento de Química-Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET. 64 and 113, 1900 Buenos Aires, Argentina
| | - Jose M Piccinini
- Department of Bioelectronic, GISENS BIOTECH, 2150 Shattuck Ave PH, Berkeley, California 94704, United States
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA)-Departamento de Química-Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CONICET. 64 and 113, 1900 Buenos Aires, Argentina
| |
Collapse
|
12
|
Roucoux G, Thonon F, Zucman D, Rey D, Abgrall S, Eriksson LE, Préau M, Michels D, Chéret A, Duracinsky M. Questioning the "Ease" in disease: Was living with HIV a burden or boost during the first wave of Covid-19 in France? A qualitative study (COVIDHIV). PLoS One 2024; 19:e0295223. [PMID: 38452028 PMCID: PMC10919596 DOI: 10.1371/journal.pone.0295223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/18/2023] [Indexed: 03/09/2024] Open
Abstract
INTRODUCTION Clinical research has focused on risk factors and treatment for severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), particularly in people with a comorbidity including the human immunodeficiency virus (HIV), but little attention has been paid to the care pathway. This article aims to show how living with HIV may have been a biopsychosocial burden or boost in care pathways for Covid-19. METHOD People living with HIV (PLHIV) from 9 clinical centers were invited to participate in this qualitative study. The sampling was purposive with a maximum variation in their sociodemographic profiles. Semi-structured interviews were conducted until data saturation, then coded for thematic analysis, using an inductive general approach. RESULTS We interviewed 34 PLHIV of which 20 had SARS-COV-2 once. They were 24 males, 26 born in France; median age: 55. Twenty had a CD4 number above 500, and all were on antiretroviral therapy (ART). HIV appeared as a burden when Covid-19 symptoms reminded HIV seroconversion, fear of contamination, and triggered questions about ART effectiveness. HIV was not considered relevant when diagnosing Covid-19, caused fear of disclosure when participants sought SARS-COV-2 testing, and its care in hospitals was disrupted by the pandemic. ART-pill fatigue caused avoidance for Covid-19 treatment. As a boost, living with HIV led participants to observe symptoms, to get advice from healthcare professionals, and screening access through them. Some participants could accept the result of screening or a clinical diagnosis out of resilience. Some could consider ART or another drug prescribed by their HIV specialist help them to recover from Covid-19. CONCLUSION Living with HIV could function as a burden and/or a boost in the care pathways for Covid-19, according to patients' relationship to their HIV history, comorbidities and representation of ART. Covid-19 in PLHIV needs further qualitative study to gain a more comprehensive assessment of the pandemic's consequences on their lives and coping strategies.
Collapse
Affiliation(s)
- Guillaume Roucoux
- ECEVE, UMR-S 1123, Inserm, Université Paris Cité, Paris, France
- Patient-Reported Outcomes Research (PROQOL), Unité de Recherche Clinique en Economie de la Santé (URC-ECO), Hôpital Hôtel-Dieu, AP-HP, Paris, France
| | - Frédérique Thonon
- ECEVE, UMR-S 1123, Inserm, Université Paris Cité, Paris, France
- Patient-Reported Outcomes Research (PROQOL), Unité de Recherche Clinique en Economie de la Santé (URC-ECO), Hôpital Hôtel-Dieu, AP-HP, Paris, France
| | | | - David Rey
- Trait d’Union–Strasbourg University Hospitals, Strasbourg, France
| | - Sophie Abgrall
- Hôpital Antoine Béclère, Service de Médecine Interne, Clamart, France
- UVSQ, INSERM U1018, CESP, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | | | - Marie Préau
- Inserm Unit 1296 « Radiations: Defense, Health, Environment », Lyon, France
- Lyon 2 Lumière University, Lyon, France
| | - David Michels
- AIDES (French HIV/AIds and Viral Hepatites Organization), Pantin, France
- Laboratoire de Recherche Communautaire, Coalition PLUS, Pantin, France
| | - Antoine Chéret
- Outpatient Medicine Service, University Hospital, Pointe-à-Pitre, Guadeloupe, France
- Internal Medicine Unit, Cochin Hospital, Paris, France
| | - Martin Duracinsky
- ECEVE, UMR-S 1123, Inserm, Université Paris Cité, Paris, France
- Patient-Reported Outcomes Research (PROQOL), Unité de Recherche Clinique en Economie de la Santé (URC-ECO), Hôpital Hôtel-Dieu, AP-HP, Paris, France
- Internal Medicine Unit, Le Kremlin Bicêtre Hospital, Bicêtre, France
| |
Collapse
|
13
|
Bharucha T, Gangadharan B, Clarke R, Fernandez LG, Arman BY, Walsby-Tickle J, Deats M, Mosca S, Lin Q, Stokes R, Dunachie S, Merchant HA, Dubot-Pérès A, Caillet C, McCullagh J, Matousek P, Zitzmann N, Newton PN. Repurposing rapid diagnostic tests to detect falsified vaccines in supply chains. Vaccine 2024; 42:1506-1511. [PMID: 38355318 DOI: 10.1016/j.vaccine.2024.01.019] [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: 03/17/2023] [Revised: 11/21/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
Substandard (including degraded) and falsified (SF) vaccines are a relatively neglected issue with serious global implications for public health. This has been highlighted during the rapid and widespread rollout of COVID-19 vaccines. There has been increasing interest in devices to screen for SF non-vaccine medicines including tablets and capsules to empower inspectors and standardise surveillance. However, there has been very limited published research focussed on repurposing or developing new devices for screening for SF vaccines. To our knowledge, rapid diagnostic tests (RDTs) have not been used for this purpose but have important potential for detecting falsified vaccines. We performed a proof-in-principle study to investigate their diagnostic accuracy using a diverse range of RDT-vaccine/falsified vaccine surrogate pairs. In an initial assessment, we demonstrated the utility of four RDTs in detecting seven vaccines. Subsequently, the four RDTs were evaluated by three blinded assessors with seven vaccines and four falsified vaccines surrogates. The results provide preliminary data that RDTs could be used by multiple international organisations, national medicines regulators and vaccine manufacturers/distributors to screen for falsified vaccines in supply chains, aligned with the WHO global 'Prevent, Detect and Respond' strategy.
Collapse
Affiliation(s)
- Tehmina Bharucha
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic.
| | - Bevin Gangadharan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Rebecca Clarke
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Laura Gomez Fernandez
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Benediktus Yohan Arman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | | | - Michael Deats
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Sara Mosca
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford-Appleton Laboratory, UKRI, Harwell Campus, Didcot OX11 0QX, UK
| | - Qianqi Lin
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford-Appleton Laboratory, UKRI, Harwell Campus, Didcot OX11 0QX, UK
| | - Robert Stokes
- Agilent Technologies LDA UK, Becquerel Avenue, Didcot OX11 0RA, UK
| | - Susanna Dunachie
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Hamid A Merchant
- Department of Bioscience, School of Health, Sport and Bioscience, University of East London, Water Lane London E15 4LZ, UK; Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic; Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK; Unité Des Virus Emergents (UVE: Aix Marseille Univ, IRD190, INSERM 1207), Marseille, France
| | - Céline Caillet
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic; Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; Infectious Diseases Data Observatory, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - James McCullagh
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Pavel Matousek
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK; Central Laser Facility, Research Complex at Harwell, STFC Rutherford-Appleton Laboratory, UKRI, Harwell Campus, Didcot OX11 0QX, UK
| | - Nicole Zitzmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic; Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; Infectious Diseases Data Observatory, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK.
| |
Collapse
|
14
|
Baldeh M, Bawa FK, Bawah FU, Chamai M, Dzabeng F, Jebreel WMA, Kabuya JBB, Molemodile Dele-Olowu SK, Odoyo E, Rakotomalala Robinson D, Cunnington AJ. Lessons from the pandemic: new best practices in selecting molecular diagnostics for point-of-care testing of infectious diseases in sub-Saharan Africa. Expert Rev Mol Diagn 2024; 24:153-159. [PMID: 37908160 DOI: 10.1080/14737159.2023.2277368] [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: 08/31/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023]
Abstract
INTRODUCTION Point-of-care molecular diagnostics offer solutions to the limited diagnostic availability and accessibility in resource-limited settings. During the COVID-19 pandemic, molecular diagnostics became essential tools for accurate detection and monitoring of SARS-CoV-2. The unprecedented demand for molecular diagnostics presented challenges and catalyzed innovations which may provide lessons for the future selection of point-of-care molecular diagnostics. AREAS COVERED We searched PubMed from January 2020 to August 2023 to identify lessons learned from the COVID-19 pandemic which may impact the selection of point-of-care molecular diagnostics for future use in sub-Saharan Africa. We evaluated this in the context of REASSURED criteria (Real-time connectivity; Ease of specimen collection; Affordable; Sensitive; Specific; User-friendly; Rapid and robust; Equipment free; and Deliverable to users at the point of need) for point-of-care diagnostics for resource-limited settings. EXPERT OPINION The diagnostic challenges and successes during the COVID-19 pandemic affirmed the importance of the REASSURED criteria but demonstrated that these are not sufficient to ensure new diagnostics will be appropriate for public health emergencies. Capacity for rapid scale-up of diagnostic testing and transferability of assays, data, and technology are also important, resulting in updated REST-ASSURED criteria. Few diagnostics will meet all criteria, and trade-offs between criteria will need to be context-specific.
Collapse
Affiliation(s)
- Mamadu Baldeh
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Flavia K Bawa
- West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Faiza U Bawah
- Department of Computer Science, University of Ghana, Accra, Ghana
- Department of Computer Science and Informatics, University of Energy and Natural Resources, Sunyani, Ghana
| | - Martin Chamai
- West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Francis Dzabeng
- West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Computer Science, University of Ghana, Accra, Ghana
| | | | | | | | - Erick Odoyo
- Masinde Muliro University of Science & Technology, Kakamega, Kenya
| | | | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease and Centre for Paediatrics and Child Health, Imperial College, London, UK
| |
Collapse
|
15
|
Yin N, Van den Wijngaert S, Wautier M, Martiny D, Hallin M, Vandenberg O. Surveillance of the respiratory syncytial virus outside infancy: impact of testing methods, a retrospective observational study. ERJ Open Res 2024; 10:00869-2023. [PMID: 38444655 PMCID: PMC10910337 DOI: 10.1183/23120541.00869-2023] [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: 11/07/2023] [Accepted: 12/20/2023] [Indexed: 03/07/2024] Open
Abstract
Background The European Medicines Agency has approved several vaccines to protect the elderly against respiratory syncytial virus (RSV) infections. However, differences in performance between antigen and PCR tests, especially in adults, can make monitoring RSV difficult. This study aims to assess the impact of the chosen diagnostic methods on the surveillance of RSV. Methods RSV and influenza test results obtained from July 2022 to June 2023 in a consolidated clinical laboratory in Brussels, Belgium, were collected. These results included antigen tests, quadruplex PCR tests and viral cultures on respiratory samples. Epidemiological trends related to the age of patients and the diagnostic methods were analysed. Results Among 14 761 RSV tests, the overall number of positive tests for infants until 1 year of age peaked on 5 November 2022 (67 per 7 days) whereas it peaked on 22 December 2022 for adults (33 per 7 days). Positive antigen tests peaked on 7 November 2022 (56 per 7 days) whereas positive PCRs peaked on 19 December 2022 (36 per 7 days). Nevertheless, the positivity rate of RSV PCRs had peaked 1 month previously. Infants were mainly diagnosed through antigen testing, contrary to older patients. The influenza epidemic was probably the cause of the increased use of a quadruplex PCR, leading to a delayed increase in the absolute number of PCRs positive for RSV. Conclusion This study shows that the use of different diagnostic methods could lead to an erroneous representation of RSV epidemiology in adults due to the lack of sensitivity of antigen detection. RSV surveillance in the elderly should rely rather on molecular methods.
Collapse
Affiliation(s)
- Nicolas Yin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sigi Van den Wijngaert
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Magali Wautier
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Faculté de Médecine et Pharmacie, Université Libre de Mons, Mons, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- These authors have contributed equally to this work and share senior authorship
| | - Olivier Vandenberg
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Clinical Research and Innovation Unit, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), ULB, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK
- These authors have contributed equally to this work and share senior authorship
| |
Collapse
|
16
|
Lee S, Park JS, Woo H, Yoo YK, Lee D, Chung S, Yoon DS, Lee KB, Lee JH. Rapid deep learning-assisted predictive diagnostics for point-of-care testing. Nat Commun 2024; 15:1695. [PMID: 38402240 PMCID: PMC10894262 DOI: 10.1038/s41467-024-46069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/12/2024] [Indexed: 02/26/2024] Open
Abstract
Prominent techniques such as real-time polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA), and rapid kits are currently being explored to both enhance sensitivity and reduce assay time for diagnostic tests. Existing commercial molecular methods typically take several hours, while immunoassays can range from several hours to tens of minutes. Rapid diagnostics are crucial in Point-of-Care Testing (POCT). We propose an approach that integrates a time-series deep learning architecture and AI-based verification, for the enhanced result analysis of lateral flow assays. This approach is applicable to both infectious diseases and non-infectious biomarkers. In blind tests using clinical samples, our method achieved diagnostic times as short as 2 minutes, exceeding the accuracy of human analysis at 15 minutes. Furthermore, our technique significantly reduces assay time to just 1-2 minutes in the POCT setting. This advancement has the potential to greatly enhance POCT diagnostics, enabling both healthcare professionals and non-experts to make rapid, accurate decisions.
Collapse
Affiliation(s)
- Seungmin Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
| | - Jeong Soo Park
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
- School of Mechanical Engineering, Korea University, 145 Anam-ro, Seoungbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyowon Woo
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Yong Kyoung Yoo
- Department of Electronic Engineering, Catholic Kwandong University, 24, Beomil-ro 579 beon-gil, Gangneung-si, Gangwon-do, 25601, Republic of Korea
| | - Dongho Lee
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi, 13449, Republic of Korea
| | - Seok Chung
- School of Mechanical Engineering, Korea University, 145 Anam-ro, Seoungbuk-gu, Seoul, 02841, Republic of Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, 145 Anam-ro, Seongbuk, Seoul, 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, Republic of Korea
- Astrion Inc, Seoul, 02841, Republic of Korea
| | - Ki-Baek Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon, Seoul, 01897, Republic of Korea.
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi, 13449, Republic of Korea.
| |
Collapse
|
17
|
Ambalavanan R, Snead RS, Marczika J, Malioukis A. Epidemiological contemplation for a currently pragmatic COVID-19 health passport: a perspective. Front Public Health 2024; 12:1347623. [PMID: 38414904 PMCID: PMC10896918 DOI: 10.3389/fpubh.2024.1347623] [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: 12/01/2023] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) has caused a global pandemic that has wreaked havoc on the lives of millions of people around the world. Confinement measures aim to reduce the epidemic's spread and minimize the burden of morbidity and mortality. In response to the challenges caused by the pandemic, digital health passports have been developed exponentially. We highlight the latent epidemiological barriers to health passports to achieve standardized digital care platforms. This review paper not only highlights the epidemiological barriers but also articulates the possible infrastructure required to make the International Standard for a multi-factor authenticated and validated health passport.
Collapse
Affiliation(s)
- Radha Ambalavanan
- Research Department, The Self Research Institute, Broken Arrow, OK, United States
| | | | | | | |
Collapse
|
18
|
Lee JC, Kim SY, Song J, Jang H, Kim M, Kim H, Choi SQ, Kim S, Jolly P, Kang T, Park S, Ingber DE. Micrometer-thick and porous nanocomposite coating for electrochemical sensors with exceptional antifouling and electroconducting properties. Nat Commun 2024; 15:711. [PMID: 38331881 PMCID: PMC10853525 DOI: 10.1038/s41467-024-44822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024] Open
Abstract
Development of coating technologies for electrochemical sensors that consistently exhibit antifouling activities in diverse and complex biological environments over extended time is vital for effective medical devices and diagnostics. Here, we describe a micrometer-thick, porous nanocomposite coating with both antifouling and electroconducting properties that enhances the sensitivity of electrochemical sensors. Nozzle printing of oil-in-water emulsion is used to create a 1 micrometer thick coating composed of cross-linked albumin with interconnected pores and gold nanowires. The layer resists biofouling and maintains rapid electron transfer kinetics for over one month when exposed directly to complex biological fluids, including serum and nasopharyngeal secretions. Compared to a thinner (nanometer thick) antifouling coating made with drop casting or a spin coating of the same thickness, the thick porous nanocomposite sensor exhibits sensitivities that are enhanced by 3.75- to 17-fold when three different target biomolecules are tested. As a result, emulsion-coated, multiplexed electrochemical sensors can carry out simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid, antigen, and host antibody in clinical specimens with high sensitivity and specificity. This thick porous emulsion coating technology holds promise in addressing hurdles currently restricting the application of electrochemical sensors for point-of-care diagnostics, implantable devices, and other healthcare monitoring systems.
Collapse
Affiliation(s)
- Jeong-Chan Lee
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Su Yeong Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
- Department of Radiology, Harvard Medical School, Boston, MA, 02114, USA
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Min Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hanul Kim
- Department of Chemical and Biomolecular Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Pawan Jolly
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do, 16419, Republic of Korea.
| | - Steve Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA.
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
19
|
Romero-Ibarguengoitia ME, Rodríguez-Torres JF, Garza-Silva A, Rivera-Cavazos A, Morales-Rodriguez DP, Hurtado-Cabrera M, Kalife-Assad R, Villarreal-Parra D, Loose-Esparza A, Gutiérrez-Arias JJ, Mata-Porras YG, Ojeda-Salazar DA, Sanz-Sánchez MA, González-Cantú A, Azzolini E, Rescigno M. Association of vaccine status, reinfections, and risk factors with Long COVID syndrome. Sci Rep 2024; 14:2817. [PMID: 38307886 PMCID: PMC10837423 DOI: 10.1038/s41598-024-52925-4] [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: 09/19/2023] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
The COVID-19 pandemic had a profound global impact, characterized by a high fatality rate and the emergence of enduring consequences known as Long COVID. Our study sought to determine the prevalence of Long COVID syndrome within a population of Northeastern Mexico, correlating it with patients' comorbidities, number of COVID-19 reinfection, and vaccination status. Employing an observational cross-sectional approach, we administered a comprehensive questionnaire covering medical history, demographics, vaccination status, COVID-related symptoms, and treatment. Our participant cohort included 807 patients, with an average age of 41.5 (SD 13.6) years, and women accounting 59.3% of the cohort. The follow-up was 488 (IQR 456) days. One hundred sixty-eight subjects (20.9%) met Long COVID criteria. Long COVID-19 was more prevalent when subjects had reinfections (p = 0.02) and less frequent when they had a complete vaccination scheme (p = 0.05). Through logistic regression, we found that male gender (OR 0.5, p ≤ 0.001), blood types of AB- (OR 0.48, p = 0.003) and O- (OR 0.27, p ≤ 0.001) in comparison with A+ and two doses of vaccines (OR 0.5, p = 006) to be protective factors against Long COVID; while higher BMI (OR 1.04, p = 0.005) was a risk factor. We saw that the prevalence of Long COVID was different within vaccinated patients and specific blood types, while being female and a higher BMI were associated with an increased risk of having long-COVID.
Collapse
Affiliation(s)
- Maria Elena Romero-Ibarguengoitia
- Research Department, Hospital Clínica Nova de Monterrey, San Nicolás de los Garza, Nuevo León, México.
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México.
| | - Juan Francisco Rodríguez-Torres
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
- Internal Medicine Department, Hospital Clínica Nova de Monterrey, San Nicolás de los Garza, Nuevo León, México
| | - Arnulfo Garza-Silva
- Research Department, Hospital Clínica Nova de Monterrey, San Nicolás de los Garza, Nuevo León, México
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Andrea Rivera-Cavazos
- Research Department, Hospital Clínica Nova de Monterrey, San Nicolás de los Garza, Nuevo León, México
| | - Devany Paola Morales-Rodriguez
- Research Department, Hospital Clínica Nova de Monterrey, San Nicolás de los Garza, Nuevo León, México
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Mauricio Hurtado-Cabrera
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Ricardo Kalife-Assad
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Diana Villarreal-Parra
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Alejandro Loose-Esparza
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Juan José Gutiérrez-Arias
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Yaressi Guadalupe Mata-Porras
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Daniela Abigail Ojeda-Salazar
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Miguel Angel Sanz-Sánchez
- Research Department, Hospital Clínica Nova de Monterrey, San Nicolás de los Garza, Nuevo León, México
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Arnulfo González-Cantú
- Research Department, Hospital Clínica Nova de Monterrey, San Nicolás de los Garza, Nuevo León, México
- Escuela de Medicina, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, San Pedro Garza García, Nuevo León, México
| | - Elena Azzolini
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072, Pieve Emanuele, Milan, Italy
| | - Maria Rescigno
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072, Pieve Emanuele, Milan, Italy
| |
Collapse
|
20
|
Song HH, Choi JC, Lee R, Yoon SK, Park HJ, Shin YH, Shin JW, Kim J. Quality and composition of archived nucleic acids after use in SARS-CoV-2 molecular testing. Clin Chim Acta 2024; 554:117755. [PMID: 38182077 DOI: 10.1016/j.cca.2023.117755] [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: 01/30/2023] [Revised: 11/27/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Reverse transcription real-time PCR (rRT-PCR) has been a gold-standard method to detect SARS-CoV-2, for which quality assessment of nucleic acids (NAs) is not needed. In order to prepare for future use, we evaluated NA quality from archived SARS-CoV-2 rRT-PCR samples. METHODS NA samples were collected in February 2021 and extracted using the QIAamp DSP Virus Spin Kit, (53 SARS-CoV-2-positive and 100 SARS-CoV-2-negative). Quality, quantity, and purity of NA were measured spectrophotometrically or fluorescently. Droplet digital PCR was used to characterize the double strand DNA (dsDNA) origin and composition by quantifying 16S rDNA and RPP30. RESULTS The RIN and purity were not significantly different between groups (p = 0.3828). RNA quantity was significantly higher than dsDNA in both groups (p < 0.0001); both dsDNA and RNA quantity were significantly higher in positive samples (dsDNA, RNA p = 0.021). For dsDNA, 16S rDNA copies were significantly greater than RPP30 in both groups (p < 0.0001), and RPP30 were significantly higher in positive samples (p < 0.0001). CONCLUSIONS Archived NA quality after SARS-CoV-2 rRT-PCR was guaranteed for subsequent molecular research using human or bacterial DNA, especially for short targets.
Collapse
Affiliation(s)
- Ho Hyun Song
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Asan, Chungcheongnam-do, Republic of Korea
| | - Jong Cheul Choi
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Ran Lee
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Sook Kyung Yoon
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Hye Jeong Park
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Young Hee Shin
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Jeong Won Shin
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea.
| | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
21
|
Liu X, Yang X, Wang C, Liu Q, Ding Y, Xu S, Wang G, Xiao R. A nanogap-enhanced SERS nanotag-based lateral flow assay for ultrasensitive and simultaneous monitoring of SARS-CoV-2 S and NP antigens. Mikrochim Acta 2024; 191:104. [PMID: 38236334 DOI: 10.1007/s00604-023-06126-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/26/2023] [Indexed: 01/19/2024]
Abstract
A lateral flow assay (LFA) strip based on dual 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB)-encoded satellite Fe3O4@Au (Mag@Au) SERS tags with nanogap is reported for ultrasensitive and simultaneous diagnosis of two SARS-CoV-2 functional proteins. Composed of Fe3O4 core, satellite gold shell with nanogaps, and double-layer DTNB, the Mag@Au nanoparticles with an average size of 238 nm were designed as multifunctional tags to efficiently enrich the target SARS-CoV-2 protein from complex samples, significantly enhancing the SERS signal of the LFA strip and provide quantitative SERS detection of analyte on test lines. The developed dual DTNB-encoded satellite Mag@Au-based LFA allowed simultaneous quantification of spike (S) protein and nucleocapsid (NP) protein with detection limits of 23 pg mL-1 and 2 pg mL-1, respectively, lower than commercial ELISA kits and reported SERS-LFA detection system-based Au NPs and Fe3O4@3 nm Au MNPs. This magnetic SERS-LFA also showed high performance of multi-variant strain detection and further distinguished clinical samples of Omicron variant infection, demonstrating the potential of in situ detection of respiratory virus diseases.
Collapse
Affiliation(s)
- Xiaoxian Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu, 210093, People's Republic of China
| | - Xingsheng Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
- Bioinformatics Center of AMMS, Beijing, 100850, People's Republic of China
| | - Chongwen Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510000, People's Republic of China
| | - Qiqi Liu
- Bioinformatics Center of AMMS, Beijing, 100850, People's Republic of China
| | - Yanlei Ding
- Bioinformatics Center of AMMS, Beijing, 100850, People's Republic of China
| | - Shiping Xu
- GI Department, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100039, People's Republic of China.
| | - Guanghui Wang
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu, 210093, People's Republic of China.
| | - Rui Xiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
| |
Collapse
|
22
|
Koo KM, Kim CD, Kim TH. Recent Advances in Electrochemical Detection of Cell Energy Metabolism. BIOSENSORS 2024; 14:46. [PMID: 38248422 PMCID: PMC10813075 DOI: 10.3390/bios14010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Cell energy metabolism is a complex and multifaceted process by which some of the most important nutrients, particularly glucose and other sugars, are transformed into energy. This complexity is a result of dynamic interactions between multiple components, including ions, metabolic intermediates, and products that arise from biochemical reactions, such as glycolysis and mitochondrial oxidative phosphorylation (OXPHOS), the two main metabolic pathways that provide adenosine triphosphate (ATP), the main source of chemical energy driving various physiological activities. Impaired cell energy metabolism and perturbations or dysfunctions in associated metabolites are frequently implicated in numerous diseases, such as diabetes, cancer, and neurodegenerative and cardiovascular disorders. As a result, altered metabolites hold value as potential disease biomarkers. Electrochemical biosensors are attractive devices for the early diagnosis of many diseases and disorders based on biomarkers due to their advantages of efficiency, simplicity, low cost, high sensitivity, and high selectivity in the detection of anomalies in cellular energy metabolism, including key metabolites involved in glycolysis and mitochondrial processes, such as glucose, lactate, nicotinamide adenine dinucleotide (NADH), reactive oxygen species (ROS), glutamate, and ATP, both in vivo and in vitro. This paper offers a detailed examination of electrochemical biosensors for the detection of glycolytic and mitochondrial metabolites, along with their many applications in cell chips and wearable sensors.
Collapse
Affiliation(s)
| | | | - Tae-Hyung Kim
- School of Integrative Engineering, Chung-Ang University, 84 Heukseuk-ro, Dongjak-gu, Seoul 06974, Republic of Korea; (K.-M.K.); (C.-D.K.)
| |
Collapse
|
23
|
Zarouri A, Barnes AMT, Aboubakr H, Thekkudan Novi V, Dong Q, Nelson A, Goyal S, Abbas A. A high-performance polymer composite column for coronavirus nucleic acid purification. Sci Rep 2024; 14:1138. [PMID: 38212439 PMCID: PMC10784286 DOI: 10.1038/s41598-024-51671-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024] Open
Abstract
Here, we report the development of a novel polymer composite (PC) purification column and kit. The performance of the PC columns was compared to conventional silica gel (SG) columns for the purification of nucleic acids from coronaviruses, including SARS-CoV-2, in 82 clinical samples. The results shows that PC-based purification outperforms silica gel (SG)-based purification by enabling a higher sensitivity (94%), accuracy (97%), and by eliminating false positives (100% specificity). The high specificity is critical for efficient patient triage and resource management during pandemics. Furthermore, PC-based purification exhibits three times higher analytical precision than a commonly used SG-based nucleic acid purification thereby enabling a more accurate quantification of viral loads and higher reproducibility.
Collapse
Affiliation(s)
- Akli Zarouri
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Aaron M T Barnes
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota Twin Cities, 420 Delaware Street SE, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota Medical School, 689 23rd Ave SE, Minneapolis, MN, USA
| | - Hamada Aboubakr
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
- Department of Veterinary Population Medicine, University of Minnesota Twin Cities, 1333 Gortner Ave., Saint Paul, MN, USA
| | - Vinni Thekkudan Novi
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Qiuchen Dong
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Andrew Nelson
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota Twin Cities, 420 Delaware Street SE, Minneapolis, MN, USA
| | - Sagar Goyal
- Department of Veterinary Population Medicine, University of Minnesota Twin Cities, 1333 Gortner Ave., Saint Paul, MN, USA
| | - Abdennour Abbas
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA.
| |
Collapse
|
24
|
Jin M, Ding J, Zhou Y, Chen J, Wang Y, Li Z. StratoLAMP: Label-free, multiplex digital loop-mediated isothermal amplification based on visual stratification of precipitate. Proc Natl Acad Sci U S A 2024; 121:e2314030121. [PMID: 38165933 PMCID: PMC10786297 DOI: 10.1073/pnas.2314030121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/05/2023] [Indexed: 01/04/2024] Open
Abstract
Multiplex, digital nucleic acid detections have important biomedical applications, but the multiplexity of existing methods is predominantly achieved using fluorescent dyes or probes, making the detection complicated and costly. Here, we present the StratoLAMP for label-free, multiplex digital loop-mediated isothermal amplification based on visual stratification of the precipitate byproduct. The StratoLAMP designates two sets of primers with different concentrations to achieve different precipitate yields when amplifying different nucleic acid targets. In the detection, deep learning image analysis is used to stratify the precipitate within each droplet and determine the encapsulated targets for nucleic acid quantification. We investigated the effect of the amplification reagents and process on the precipitate generation and optimized the assay conditions. We then implemented a deep-learning image analysis pipeline for droplet detection, achieving an overall accuracy of 94.3%. In the application, the StratoLAMP successfully achieved the simultaneous quantification of two nucleic acid targets with high accuracy. By eliminating the need for fluorescence, StratoLAMP represents a unique concept toward label-free, multiplex nucleic acid assays and an analytical tool with great cost-effectiveness.
Collapse
Affiliation(s)
- Meichi Jin
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
| | - Jingyi Ding
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
| | - Yu Zhou
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
- Smart Medical Imaging, Learning and Engineering Lab, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
| | - Jiazhao Chen
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
- Smart Medical Imaging, Learning and Engineering Lab, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
| | - Yi Wang
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
- Smart Medical Imaging, Learning and Engineering Lab, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
| | - Zida Li
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen518060, China
| |
Collapse
|
25
|
von Possel R, Menge B, Deschermeier C, Fritzsche C, Hemmer C, Geerdes-Fenge H, Loebermann M, Schulz A, Lattwein E, Steinhagen K, Tönnies R, Ahrendt R, Emmerich P. Performance Analysis of Serodiagnostic Tests to Characterize the Incline and Decline of the Individual Humoral Immune Response in COVID-19 Patients: Impact on Diagnostic Management. Viruses 2024; 16:91. [PMID: 38257792 PMCID: PMC10820597 DOI: 10.3390/v16010091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Serodiagnostic tests for antibody detection to estimate the immunoprotective status regarding SARS-CoV-2 support diagnostic management. This study aimed to investigate the performance of serological assays for COVID-19 and elaborate on test-specific characteristics. Sequential samples (n = 636) of four panels (acute COVID-19, convalescent COVID-19 (partly vaccinated post-infection), pre-pandemic, and cross-reactive) were tested for IgG by indirect immunofluorescence test (IIFT) and EUROIMMUN EUROLINE Anti-SARS-CoV-2 Profile (IgG). Neutralizing antibodies were determined by a virus neutralization test (VNT) and two surrogate neutralization tests (sVNT, GenScript cPass, and EUROIMMUN SARS-CoV-2 NeutraLISA). Analysis of the acute and convalescent panels revealed high positive (78.3% and 91.6%) and negative (91.6%) agreement between IIFT and Profile IgG. The sVNTs revealed differences in their positive (cPass: 89.4% and 97.0%, NeutraLISA: 71.5% and 72.1%) and negative agreement with VNT (cPass: 92.3% and 50.0%, NeutraLISA: 95.1% and 92.5%) at a diagnostic specificity of 100% for all tests. The cPass showed higher inhibition rates than NeutraLISA at VNT titers below 1:640. Cross-reactivities were only found by cPass (57.1%). Serodiagnostic tests, which showed substantial agreement and fast runtime, could provide alternatives for cell-based assays. The findings of this study suggest that careful interpretation of serodiagnostic results obtained at different times after SARS-CoV-2 antigen exposure is crucial to support decision-making in diagnostic management.
Collapse
Affiliation(s)
- Ronald von Possel
- Department for Virology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- Department of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, University of Rostock, 18057 Rostock, Germany
| | - Babett Menge
- Institute for Experimental Immunology, EUROIMMUN Medizinische Labordiagnostika AG, 23560 Lübeck, Germany
| | - Christina Deschermeier
- Diagnostics Development Laboratory, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Carlos Fritzsche
- Department of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, University of Rostock, 18057 Rostock, Germany
| | - Christoph Hemmer
- Department of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, University of Rostock, 18057 Rostock, Germany
| | - Hilte Geerdes-Fenge
- Department of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, University of Rostock, 18057 Rostock, Germany
| | - Micha Loebermann
- Department of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, University of Rostock, 18057 Rostock, Germany
| | - Anette Schulz
- Institute for Experimental Immunology, EUROIMMUN Medizinische Labordiagnostika AG, 23560 Lübeck, Germany
| | - Erik Lattwein
- Institute for Experimental Immunology, EUROIMMUN Medizinische Labordiagnostika AG, 23560 Lübeck, Germany
| | - Katja Steinhagen
- Institute for Experimental Immunology, EUROIMMUN Medizinische Labordiagnostika AG, 23560 Lübeck, Germany
| | | | | | - Petra Emmerich
- Department for Virology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- Department of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, University of Rostock, 18057 Rostock, Germany
| |
Collapse
|
26
|
Matic N, Lawson T, Ritchie G, Lowe CF, Romney MG. Testing the limits of multiplex respiratory virus assays for SARS-CoV-2 at high cycle threshold values: Comparative performance of cobas 6800/8800 SARS-CoV-2 & Influenza A/B, Xpert Xpress SARS-CoV-2/Flu/RSV, and cobas Liat SARS-CoV-2 & Influenza A/B. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA = JOURNAL OFFICIEL DE L'ASSOCIATION POUR LA MICROBIOLOGIE MEDICALE ET L'INFECTIOLOGIE CANADA 2024; 8:328-335. [PMID: 38250621 PMCID: PMC10797767 DOI: 10.3138/jammi-2022-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 01/23/2024]
Abstract
Background Multiplex real-time RT-PCR assays for respiratory pathogens are valuable tools to optimize laboratory workflow and turnaround time. At a time when resurgence of influenza and respiratory syncytial virus (RSV) cases have been widely observed along with continued transmission of SARS-CoV-2, timely identification of all circulating respiratory viruses is crucial. This study evaluates the detection of low viral loads of SARS-CoV-2 by four multiplex molecular assays: Roche cobas 6800/8800 SARS-CoV-2 & Influenza A/B Test, Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV, cobas Liat SARS-CoV-2 & Influenza A/B, and a laboratory-developed test (LDT). Methods Retrospective upper respiratory tract specimens positive for various respiratory viruses at a range of cycle threshold (Ct) values (18-40) were tested by four multiplex assays. Positive and negative percent agreement (PPA and NPA) with validated RT-PCR assays were calculated. Results A total of 82 samples were assessed, with discordant results observed in a portion of the samples (10/82, 12.2%) where Ct values were >33. The majority of the discordant results (6/10, 60%) were false negatives. Overall, PPA was 100% (58/58) for cobas 6800, 97.4% (38/39) for GeneXpert, 100% (17/17) for Liat, and 90.5% (57/63) for the LDT. PPA for the LDT increased to 92.1% after manual review of amplification curves. Conclusions Commercial multiplex respiratory virus assays have good performance for samples with medium to high viral loads (Ct values <33). Laboratories should consider appropriate test result review and confirmation protocols to optimize sensitivity, and may consider reporting samples with additional interpretive comments when low viral loads are detected.
Collapse
Affiliation(s)
- Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| |
Collapse
|
27
|
Hempel EM, Bharmal A, Li G, Minhas A, Manan R, Doull K, Hamilton L, Cheung B, Chan M, Gunadasa K, Chow R, Lee T, Tsang F, Krajden M, Mooder K, Kassan T, Prystajecky N, Jassem A, Hoang LMN. Prospective, clinical comparison of self-collected throat-bilateral nares swabs and saline gargle compared to health care provider collected nasopharyngeal swabs among symptomatic outpatients with potential SARS-CoV-2 infection. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA = JOURNAL OFFICIEL DE L'ASSOCIATION POUR LA MICROBIOLOGIE MEDICALE ET L'INFECTIOLOGIE CANADA 2024; 8:283-298. [PMID: 38250616 PMCID: PMC10797771 DOI: 10.3138/jammi-2023-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/27/2023] [Accepted: 06/15/2023] [Indexed: 01/23/2024]
Abstract
Background In British Columbia (BC), self-collected saline gargle (SG) is the only alternative to health care provider (HCP)-collected nasopharyngeal (NP) swabs to detect SARS-CoV-2 in an outpatient setting by polymerase chain reaction (PCR). However, some individuals cannot perform a SG. Our study aimed to assess combined throat-bilateral nares (TN) swabbing as a swab-based alternative. Methods Symptomatic individuals greater than 12 years of age seeking a COVID-19 PCR test at one of two COVID-19 collection centres in Metro Vancouver were asked to participate in this study. Participants provided a HCP-collected NP sample and a self-collected SG and TN sample for PCR testing, which were either HCP observed or unobserved. Results Three-hundred and eleven individuals underwent all three collections. Compared against HCP-NP, SG was 99% sensitive and 98% specific (kappa 0.97) and TN was 99% sensitive and 99% specific (kappa 0.98). Using the final clinical test interpretation as the reference standard, NP was 98% sensitive and 100% specific (kappa 0.98), and both SG and TN were 99% sensitive and 100% specific (both kappa 0.99). Mean cycle threshold values for each viral target were higher in SG specimens compared to the other sample types; however, this did not significantly impact the clinical performance, because the positivity rates were similar. The clinical performance of all specimen types was comparable within the first 7 days of symptom onset, regardless of the observation method. SG self-collections were rated the most acceptable, followed by TN. Conclusions TN provides another less invasive self-collection modality for symptomatic outpatient SARS-CoV-2 PCR testing.
Collapse
Affiliation(s)
- Eric M Hempel
- Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Aamir Bharmal
- British Columbia Centre for Disease Control Public Health Response, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guiyun Li
- Fraser Health Authority, Surrey, British Columbia, Canada
| | - Aileen Minhas
- Fraser Health Authority, Surrey, British Columbia, Canada
| | - Ramndip Manan
- Fraser Health Authority, Surrey, British Columbia, Canada
| | - Kathy Doull
- Fraser Health Authority, Surrey, British Columbia, Canada
| | - Lynsey Hamilton
- British Columbia Centre for Disease Control Knowledge Translation, Vancouver, British Columbia, Canada
| | - Branco Cheung
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Michael Chan
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Kingsley Gunadasa
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Ron Chow
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Tracy Lee
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Frankie Tsang
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Mooder
- Provincial Health Services Authority, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Trushna Kassan
- Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | - Natalie Prystajecky
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Agatha Jassem
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Linda MN Hoang
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
28
|
Ebbah E, Amissah A, Kim JH, Driskell JD. SERS-based immunoassay on a plasmonic syringe filter for improved sampling and labeling efficiency of biomarkers. Analyst 2023; 149:221-230. [PMID: 38018888 DOI: 10.1039/d3an01899g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Rapid, sensitive, and quantitative detection of biomarkers is needed for early diagnosis of disease and surveillance of infectious outbreaks. Here, we exploit a plasmonic syringe filter and surface-enhanced Raman spectroscopy (SERS) in the development of a rapid detection system, using human IgG as a model diagnostic biomarker. The novel assay design facilitates multiple passages of the sample and labeling solution through the detection zone enabling us to investigate and maximize sampling efficiency to the capture substrate. The vertical flow immunoassay process in this study involves the utilization of filter paper embedded with gold nanoparticles (AuNPs) to form a plasmonic substrate. Capture antibody (anti-human IgG) is then immobilized onto the prepared plasmonic paper and inserted into a vertical flow device (syringe filter holder). Sample solution is passed through the filter paper and the target antigen (human IgG) is selectively captured by the immobilized antibody to form an antibody-antigen complex. Next, functionalized AuNPs as extrinsic Raman labels (ERLs) are passed through the filter paper to label the captured biomarker molecules forming a layered structure. This sandwiched geometry enhances plasmonic coupling and SERS signal to provide highly sensitive detection of biomolecules. Systematic studies to investigate the impact of multiple infuse/withdraw cycles of the sample and labeling solutions reveal that antigen and ERL binding are maximized with 10 and 20 cycles, respectively. The optimized assay achieves a detection limit of ∼0.2 ng mL-1 for human IgG with a total assay time of less than 5 minutes, meeting the demands for rapid point of care diagnostics. Additionally, the optimized platform was implemented in the quantitative analysis of the SARS-CoV-2 nucleocapsid protein, the typical target in commercial, FDA-approved rapid antigen tests for COVID-19.
Collapse
Affiliation(s)
- Eunice Ebbah
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA.
| | - Anthony Amissah
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA.
| | - Jun-Hyun Kim
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA.
| | - Jeremy D Driskell
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA.
| |
Collapse
|
29
|
Ota K, Kodama H, Kawamoto Y, Sasaki D, Mitsumoto-Kaseida F, Sakamoto K, Kosai K, Hasegawa H, Takazono T, Izumikawa K, Mukae H, Tun MMN, Morita K, Yanagihara K. The evaluation of a rapid microfluidic immunofluorescence antigen test in detecting the infectiousness of COVID-19 patients. BMC Infect Dis 2023; 23:823. [PMID: 37996783 PMCID: PMC10668452 DOI: 10.1186/s12879-023-08821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND A test-based strategy against coronavirus disease 2019 (COVID-19) is one of the measures to assess the need for isolation and prevention of infection. However, testing with high sensitivity methods, such as quantitative RT-PCR, leads to unnecessary isolation, whereas the lateral flow antigen test shows low sensitivity and false negative results. The purpose of this study was to evaluate the performance of the LumiraDx SARS-CoV-2 Ag test (Lumira Ag), a rapid microfluidic immunofluorescence method, in assessing infectivity. METHODS This study was performed from March 2022 to July 2022. A pair of nasopharyngeal swab samples were obtained from each patient with mild COVID-19. One swab was used for Lumira Ag testing, and the other for quantitative RT-PCR testing and virus culture. RESULTS A total of 84 patients were included in the study. Among them, PCR, Lumira Ag test, and virus culture indicated positivity for 82, 66, and 24 patients, respectively. When comparing the Lumira Ag test to virus culture, its sensitivity was 100.0% (24/24), specificity, 30.0% (18/60); positive predictive value, 36.3% (24/66); and negative predictive value (NPV), 100.0% (18/18). The positive sample for virus culture was observed until the ninth day from the onset of symptoms, while the Lumira Ag test was observed until day 11. CONCLUSIONS The Lumira Ag test showed high sensitivity and NPV (100% each) compared to virus culture. A test-based strategy using the Lumira Ag test can effectively exclude COVID-19 infectiousness.
Collapse
Affiliation(s)
- Kenji Ota
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan.
| | - Hina Kodama
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Yasuhide Kawamoto
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Daisuke Sasaki
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Fujiko Mitsumoto-Kaseida
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Kei Sakamoto
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
- Department of Microbiology, Graduate School of Medicine, Yamaguchi University, 1-1-1, Minami-Kogushi, Ube, 755-8505, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Takahiro Takazono
- Department of Respiratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Koichi Izumikawa
- Infection Control and Education Center, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
- Dejima Infectious Disease Research Alliance, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8102, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| |
Collapse
|
30
|
Ramos-Mandujano G, Grünberg R, Zhang Y, Bi C, Guzmán-Vega FJ, Shuaib M, Gorchakov RV, Xu J, Tehseen M, Takahashi M, Takahashi E, Dada A, Ahmad AN, Hamdan SM, Pain A, Arold ST, Li M. An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing. Sci Rep 2023; 13:20349. [PMID: 37990068 PMCID: PMC10663496 DOI: 10.1038/s41598-023-47190-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use-with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses.
Collapse
Affiliation(s)
- Gerardo Ramos-Mandujano
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Raik Grünberg
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Yingzi Zhang
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Francisco J Guzmán-Vega
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Shuaib
- Pathogen Genomics Laboratory, Bioscience Program, Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Rodion V Gorchakov
- Health, Safety and Environment Department, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Jinna Xu
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Etsuko Takahashi
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Ashraf Dada
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
- College of Medicine, Al Faisal University, Riyadh, Kingdom of Saudi Arabia
| | - Adeel Nazir Ahmad
- KAUST Health, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Bioscience Program, Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Stefan T Arold
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
| | - Mo Li
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
- Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
| |
Collapse
|
31
|
Bertels X, Hanoteaux S, Janssens R, Maloux H, Verhaegen B, Delputte P, Boogaerts T, van Nuijs ALN, Brogna D, Linard C, Marescaux J, Didy C, Pype R, Roosens NHC, Van Hoorde K, Lesenfants M, Lahousse L. Time series modelling for wastewater-based epidemiology of COVID-19: A nationwide study in 40 wastewater treatment plants of Belgium, February 2021 to June 2022. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165603. [PMID: 37474075 DOI: 10.1016/j.scitotenv.2023.165603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Wastewater-based epidemiology (WBE) has been implemented to monitor surges of COVID-19. Yet, multiple factors impede the usefulness of WBE and quantitative adjustment may be required. AIM We aimed to model the relationship between WBE data and incident COVID-19 cases, while adjusting for confounders and autocorrelation. METHODS This nationwide WBE study includes data from 40 wastewater treatment plants (WWTPs) in Belgium (02/2021-06/2022). We applied ARIMA-based modelling to assess the effect of daily flow rate, pepper mild mottle virus (PMMoV) concentration, a measure of human faeces in wastewater, and variants (alpha, delta, and omicron strains) on SARS-CoV-2 RNA levels in wastewater. Secondly, adjusted WBE metrics at different lag times were used to predict incident COVID-19 cases. Model selection was based on AICc minimization. RESULTS In 33/40 WWTPs, RNA levels were best explained by incident cases, flow rate, and PMMoV. Flow rate and PMMoV were associated with -13.0 % (95 % prediction interval: -26.1 to +0.2 %) and +13.0 % (95 % prediction interval: +5.1 to +21.0 %) change in RNA levels per SD increase, respectively. In 38/40 WWTPs, variants did not explain variability in RNA levels independent of cases. Furthermore, our study shows that RNA levels can lead incident cases by at least one week in 15/40 WWTPs. The median population size of leading WWTPs was 85.1 % larger than that of non‑leading WWTPs. In 17/40 WWTPs, however, RNA levels did not lead or explain incident cases in addition to autocorrelation. CONCLUSION This study provides quantitative insights into key determinants of WBE, including the effects of wastewater flow rate, PMMoV, and variants. Substantial inter-WWTP variability was observed in terms of explaining incident cases. These findings are of practical importance to WBE practitioners and show that the early-warning potential of WBE is WWTP-specific and needs validation.
Collapse
Affiliation(s)
- Xander Bertels
- Department of Bioanalysis, Ghent University, 9000 Ghent, Belgium
| | - Sven Hanoteaux
- Epidemiology and Public Health, Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | - Raphael Janssens
- Epidemiology and Public Health, Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | - Hadrien Maloux
- Epidemiology and Public Health, Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | - Bavo Verhaegen
- Infectious Diseases in Humans, Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium
| | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, 2610 Wilrijk, Belgium
| | - Tim Boogaerts
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Delphine Brogna
- Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - Catherine Linard
- Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - Jonathan Marescaux
- Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium; E-BIOM SA, 5000 Namur, Belgium
| | - Christian Didy
- Société Publique de Gestion de l'Eau, 4800 Verviers, Belgium
| | - Rosalie Pype
- Société Publique de Gestion de l'Eau, 4800 Verviers, Belgium
| | - Nancy H C Roosens
- Biological Health Risks, Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koenraad Van Hoorde
- Infectious Diseases in Humans, Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium
| | - Marie Lesenfants
- Epidemiology and Public Health, Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, 9000 Ghent, Belgium.
| |
Collapse
|
32
|
Ahmad I, Merla A, Ali F, Shah B, AlZubi AA, AlZubi MA. A deep transfer learning approach for COVID-19 detection and exploring a sense of belonging with Diabetes. Front Public Health 2023; 11:1308404. [PMID: 38026271 PMCID: PMC10657998 DOI: 10.3389/fpubh.2023.1308404] [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: 10/06/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
COVID-19 is an epidemic disease that results in death and significantly affects the older adult and those afflicted with chronic medical conditions. Diabetes medication and high blood glucose levels are significant predictors of COVID-19-related death or disease severity. Diabetic individuals, particularly those with preexisting comorbidities or geriatric patients, are at a higher risk of COVID-19 infection, including hospitalization, ICU admission, and death, than those without Diabetes. Everyone's lives have been significantly changed due to the COVID-19 outbreak. Identifying patients infected with COVID-19 in a timely manner is critical to overcoming this challenge. The Real-Time Polymerase Chain Reaction (RT-PCR) diagnostic assay is currently the gold standard for COVID-19 detection. However, RT-PCR is a time-consuming and costly technique requiring a lab kit that is difficult to get in crises and epidemics. This work suggests the CIDICXR-Net50 model, a ResNet-50-based Transfer Learning (TL) method for COVID-19 detection via Chest X-ray (CXR) image classification. The presented model is developed by substituting the final ResNet-50 classifier layer with a new classification head. The model is trained on 3,923 chest X-ray images comprising a substantial dataset of 1,360 viral pneumonia, 1,363 normal, and 1,200 COVID-19 CXR images. The proposed model's performance is evaluated in contrast to the results of six other innovative pre-trained models. The proposed CIDICXR-Net50 model attained 99.11% accuracy on the provided dataset while maintaining 99.15% precision and recall. This study also explores potential relationships between COVID-19 and Diabetes.
Collapse
Affiliation(s)
- Ijaz Ahmad
- Digital Transition, Innovation and Health Service, Leonardo da Vinci Telematic University, Chieti, Italy
| | - Arcangelo Merla
- Department of Engineering and Geology (INGEO) University "G. d’Annunzio" Chieti-Pescara, Pescara, Italy
| | - Farman Ali
- Department of Computer Science and Engineering, School of Convergence, College of Computing and Informatics, Sungkyunkwan University, Seoul, Republic of Korea
| | - Babar Shah
- College of Technological Innovation, Zayed University, Dubai, United Arab Emirates
| | - Ahmad Ali AlZubi
- Department of Computer Science, Community College, King Saud University, Riyadh, Saudi Arabia
| | - Mallak Ahmad AlZubi
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| |
Collapse
|
33
|
Boujemaa S, Suri GS, Kaur G. Diagnostic evaluation of Panbio™ antigen rapid diagnostic test for SARS-CoV-2: A systematic review and meta-analysis. J Virol Methods 2023; 321:114811. [PMID: 37696303 DOI: 10.1016/j.jviromet.2023.114811] [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: 05/01/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
INTRODUCTION The reverse transcriptase polymerase chain reaction (RT-PCR) is the reference diagnostic method for the confirmation of SARS-CoV-2 infected cases. However, various antigen rapid diagnostic tests (Ag-RDTs) have been developed. The purpose of this meta-analysis study was to assess the diagnostic performance of Panbio™ Ag-RDT (Abbott Point of Care) in identifying the SARS-CoV-2 virus. METHODS We systematically searched eight databases from March 2020 until March 2023 to look for potentially eligible articles. Diagnostic meta-analysis of Panbio™ Ag-RDT used diverse evaluation indicators, including sensitivity, specificity, Diagnostic Odds Ratio (DOR), and the area under the curve (AUC) value. RESULTS Of the 794 articles identified, 49 studies met the inclusion criteria. The pooled estimates of Panbio™ Ag-RDT for the diagnosis of SARS-CoV-2 were 0,65 (95% CI: 0,64-0,66), 0,99 (95% CI: 0,99-1,00), 578,03 (95% CI: 333,37-1002,26) for sensitivity, specificity, and DOR, respectively. Moreover, the summary receiver operating characteristic (SROC) curve revealed an AUC value of 0,942 (95% CI: 0,941-0,943), suggesting an outstanding diagnostic accuracy. Subgroup and meta-regression analyses showed that continent, study period, age, study population and cycle threshold (Ct) values constituted a source of heterogeneity. Furthermore, we demonstrated proof of publication bias for DOR values analyzed using Deek's test (p = 0,001) and funnel plot. CONCLUSION Panbio™ Ag-RDT presented an outstanding diagnostic accuracy in the detection of the SARS-CoV-2 virus in both adults and children with or without symptoms.
Collapse
Affiliation(s)
- Safa Boujemaa
- Biologica Training and Consulting, 2078 Tunis, Tunisia.
| | | | | |
Collapse
|
34
|
Nahiduzzaman M, Goni MOF, Hassan R, Islam MR, Syfullah MK, Shahriar SM, Anower MS, Ahsan M, Haider J, Kowalski M. Parallel CNN-ELM: A multiclass classification of chest X-ray images to identify seventeen lung diseases including COVID-19. EXPERT SYSTEMS WITH APPLICATIONS 2023; 229:120528. [PMID: 37274610 PMCID: PMC10223636 DOI: 10.1016/j.eswa.2023.120528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023]
Abstract
Numerous epidemic lung diseases such as COVID-19, tuberculosis (TB), and pneumonia have spread over the world, killing millions of people. Medical specialists have experienced challenges in correctly identifying these diseases due to their subtle differences in Chest X-ray images (CXR). To assist the medical experts, this study proposed a computer-aided lung illness identification method based on the CXR images. For the first time, 17 different forms of lung disorders were considered and the study was divided into six trials with each containing two, two, three, four, fourteen, and seventeen different forms of lung disorders. The proposed framework combined robust feature extraction capabilities of a lightweight parallel convolutional neural network (CNN) with the classification abilities of the extreme learning machine algorithm named CNN-ELM. An optimistic accuracy of 90.92% and an area under the curve (AUC) of 96.93% was achieved when 17 classes were classified side by side. It also accurately identified COVID-19 and TB with 99.37% and 99.98% accuracy, respectively, in 0.996 microseconds for a single image. Additionally, the current results also demonstrated that the framework could outperform the existing state-of-the-art (SOTA) models. On top of that, a secondary conclusion drawn from this study was that the prospective framework retained its effectiveness over a range of real-world environments, including balanced-unbalanced or large-small datasets, large multiclass or simple binary class, and high- or low-resolution images. A prototype Android App was also developed to establish the potential of the framework in real-life implementation.
Collapse
Affiliation(s)
- Md Nahiduzzaman
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi 6204, Bangladesh
| | - Md Omaer Faruq Goni
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi 6204, Bangladesh
| | - Rakibul Hassan
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi 6204, Bangladesh
| | - Md Robiul Islam
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi 6204, Bangladesh
| | - Md Khalid Syfullah
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi 6204, Bangladesh
| | - Saleh Mohammed Shahriar
- Department of Electrical & Computer Engineering, Rajshahi University of Engineering & Technology, Rajshahi 6204, Bangladesh
| | - Md Shamim Anower
- Department of Electrical & Electronic Engineering, Rajshahi University of Engineering & Technology, Rajshahi 6204, Bangladesh
| | - Mominul Ahsan
- Department of Computer Science, University of York, Deramore Lane, Heslington, York YO10 5GH, UK
| | - Julfikar Haider
- Department of Engineering, Manchester Metropolitan University, Chester St, Manchester M1 5GD, UK
| | - Marcin Kowalski
- Institute of Optoelectronics, Military University of Technology, Gen. S. Kaliskiego 2, 00-908 Warsaw, Poland
| |
Collapse
|
35
|
Zhou S, Feng X, Hu Y, Yang J, Chen Y, Bastow J, Zheng ZJ, Xu M. Factors associated with the utilization of diagnostic tools among countries with different income levels during the COVID-19 pandemic. Glob Health Res Policy 2023; 8:45. [PMID: 37885008 PMCID: PMC10605783 DOI: 10.1186/s41256-023-00330-1] [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: 05/05/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Disparities in the utilization of essential medical products are a key factor contributing to inequality in health outcomes. We aimed to analyze the trends and influencing factors in using Coronavirus disease 2019 (COVID-19) diagnostic tools and disparities in countries with different income levels. METHODS We conducted a cross-sectional study using open and publicly available data sources. Data were mainly collected from the Foundation for Innovative New Diagnostics, "Our World in Data," and the Global Burden of Disease databases. Negative binomial regression model and generalized linear mixed model were employed to investigate into five sets of factors associated with the usage of diagnostics: severity of COVID-19, socioeconomic status, health status, medical service capacity, and rigidity of response. Dominance analysis was utilized to compare the relative importance of these factors. The Blinder-Oaxaca decomposition was used to decompose the difference in the usage of diagnostics between countries. RESULTS The total COVID-19 testing rate ranged from 5.13 to 22,386.63 per 1000 people from March 2020 to October 2022 and the monthly testing rate declined dramatically from January 2022 to October 2022 (52.37/1000 vs 5.91/1000).. The total testing rate was primarily associated with socioeconomic status (37.84%), with every 1 standard deviation (SD) increase in Gross Domestic Product per capita and the proportion of people aged ≥ 70, the total testing rate increased by 88% and 31%. And so is the medical service capacity (33.66%), with every 1 SD increase in health workforce density, the number increased by 38%. The monthly testing rate was primarily associated with socioeconomic status (34.72%) and medical service capacity (28.67%), and the severity of COVID-19 (21.09%). The average difference in the total testing rates between high-income and low-income countries was 2726.59 per 1000 people, and 2493.43 (91.45%) of the differences could be explained through the five sets of factors. CONCLUSIONS Redoubling the efforts, such as local manufacturing, regulatory reliance, and strengthening the community health workforce and laboratory capacity in low- and middle-income countries (LMICs) cannot be more significant for ensuring sustainable and equitable access to diagnostic tools during pandemic.
Collapse
Affiliation(s)
- Shuduo Zhou
- Department of Global Health, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing, 100191, China
- Institute for Global Health and Development, Peking University, Beijing, China
| | - Xiangning Feng
- Department of Global Health, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing, 100191, China
- Institute for Global Health and Development, Peking University, Beijing, China
| | - Yunxuan Hu
- Department of Global Health, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing, 100191, China
- Institute for Global Health and Development, Peking University, Beijing, China
| | - Jian Yang
- Department of Global Health, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing, 100191, China
- Institute for Global Health and Development, Peking University, Beijing, China
| | - Ying Chen
- Department of Global Health, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing, 100191, China
- Institute for Global Health and Development, Peking University, Beijing, China
| | - Jon Bastow
- Independent Diagnostics and Health Systems Expert, Geneva, Switzerland
| | - Zhi-Jie Zheng
- Department of Global Health, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing, 100191, China
- Institute for Global Health and Development, Peking University, Beijing, China
| | - Ming Xu
- Department of Global Health, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing, 100191, China.
- Institute for Global Health and Development, Peking University, Beijing, China.
| |
Collapse
|
36
|
Kang BH, Jang KW, Yu ES, Jeong H, Jeong KH. Single-shot multi-channel plasmonic real-time polymerase chain reaction for multi-target point-of-care testing. LAB ON A CHIP 2023; 23:4701-4707. [PMID: 37823261 DOI: 10.1039/d3lc00687e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Plasmonic nucleic acid amplification tests demand high-throughput and multi-target detection of infectious diseases as well as short turnaround time and small size for point-of-care molecular diagnostics. Here, we report a multi-channel plasmonic real-time reverse-transcription polymerase chain reaction (mpRT-qPCR) assay for ultrafast and on-chip multi-target detection. The mpRT-qPCR system features two pairs of plasmonic thermocyclers for rapid nanostructure-driven amplification and microlens array fluorescence microscopes for in situ multi-color fluorescence quantification. Each channel shows a physical dimension of 32 mm, 75 mm, and 25 mm in width, length, and thickness. The ultrathin microscopes simultaneously capture four different fluorescence images from two PCR chambers of a single cartridge at a single shot exposure per PCR cycle of four different excitation light sources. The experimental results demonstrate a single assay result of high-throughput amplification and multi-target quantification for RNA-dependent RNA polymerase, nucleocapsid, and human ribonuclease P genes in SARS-CoV-2 RNA detection. The mpRT-PCR increases the number of tests four times over the single RT-PCR and exhibits a short detection time of 15 min for the four RT-PCR reactions. This point-of-care molecular diagnostic platform can reduce false negative results in clinical applications of virus detection and decentralize healthcare facilities with limited infrastructure.
Collapse
Affiliation(s)
- Byoung-Hoon Kang
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyung-Won Jang
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Eun-Sil Yu
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyejeong Jeong
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ki-Hun Jeong
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| |
Collapse
|
37
|
Ansu-Mensah M, Kuupiel D, Bawontuo V, Ginindza TG. Availability, stock levels and usage of In-vitro diagnostics in the Bono region, Ghana: A cross-sectional study. Afr J Prim Health Care Fam Med 2023; 15:e1-e10. [PMID: 37916723 PMCID: PMC10623501 DOI: 10.4102/phcfm.v15i1.4114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Point-of-care (POC) diagnostic tests play essential roles in diagnosis, surveillance, and disease management in health settings. Nevertheless, implementation challenges may hamper POC test accessibility. This study evaluated the availability and stock levels of the World Health Organization (WHO) prequalified existing in-vitro diagnostics (IVDs) for use in health facilities without laboratories. AIM To evaluate the availability, stock levels, and usage of POC diagnostic tests. SETTING Bono Region, Ghana. METHODS This cross-sectional survey involved 102 randomly selected Community Health-based and Planning Services (CHPS), 12 district health depots, and a regional medical depot. Using a survey tool, data were collected on clinic staffing, availability and stock levels of tests, and funding sources. STATA 17 was employed for data analysis. RESULTS Majority (37.3%) of the respondents were community health nurses, with 4.4 mean years of work experience and 38 working hours per week. Of the 18 existing WHO prequalified POC tests for use at facilities without laboratories, 10 (56%), 2 (11%) and 0 (0%) were found at CHPS, regional, and district depots, respectively. Majority (183 out of 301) stock levels were low. Of the 10 available tests found, 7 scored 111 (36%) of 'high use'. Supply chain management compliance was 5 (31%) out of 16. All CHPS received government funding with 25.5% of them receiving additional donor or internally generated funding. CONCLUSION This study found poor supply chain management compliance, and low availability of POC tests in the Bono Region of Ghana.Contribution: The study outlines POC tests availability and usage in low-resourced setting.
Collapse
Affiliation(s)
- Monica Ansu-Mensah
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa; and, Health Economics and HIV and AIDS Research Division (HEARD), University of KwaZulu-Natal, Durban, South Africa; and, Clinic, Sunyani Technical University, Sunyani.
| | | | | | | |
Collapse
|
38
|
Link JS, Carrell CS, Jang I, Barstis EJO, Call ZD, Bellows RA, O'Donnell-Sloan JJ, Terry JS, Anderson LBR, Panraksa Y, Geiss BJ, Dandy DS, Henry CS. Capillary flow-driven immunoassay platform for COVID-19 antigen diagnostics. Anal Chim Acta 2023; 1277:341634. [PMID: 37604607 PMCID: PMC10476143 DOI: 10.1016/j.aca.2023.341634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 08/23/2023]
Abstract
Over the last few years, the SARS-CoV-2 pandemic has made the need for rapid, affordable diagnostics more compelling than ever. While traditional laboratory diagnostics like PCR and well-plate ELISA are sensitive and specific, they can be costly and take hours to complete. Diagnostic tests that can be used at the point-of-care or at home, like lateral flow assays (LFAs) are a simple, rapid alternative, but many commercially available LFAs have been criticized for their lack of sensitivity compared to laboratory methods like well-plate ELISAs. The Capillary-Driven Immunoassay (CaDI) device described in this work uses microfluidic channels and capillary action to passively automate the steps of a traditional well-plate ELISA for visual read out. This work builds on prior capillary-flow devices by further simplifying operation and use of colorimetric detection. Upon adding sample, an enzyme-conjugated secondary antibody, wash steps, and substrate are sequentially delivered to test and control lines on a nitrocellulose strip generating a colorimetric response. The end user can visually detect SARS-CoV-2 antigen in 15-20 min by naked eye, or results can be quantified using a smartphone and software such as ImageJ. An analytical detection limit of 83 PFU/mL for SARS-CoV-2 was determined for virus in buffer, and 222 PFU/mL for virus spiked into nasal swabs using image analysis, similar to the LODs determined by traditional well-plate ELISA. Additionally, a visual detection limit of 100 PFU/mL was determined in contrived nasal swab samples by polling 20 untrained end-users. While the CaDI device was used for detecting clinically relevant levels of SARS-CoV-2 in this study, the CaDI device can be easily adapted to other immunoassay applications by changing the reagents and antibodies.
Collapse
Affiliation(s)
- Jeremy S Link
- Department of Chemistry, Colorado State University, USA
| | | | - Ilhoon Jang
- Department of Chemistry, Colorado State University, USA; Institute of Nano Science and Technology, Hanyang University, South Korea
| | | | | | - Rae A Bellows
- Department of Chemistry, Colorado State University, USA
| | | | - James S Terry
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA
| | - Loran B R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA
| | - Yosita Panraksa
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA; Myobacteria Research Laboratories, Colorado State University, USA
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA; School of Biomedical Engineering, Colorado State University, USA
| | - David S Dandy
- Department of Chemical and Biological Engineering, Colorado State University, USA; School of Biomedical Engineering, Colorado State University, USA
| | - Charles S Henry
- Department of Chemistry, Colorado State University, USA; Department of Chemical and Biological Engineering, Colorado State University, USA; School of Biomedical Engineering, Colorado State University, USA; Metalluragy and Materials Research Institute, Chulalongkorn University, Bangkok, Thailand.
| |
Collapse
|
39
|
Calorenni P, Leonardi AA, Sciuto EL, Rizzo MG, Faro MJL, Fazio B, Irrera A, Conoci S. PCR-Free Innovative Strategies for SARS-CoV-2 Detection. Adv Healthc Mater 2023; 12:e2300512. [PMID: 37435997 DOI: 10.1002/adhm.202300512] [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: 02/16/2023] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 07/13/2023]
Abstract
The pandemic outbreak caused by SARS-CoV-2 coronavirus brought a crucial issue in public health causing up to now more than 600 million infected people and 6.5 million deaths. Conventional diagnostic methods are based on quantitative reverse transcription polymerase chain reaction (RT-qPCR assay) and immuno-detection (ELISA assay). However, despite these techniques have the advantages of being standardized and consolidated, they keep some main limitations in terms of accuracy (immunoassays), time/cost consumption of analysis, the need for qualified personnel, and lab constrain (molecular assays). There is crucial the need to develop new diagnostic approaches for accurate, fast and portable viral detection and quantification. Among these, PCR-free biosensors represent the most appealing solution since they can allow molecular detection without the complexity of the PCR. This will enable the possibility to be integrated in portable and low-cost systems for massive and decentralized screening of SARS-CoV-2 in a point-of-care (PoC) format, pointing to achieve a performant identification and control of infection. In this review, the most recent approaches for the SARS-CoV-2 PCR-free detection are reported, describing both the instrumental and methodological features, and highlighting their suitability for a PoC application.
Collapse
Affiliation(s)
- Paolo Calorenni
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Antonio A Leonardi
- Department of Physics and Astronomy, University of Catania, Via Santa Sofia 64, Catania, 95123, Italy
| | - Emanuele L Sciuto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Maria G Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Maria J Lo Faro
- Department of Physics and Astronomy, University of Catania, Via Santa Sofia 64, Catania, 95123, Italy
| | - Barbara Fazio
- URT Lab Sens Beyond Nano, CNR-DSFTM, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Alessia Irrera
- URT Lab Sens Beyond Nano, CNR-DSFTM, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
| | - Sabrina Conoci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
- URT Lab Sens Beyond Nano, CNR-DSFTM, Viale F. Stagno D'Alcontres 37, Messina, 98158, Italy
- Department of Chemistry ''Giacomo Ciamician'', University of Bologna, Via Selmi 2, Bologna, 40126, Italy
- CNR-IMM, Institute for Microelectronics and Microsystems, Ottava Strada n.5, Catania, I-95121, Italy
| |
Collapse
|
40
|
Dou X, Zhang Z, Liu B, Li C, Du Y, Tian F. Highly sensitive digital detection of SARS-CoV-2 nucleocapsid protein through single-molecule counting. Anal Bioanal Chem 2023; 415:6155-6164. [PMID: 37596347 DOI: 10.1007/s00216-023-04886-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 08/20/2023]
Abstract
Nucleocapsid protein (NP) is one of the structural proteins of SARS-CoV-2 which is stable, well-conserved, highly immunogenic, and abundantly expressed due to the host's adaptive immune response, making it a promising antigenic biomarker for the early and rapid identification and diagnosis of SARS-CoV-2. Traditional antigen analytical methods with NP as the detection marker often have insufficient sensitivity. To achieve rapid and highly sensitive detection of NP, we constructed a novel single-molecule (digital) fluorescence-linked immunosorbent assay (FLISA) based on streptavidin-modified transparent 96-well microplates. Streptavidin was immobilized on the microplate under optimized conditions with a 15 mM carbonate buffer solution (pH 9.6) as the coating solution, biotinylated antibodies conjugated with streptavidin as capture probes, and carboxylated fluorescent microsphere-conjugated monoclonal antibodies (FMs-mAbs) as fluorescent probes. Individual sandwich immunolabeled complexes of the SARS-CoV-2 diagnostic marker NP were detected and counted though wide-field inverted fluorescence microscopy (1.1 × 1.4 mm2). FLISA had a linear detection range of 0.2 pg/mL to 200 ng/mL and a limit of detection (LOD) of 0.73 fg/mL and 8 fg/mL for NP in phosphate buffer saline and spiked nasal swab samples, respectively. The sensitivity was much higher than commercial antigen detection kits, providing wide detection prospects in future clinical diagnosis, environmental monitoring, and other fields.
Collapse
Affiliation(s)
- Xuechen Dou
- Medical Support Technology Research Department, Systems Engineering Institute, Academy of Military Sciences, People's Liberation Army, Tianjin, 30161, China
| | - Zhiwei Zhang
- Medical Support Technology Research Department, Systems Engineering Institute, Academy of Military Sciences, People's Liberation Army, Tianjin, 30161, China
| | - Bo Liu
- Medical Support Technology Research Department, Systems Engineering Institute, Academy of Military Sciences, People's Liberation Army, Tianjin, 30161, China
| | - Chao Li
- Medical Support Technology Research Department, Systems Engineering Institute, Academy of Military Sciences, People's Liberation Army, Tianjin, 30161, China
- National Bio-Protection Engineering Center, Tianjin, 300161, China
| | - Yaohua Du
- Medical Support Technology Research Department, Systems Engineering Institute, Academy of Military Sciences, People's Liberation Army, Tianjin, 30161, China.
- National Bio-Protection Engineering Center, Tianjin, 300161, China.
| | - Feng Tian
- Medical Support Technology Research Department, Systems Engineering Institute, Academy of Military Sciences, People's Liberation Army, Tianjin, 30161, China.
| |
Collapse
|
41
|
de Souza LR, da Silva IEP, Celis-Silva G, Raddatz BW, Imamura LM, Kim EYS, Valderrama GV, Riedi HDP, Rogal SR, de Almeida BMM, Figueredo MVM, Bengtson MH, Massirer KB. Improved protocol for Bst polymerase and reverse transcriptase production and application to a point-of-care diagnostics system. Exp Biol Med (Maywood) 2023; 248:1671-1683. [PMID: 38088106 PMCID: PMC10723028 DOI: 10.1177/15353702231215815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised awareness in the scientific community about the importance of being prepared for sanitary emergencies. Many measures implemented during the COVID pandemic are now being expanded to other applications. In the field of molecular and immunological diagnostics, the need to massively test the population worldwide resulted in the application of a variety of methods to detect viral infection. Besides gold standard reverse transcription quantitative polymerase chain reaction (RT-qPCR), the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) arose as an alternative and sensitive method to amplify and detect viral genetic material. We have used openly available protocols and have improved the protein production of RT-LAMP enzymes Bst polymerase and HIV-reverse transcriptase. To optimize enzyme production, we tested different protein tags, and we shortened the protein purification protocol, resulting in reduced processing time and handling of the enzymes and, thus, preserved the protein activity with high purity. The enzymes showed significant stability at 4 °C and 25 °C, over 60 days, and were highly reliable when used as a one-step RT-LAMP reaction in a portable point-of-care device with clinical samples. The enzymes and the reaction setup can be further expanded to detect other infectious diseases agents.
Collapse
Affiliation(s)
- Lucas Rodrigo de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | - Italo Esposti Poly da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-862, Brazil
| | - Gabriele Celis-Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | | | | | | | - Gabriel Vieira Valderrama
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | | | | | | | | | - Mario Henrique Bengtson
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-862, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| |
Collapse
|
42
|
Hu S, Li Y, Dong B, Tang Z, Zhou B, Wang Y, Sun L, Xu L, Wang L, Zhang X, Alifu N, Sun L, Song H. Highly hydrostable and flexible opal photonic crystal film for enhanced up-conversion fluorescence sensor of COVID-19 antibody. Biosens Bioelectron 2023; 237:115484. [PMID: 37352761 DOI: 10.1016/j.bios.2023.115484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023]
Abstract
Efficient detection of related markers is significant for the early screening of COVID-19. Near infrared (NIR) light excited up-conversion fluorescence probes are ideal for biosensing but limited by the low luminescence efficiency. In this work, a novel highly stable opal photonic crystal (OPC) structure was designed to provide an OPC effect for up-conversion fluorescence enhancement, and sensitive Novel Coronavirus IgG up-conversion FRET-based sensor was further constructed. For the problems of water stability and mechanical stability of polymer OPC which cannot be solved for a long time, polymer spray combined with a flipped OPC film strategy is presented. Fragmented size OPC film was firmly fixed by polymer modification layer, which gave large size OPC film great water stability, mechanical stability and bending performance without affecting the fluorescence enhancement property. On this basis, the up-conversion emission intensity was enhanced significantly, and fluorescence resonant energy transfer (FRET) based Novel Coronavirus IgG antibody sensor was constructed. Monolayer up-conversion nanoparticles (UCNPs) on the surface of the polydopamine (PDA)/OPC film can make the fluorescent signal more sensitive, and effectively reduce the detection limit. The test device integrating NIR excitation and mobile phone realized the visual fast detection, showing remarkable sensing performance for COVID-19 antibodies with the limit of detection (LOD) of 0.1 ng mL-1. This detection platform will provide a more effective tool for early detection of the novel coronavirus.
Collapse
Affiliation(s)
- Songtao Hu
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Yige Li
- Department of Oral Implantology, School and Hospital of Stomatology, Jilin University, Changchun, 130021, PR China
| | - Biao Dong
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China.
| | - Zixin Tang
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Bingshuai Zhou
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Yue Wang
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Liheng Sun
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Lin Xu
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Lin Wang
- Department of Oral Implantology, School and Hospital of Stomatology, Jilin University, Changchun, 130021, PR China
| | - Xueliang Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830011, PR China
| | - Nuernisha Alifu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830011, PR China.
| | - Liankun Sun
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China
| | - Hongwei Song
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China.
| |
Collapse
|
43
|
Nishimura K, Kitazawa H, Kawahata T, Yuhara K, Masuya T, Kuroita T, Waki K, Koike S, Isobe M, Kurosawa N. The development of a highly sensitive and quantitative SARS-CoV-2 rapid antigen test applying newly developed monoclonal antibodies to an automated chemiluminescent flow-through membrane immunoassay device. BMC Immunol 2023; 24:34. [PMID: 37752417 PMCID: PMC10523765 DOI: 10.1186/s12865-023-00567-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Rapid and accurate diagnosis of individuals with SARS-CoV-2 infection is an effective way to prevent and control the spread of COVID-19. Although the detection of SARS-CoV-2 viral RNA by RT-qPCR is the gold standard for COVID-19 testing, the use of antigen-detecting rapid diagnostic tests (Ag-RDTs) is emerging as a complementary surveillance tool as Omicron case numbers skyrocket worldwide. However, the results from Ag-RDTs are less accurate in individuals with low viral loads. RESULTS To develop a highly sensitive and accurate Ag-RDT, 90 monoclonal antibodies were raised from guinea pigs immunized with SARS CoV-2 nucleocapsid protein (CoV-2-NP). By applying a capture antibody recognizing the structural epitope of the N-terminal domain of CoV-2-NP and a detection antibody recognizing the C-terminal tail of CoV-2-NP to an automated chemiluminescence flow-through membrane immunoassay device, we developed a novel Ag-RDT, CoV-2-POCube. The CoV-2-POCube exclusively recognizes CoV-2-NP variants but not the nucleocapsid proteins of other human coronaviruses. The CoV-2-POCube achieved a limit of detection sensitivity of 0.20 ~ 0.66 pg/mL of CoV-2-NPs, demonstrating more than 100 times greater sensitivity than commercially available SARS-CoV-2 Ag-RDTs. CONCLUSIONS CoV-2-POCube has high analytical sensitivity and can detect SARS-CoV-2 variants in 15 min without observing the high-dose hook effect, thus meeting the need for early SARS-CoV-2 diagnosis with lower viral load. CoV-2-POCube is a promising alternative to currently available diagnostic devices for faster clinical decision making in individuals with suspected COVID-19 in resource-limited settings.
Collapse
Affiliation(s)
- Kengo Nishimura
- Bio-Science & Medical Research Unit, Corporate Research Center, TOYOBO CO., LTD., 2-1-1 Katata, Otsu-Shi, Shiga, 520-0243, Japan
| | - Hiroaki Kitazawa
- Biotechnology Research Laboratory, TOYOBO CO., LTD., 10-24, Toyo-Cho, Tsuruga-Shi, Fukui, 914-8550, Japan
| | - Takashi Kawahata
- Biotechnology Research Laboratory, TOYOBO CO., LTD., 10-24, Toyo-Cho, Tsuruga-Shi, Fukui, 914-8550, Japan
| | - Kosuke Yuhara
- Biotechnology Research Laboratory, TOYOBO CO., LTD., 10-24, Toyo-Cho, Tsuruga-Shi, Fukui, 914-8550, Japan
| | - Takahiro Masuya
- Biotechnology Research Laboratory, TOYOBO CO., LTD., 10-24, Toyo-Cho, Tsuruga-Shi, Fukui, 914-8550, Japan
| | - Toshihiro Kuroita
- Biotechnology Operating Department, TOYOBO CO., LTD., 1-13-1 Umeda, Kita-Ku, Osaka, 530-0001, Japan
| | - Kentarou Waki
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Education, University of Toyama, Toyama-Shi, Gofuku, Toyama, 930-8555, Japan
| | - Seiichi Koike
- Laboratory of Molecular and Cellular Biology, Graduate School of Innovative Life Science, University of Toyama, 3190 Gofuku, Toyama-Shi, Toyama, 930-8555, Japan
| | - Masaharu Isobe
- Laboratory of Molecular and Cellular Biology, Graduate School of Innovative Life Science, University of Toyama, 3190 Gofuku, Toyama-Shi, Toyama, 930-8555, Japan
| | - Nobuyuki Kurosawa
- Laboratory of Molecular and Cellular Biology, Graduate School of Innovative Life Science, University of Toyama, 3190 Gofuku, Toyama-Shi, Toyama, 930-8555, Japan.
| |
Collapse
|
44
|
Bao M, Waitkus J, Liu L, Chang Y, Xu Z, Qin P, Chen J, Du K. Micro- and nanosystems for the detection of hemorrhagic fever viruses. LAB ON A CHIP 2023; 23:4173-4200. [PMID: 37675935 DOI: 10.1039/d3lc00482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.
Collapse
Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Jacob Waitkus
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Yu Chang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Zhiheng Xu
- Department of Industrial Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| |
Collapse
|
45
|
Rebbapragada A, Cariazo L, Elchuk D, Abdelrahman H, Pham D, Raveendraraj J, Chokshi K, Joseph N, Gouzenkova E, Gill H, Blecher P. Performance of the Cue COVID-19 point-of-care molecular test: insights from a multi-site clinic service model. Microbiol Spectr 2023; 11:e0406422. [PMID: 37728337 PMCID: PMC10580901 DOI: 10.1128/spectrum.04064-22] [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: 11/21/2022] [Accepted: 07/26/2023] [Indexed: 09/21/2023] Open
Abstract
The COVID-19 pandemic highlighted the critical need for rapid and accurate molecular diagnostic testing. The Cue COVID-19 Point-of-Care Test (Cue POCT) is a nucleic acid amplification test (NAAT), authorized by Health Canada and FDA as a POCT for SARS-CoV-2 detection. Cue POCT was deployed at a network of clinics in Ontario, Canada with n = 13,848 patrons tested between 17 July 2021 and 31 January 2022. The clinical performance and operational experience with Cue POCT were examined for this testing population composed mostly of asymptomatic individuals (93.7%). A head-to-head prospective clinical verification was performed between 17 July and 4 October for all POCT service clients (n = 3,037) with paired COVID-19 testing by Cue and RT-PCR. Prospective verification demonstrated a clinical sensitivity of 100% and clinical specificity of 99.4% for Cue COVID-19 POCT. The lack of false negatives and low false positive rate (0.64%), underscores the high accuracy (99.4%) of Cue POCT to provide rapid PCR quality results. Low error rates (cancellation rate of 0% and invalid rate of 0.63%) with the current software version were additionally noted. Taken together, these findings highlight the value of accurate molecular COVID-19 POCT in a distributed service delivery model to rapidly detect cases in the community with the potential to curb transmission in high-exposure settings (i.e., in-flight, congregate workplace, and social events). The insights gleaned from this operational implementation are readily transferable to future POCT diagnostic services. IMPORTANCE This manuscript reports on the findings of a large asymptomatic population who underwent surveillance COVID testing on the Cue COVID-19 Point-of-Care Test (POCT). Review of test performance of this rapid molecular POCT, as compared to gold standard RT-PCR, is valuable to many audiences, including public health, emergency testing services, employers, and the general population of consumers who are seeking a user-friendly, accurate, cost-effective, and sustainable testing model for COVID screening. The findings from this operational experience also inform future models of POCT services beyond COVID.
Collapse
|
46
|
Miglietta L, Chen Y, Luo Z, Xu K, Ding N, Peng T, Moniri A, Kreitmann L, Cacho-Soblechero M, Holmes A, Georgiou P, Rodriguez-Manzano J. Smart-Plexer: a breakthrough workflow for hybrid development of multiplex PCR assays. Commun Biol 2023; 6:922. [PMID: 37689821 PMCID: PMC10492832 DOI: 10.1038/s42003-023-05235-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/10/2023] [Indexed: 09/11/2023] Open
Abstract
Developing multiplex PCR assays requires extensive experimental testing, the number of which exponentially increases by the number of multiplexed targets. Dedicated efforts must be devoted to the design of optimal multiplex assays ensuring specific and sensitive identification of multiple analytes in a single well reaction. Inspired by data-driven approaches, we reinvent the process of developing and designing multiplex assays using a hybrid, simple workflow, named Smart-Plexer, which couples empirical testing of singleplex assays and computer simulation to develop optimised multiplex combinations. The Smart-Plexer analyses kinetic inter-target distances between amplification curves to generate optimal multiplex PCR primer sets for accurate multi-pathogen identification. In this study, the Smart-Plexer method is applied and evaluated for seven respiratory infection target detection using an optimised multiplexed PCR assay. Single-channel multiplex assays, together with the recently published data-driven methodology, Amplification Curve Analysis (ACA), were demonstrated to be capable of classifying the presence of desired targets in a single test for seven common respiratory infection pathogens.
Collapse
Affiliation(s)
- Luca Miglietta
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Yuwen Chen
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Zhi Luo
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Ke Xu
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Ning Ding
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Tianyi Peng
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Ahmad Moniri
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Louis Kreitmann
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Miguel Cacho-Soblechero
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | | |
Collapse
|
47
|
Tayyab M, Barrett D, van Riel G, Liu S, Reinius B, Scharfe C, Griffin P, Steinmetz LM, Javanmard M, Pelechano V. Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs. SCIENCE ADVANCES 2023; 9:eadi4997. [PMID: 37672583 PMCID: PMC10482329 DOI: 10.1126/sciadv.adi4997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Fast and accurate detection of nucleic acids is key for pathogen identification. Methods for DNA detection generally rely on fluorescent or colorimetric readout. The development of label-free assays decreases costs and test complexity. We present a novel method combining a one-pot isothermal generation of DNA nanoballs with their detection by electrical impedance. We modified loop-mediated isothermal amplification by using compaction oligonucleotides that self-assemble the amplified target into nanoballs. Next, we use capillary-driven flow to passively pass these nanoballs through a microfluidic impedance cytometer, thus enabling a fully compact system with no moving parts. The movement of individual nanoballs is detected by a change in impedance providing a quantized readout. This approach is flexible for the detection of DNA/RNA of numerous targets (severe acute respiratory syndrome coronavirus 2, HIV, β-lactamase gene, etc.), and we anticipate that its integration into a standalone device would provide an inexpensive (<$5), sensitive (10 target copies), and rapid test (<1 hour).
Collapse
Affiliation(s)
- Muhammad Tayyab
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Gijs van Riel
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Shujing Liu
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- International Institute of Tea Industry Innovation for the Belt and Road, Nanjing Agricultural University, Nanjing 210095, China
| | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | | | - Peter Griffin
- Stanford Genome Technology Center, Stanford, CA, USA
| | - Lars M. Steinmetz
- Stanford Genome Technology Center, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mehdi Javanmard
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| |
Collapse
|
48
|
Yadav SK, Verma D, Yadav U, Kalkal A, Priyadarshini N, Kumar A, Mahato K. Point-of-Care Devices for Viral Detection: COVID-19 Pandemic and Beyond. MICROMACHINES 2023; 14:1744. [PMID: 37763907 PMCID: PMC10535693 DOI: 10.3390/mi14091744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
The pandemic of COVID-19 and its widespread transmission have made us realize the importance of early, quick diagnostic tests for facilitating effective cure and management. The primary obstacles encountered were accurately distinguishing COVID-19 from other illnesses including the flu, common cold, etc. While the polymerase chain reaction technique is a robust technique for the determination of SARS-CoV-2 in patients of COVID-19, there arises a high demand for affordable, quick, user-friendly, and precise point-of-care (POC) diagnostic in therapeutic settings. The necessity for available tests with rapid outcomes spurred the advancement of POC tests that are characterized by speed, automation, and high precision and accuracy. Paper-based POC devices have gained increasing interest in recent years because of rapid, low-cost detection without requiring external instruments. At present, microfluidic paper-based analysis devices have garnered public attention and accelerated the development of such POCT for efficient multistep assays. In the current review, our focus will be on the fabrication of detection modules for SARS-CoV-2. Here, we have included a discussion on various strategies for the detection of viral moieties. The compilation of these strategies would offer comprehensive insight into the detection of the causative agent preparedness for future pandemics. We also provide a descriptive outline for paper-based diagnostic platforms, involving the determination mechanisms, as well as a commercial kit for COVID-19 as well as their outlook.
Collapse
Affiliation(s)
- Sumit K. Yadav
- Department of Biotechnology, Vinoba Bhave University, Hazaribagh 825301, Jharkhand, India
| | - Damini Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ujala Yadav
- Department of Life Sciences, Central University of Jharkhand, Ranchi 835205, Jharkhand, India
| | - Ashish Kalkal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Nivedita Priyadarshini
- Department of Zoology, DAV PG College Siwan, Jai Prakash University, Chhapra 841226, Bihar, India
| | - Ashutosh Kumar
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46637, USA
| | - Kuldeep Mahato
- Department of Nanoengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, San Diego, CA 92093, USA
| |
Collapse
|
49
|
Anand A, Gupta A, Singh S, Pyakurel S, Karkee R, Pyakurel P. Knowledge and attitude regarding the COVID-19 pandemic among undergraduate health science students of Nepal: An online survey. SAGE Open Med 2023; 11:20503121231196703. [PMID: 37694131 PMCID: PMC10486226 DOI: 10.1177/20503121231196703] [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: 05/15/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Objectives This study aims to assess health science students' knowledge and attitude about COVID-19 epidemiology, management, and prevention; and the association of knowledge and attitude with various sociodemographic characteristics. Methods An online survey was done among 524 undergraduate health science students using a pre-tested questionnaire across 19 health science institutions in Nepal from 30 June to 11 August 2021. All subjects were enrolled in the study after informed consent. Outcomes were Knowledge level, attitude level, and predictors of knowledge level and attitude level. Bivariate analysis was done to determine the association between variables. Results Of 524 students, 42.9% were male, and 57.1% were female. More than half (54.6%) and the majority (85.1%) participants had good knowledge and attitude, respectively. Approximately three-fifths (59.4%) of the participants were from the B. P. Koirala Institute of Health Sciences (BPKIHS). Students in BPKIHS (odds ratio = 1.774; 95% confidence interval = 1.243-2.533), junior years (odds ratio = 8.892; 95% confidence interval = 5.814-13.599), age less than 23 years (odds ratio = 2.985; 95% confidence interval = 2.089-4.266) were more likely to have good knowledge. Students under 23 years (odds ratio = 24.160; 95% confidence interval: 9.570-60.992) and those in junior years (odds ratio = 4.460; 95% confidence interval = 3.753-5.300) were likely to have a good attitude level. Students in BPKIHS (odds ratio = 0.443; 95% confidence interval = 0.272-0.722) were less likely to have a good attitude. Conclusions Overall, health science students had adequate knowledge and a good attitude regarding COVID-19. However, students lacked knowledge regarding infectiousness, transmission, post-vaccination observation period, remdesivir use, convalescent plasma therapy, and awake-prone positioning. Knowledge and attitude scores were associated with age, stream, and study institution.
Collapse
Affiliation(s)
- Ayush Anand
- B. P. Koirala Institute of Health Sciences, Sunsari, Nepal
| | - Ashwini Gupta
- B. P. Koirala Institute of Health Sciences, Sunsari, Nepal
| | - Sweta Singh
- B. P. Koirala Institute of Health Sciences, Sunsari, Nepal
| | - Sulav Pyakurel
- Lumbini Medical College & Teaching Hospital, Palpa, Nepal
| | - Rajendra Karkee
- School of Public Health and Community Medicine, B. P. Koirala Institute of Health Sciences, Sunsari, Nepal
| | - Prajjwal Pyakurel
- School of Public Health and Community Medicine, B. P. Koirala Institute of Health Sciences, Sunsari, Nepal
| |
Collapse
|
50
|
Pilipenco A, Forinová M, Mašková H, Hönig V, Palus M, Lynn Jr. NS, Víšová I, Vrabcová M, Houska M, Anthi J, Spasovová M, Mustacová J, Štěrba J, Dostálek J, Tung CP, Yang AS, Jack R, Dejneka A, Hajdu J, Vaisocherová-Lísalová H. Negligible risk of surface transmission of SARS-CoV-2 in public transportation. J Travel Med 2023; 30:taad065. [PMID: 37133444 PMCID: PMC10481417 DOI: 10.1093/jtm/taad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Exposure to pathogens in public transport systems is a common means of spreading infection, mainly by inhaling aerosol or droplets from infected individuals. Such particles also contaminate surfaces, creating a potential surface-transmission pathway. METHODS A fast acoustic biosensor with an antifouling nano-coating was introduced to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on exposed surfaces in the Prague Public Transport System. Samples were measured directly without pre-treatment. Results with the sensor gave excellent agreement with parallel quantitative reverse-transcription polymerase chain reaction (qRT-PCR) measurements on 482 surface samples taken from actively used trams, buses, metro trains and platforms between 7 and 9 April 2021, in the middle of the lineage Alpha SARS-CoV-2 epidemic wave when 1 in 240 people were COVID-19 positive in Prague. RESULTS Only ten of the 482 surface swabs produced positive results and none of them contained virus particles capable of replication, indicating that positive samples contained inactive virus particles and/or fragments. Measurements of the rate of decay of SARS-CoV-2 on frequently touched surface materials showed that the virus did not remain viable longer than 1-4 h. The rate of inactivation was the fastest on rubber handrails in metro escalators and the slowest on hard-plastic seats, window glasses and stainless-steel grab rails. As a result of this study, Prague Public Transport Systems revised their cleaning protocols and the lengths of parking times during the pandemic. CONCLUSIONS Our findings suggest that surface transmission played no or negligible role in spreading SARS-CoV-2 in Prague. The results also demonstrate the potential of the new biosensor to serve as a complementary screening tool in epidemic monitoring and prognosis.
Collapse
Affiliation(s)
- Alina Pilipenco
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Michala Forinová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Hana Mašková
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Václav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Nicholas Scott Lynn Jr.
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Ivana Víšová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Markéta Vrabcová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Milan Houska
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Judita Anthi
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Monika Spasovová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Johana Mustacová
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Ján Štěrba
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic
| | - Jakub Dostálek
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Rachael Jack
- The European Extreme Light Infrastructure, ERIC, Za Radnici 835, 25241 Dolní Břežany, Czech Republic
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Janos Hajdu
- The European Extreme Light Infrastructure, ERIC, Za Radnici 835, 25241 Dolní Břežany, Czech Republic
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | | |
Collapse
|