A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field.

Autor: Ceruti A; Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Germany. Electronic address: arianna.ceruti@uni-leipzig.de., Dia N; Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal., Bakarey AS; Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Nigeria., Ssekitoleko J; College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.o.Box 7062 Uganda., Andriamandimby SF; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Malwengo-Kasongo P; Department of Virology at the Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo (DRC); Faculty of Medicine, University of Kinshasa, Democratic Republic of the Congo (DRC)., Ahmed RHA; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Kobialka RM; Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Germany., Heraud JM; Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal., Diagne MM; Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal., Dione MHD; Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal., Dieng I; Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal., Faye M; Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal., Faye O; Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal., Rafisandratantsoa JT; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Ravalohery JP; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Raharinandrasana C; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Randriambolamanantsoa TH; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Razanajatovo N; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Razanatovo I; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Rabarison JH; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Dussart P; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Kyei-Tuffuor L; Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Ghana., Agbanyo A; Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Ghana., Adewumi OM; Department of Virology, College of Medicine, University of Ibadan, Nigeria., Fowotade A; Department of Medical Microbiology and Parasitology, College of Medicine, University of Ibadan, Nigeria., Raifu MK; Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Nigeria., Okitale-Talunda P; Department of Virology at the Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo (DRC); Faculty of Medicine, University of Kinshasa, Democratic Republic of the Congo (DRC)., Kashitu-Mujinga G; Department of Virology at the Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo (DRC); Faculty of Medicine, University of Kinshasa, Democratic Republic of the Congo (DRC)., Mbelu-Kabongo C; Department of Virology at the Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo (DRC); Faculty of Medicine, University of Kinshasa, Democratic Republic of the Congo (DRC)., Ahuka-Mundeke S; Department of Virology at the Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo (DRC); Faculty of Medicine, University of Kinshasa, Democratic Republic of the Congo (DRC)., Makaka-Mutondo A; Department of Virology at the Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo (DRC); Faculty of Medicine, University of Kinshasa, Democratic Republic of the Congo (DRC)., Abdalla EM; Unit of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, 13314 Khartoum North, Sudan., Idris SM; Unit of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, 13314 Khartoum North, Sudan., Elmagzoub WA; Unit of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, 13314 Khartoum North, Sudan., Ali RH; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Nour EOM; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Ebraheem RSM; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Ahmed HHH; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Abdalla HE; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Elnegoumi M; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Mukhtar I; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Adam MAM; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Mohamed NYI; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Bedri SA; Tuberculosis National Reference Laboratory, National Public Health Laboratory, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Hamdan HM; MDR Focal Point, El Qasr Avenue, Federal Ministry of Health, Khartoum, Sudan., Kisekka M; College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.o.Box 7062 Uganda., Mpumwiire M; College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.o.Box 7062 Uganda., Aloyo SM; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda., Wandera JN; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda., Agaba A; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda., Kamulegeya R; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda., Kiprotich H; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda., Kateete DP; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda., Kadetz P; Institute for Global Health and Development, Queen Margaret University, United Kingdom., Truyen U; Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Germany., Eltom KH; Unit of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, 13314 Khartoum North, Sudan., Sakuntabhai A; Functional Genetics of Infectious Diseases Unit, Institut Pasteur, France., Okuni JB; College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.o.Box 7062 Uganda., Makiala-Mandanda S; Department of Virology at the Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo (DRC); Faculty of Medicine, University of Kinshasa, Democratic Republic of the Congo (DRC)., Lacoste V; Virology Unit, Institut Pasteur de Madagascar, Republic of Madagascar., Ademowo GO; Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Nigeria., Frimpong M; Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Ghana; Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Ghana., Sall AA; Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal., Weidmann M; Institute of Microbiology and Virology, Medizinische Hochschule Brandenburg Theodor Fontane, Germany., Abd El Wahed A; Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Germany.
Jazyk: angličtina
Zdroj: Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology [J Clin Virol] 2023 May; Vol. 162, pp. 105422. Date of Electronic Publication: 2023 Mar 03.
DOI: 10.1016/j.jcv.2023.105422
Abstrakt: Background: The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings.
Objectives: To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries.
Study Design: In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 min. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied.
Results: Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay).
Conclusion: Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2023. Published by Elsevier B.V.)
Databáze: MEDLINE
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