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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.
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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
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Johnson G, Gregorchuk BSJ, Zubrzycki A, Kolsun K, Meyers AFA, Sandstrom PA, Becker MG. Clinical evaluation of the GeneXpert ® Xpert ® Xpress SARS-CoV-2/Flu/RSV PLUS combination test. Can J Microbiol 2023; 69:146-150. [PMID: 36657122 DOI: 10.1139/cjm-2022-0204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The GeneXpert® Xpert® Xpress SARS-CoV-2/Flu/RSV PLUS combination test (PLUS assay) received Health Canada approval in January 2022. The PLUS assay is similar to the SARS-CoV-2/Flu/RSV combination test, with modifications to improve assay robustness against circulating and emerging variants. The performance characteristics of the PLUS assay were assessed at the Lakeridge Health Oshawa Hospital Centre and the National Microbiology Laboratory of Canada. The PLUS assay was directly compared to the SARS-CoV-2/Flu/RSV combination test using SARS-CoV-2 culture from five variants and remnant clinical specimens collected across the coronavirus disease 2019 pandemic. This included 50 clinical specimens negative for all pathogens, 110 clinical specimens positive for SARS-CoV-2, influenza A, influenza B, RSVA, and(or) RSVB and an additional 11 mixed samples to screen for target interactions. The PLUS assay showed a high % agreement with the widely used SARS-CoV-2/Flu/RSV combination test. Based on these findings, the PLUS assay and the Xpert SARS-CoV-2/Flu/RSV combination test results are largely consistent with no observed difference in sensitivity, specificity, or time to result when challenged with various SARS-CoV-2 variants. The reported cycle threshold (Ct) values provided by the new PLUS assay were also unchanged, with the exception of a possible 1-2 decrease reported in Ct for RSVA across a limited sample size.
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Affiliation(s)
- Grant Johnson
- Laboratory Medicine and Infection Prevention and Control, Lakeridge Health, Oshawa, ON, Canada.,Ontario Tech University, Oshawa, ON, Canada
| | - Branden S J Gregorchuk
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory Branch, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Arek Zubrzycki
- Laboratory Medicine and Infection Prevention and Control, Lakeridge Health, Oshawa, ON, Canada
| | - Kurt Kolsun
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory Branch, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Adrienne F A Meyers
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory Branch, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Paul A Sandstrom
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory Branch, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Michael G Becker
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory Branch, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Performing under Pressure: Insights into the Diagnostic Testing Burden at a UK National Health Service Clinical Virology Laboratory during the SARS-CoV-2 Pandemic. Viruses 2022; 14:v14102233. [PMID: 36298788 PMCID: PMC9609557 DOI: 10.3390/v14102233] [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: 09/12/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/23/2022] Open
Abstract
UK National Health Service (NHS) Clinical Virology Departments provide a repertoire of tests on clinical samples to detect the presence of viral genomic material or host immune responses to viral infection. In December 2019, a novel coronavirus (SARS-CoV-2) emerged which quickly developed into a global pandemic; NHS laboratories responded rapidly to upscale their testing capabilities. To date, there is little information on the impact of increased SARS-CoV-2 screening on non-SARS-CoV-2 testing within NHS laboratories. This report details the virology test requests received by the Leicester-based NHS Virology laboratory from January 2018 to May 2022. Data show that in spite of a dramatic increase in screening, along with multiple logistic and staffing issues, the Leicester Virology Department was mostly able to maintain the same level of service for non-respiratory virus testing while meeting the new increase in SARS-CoV-2 testing.
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Feasibility of Rapid Diagnostic Technology for SARS-CoV-2 Virus Using a Trace Amount of Saliva. Diagnostics (Basel) 2021; 11:diagnostics11112024. [PMID: 34829371 PMCID: PMC8625231 DOI: 10.3390/diagnostics11112024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 12/23/2022] Open
Abstract
Containment of SARS-CoV-2 has become an urgent global issue. To overcome the problems of conventional quantitative polymerase chain reaction (qPCR) tests, we verified the usefulness of a mobile qPCR device that utilizes mouthwash to obtain a saliva sample with the aim of developing a rapid diagnostic method for SARS-CoV-2. First, we examined whether anyone could easily operate this device. Then, we examined whether RNA in the mouthwash could be detected in a short time. In addition, we investigated whether it was possible to diagnose SARS-CoV-2 infection using mouthwash obtained from COVID-19 patients undergoing hospitalization. The results revealed that all subjects were able to complete the operation properly without error. In addition, RNase P was detected in the mouthwash without pretreatment. The average detection time was 18 min, which is significantly shorter than conventional qPCR devices. Furthermore, this device detected SARS-CoV-2 in the mouthwash of a COVID-19 patient undergoing hospitalization. The above findings verified the efficacy of this diagnostic method, which had a low risk of infection, was technically simple, and provided stable results. Therefore, this method is useful for the rapid detection of SARS-CoV-2.
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Dancer SJ. Reducing the risk of COVID-19 transmission in hospitals: focus on additional infection control strategies. ACTA ACUST UNITED AC 2021; 39:752-758. [PMID: 34658477 PMCID: PMC8511651 DOI: 10.1016/j.mpsur.2021.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hospitals under pressure from the COVID-19 pandemic have experienced an additional challenge due to clusters of hospital-acquired COVID-19 infection occurring on non-COVID-19 wards. These clusters have involved both staff and patients and compromise staffing, bed management and routine care, especially delivery of elective surgical procedures. They have also contributed towards the overall morbidity and mortality of the pandemic. COVID-19 infection rates are rising again, so it is important to consider implementing additional activities designed to impede transmission of SARS-CoV-2 in acute hospitals. These aim to protect staff, patients and visitors, and conserve safe and continued access for patients needing routine and emergency surgical interventions. Current infection prevention strategies include hand hygiene; patient and staff screening; surveillance; personal protective equipment; cohorting and isolation; and enhanced cleaning. Additional activities include restriction of staff and patient movement; COVID-19 pathways for wards, operating theatres and outpatient services; bathroom management; and ensuring fresh air in the absence of effective mechanical ventilation systems. Seasonal pressures and spread of more contagious and/or vaccine-tolerant variants will continue to disrupt routine and emergency care of non-COVID-19 patients, as well as increase the risk of COVID-19 infection for staff and patients. Supplementary practical and cost-effective actions to limit spread in hospitals are explored in this article.
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Affiliation(s)
- Stephanie J Dancer
- is a Consultant Microbiologist in NHS Lanarkshire and Professor of Microbiology at Edinburgh Napier University, Edinburgh, UK. Conflicts of interest: The author is a member of the 'Group of 36', which is an international collaboration of scientists and clinicians working on the role of airborne transmission of SARS-CoV-2; she was also a member of the 2020 COVID-19 DEFRA committee reporting to SAGE
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