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
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Date
2023-03-03Author
Ceruti, Arianna
Dia, Ndongo
Bakarey, Adeleye Solomon
Ssekitoleko, Judah
Andriamandimby, Soa Fy
Malwengo-Kasongo, Padra
Ahmed, Rasheeda H.A.
Kobialka, Rea Maja
Heraud, Jean Michel
Diagne, Moussa Moise
Dione, Marie Henriette Dior
Dieng, Idrissa
Faye, Martin
Faye, Ousmane
Rafisandratantsoa, Jean Théophile
Ravalohery, Jean-Pierre
Raharinandrasana, Claudio
Randriambolamanantsoa, Tsiry H.
Razanajatovo, Norosoa
Razanatovo, Iony
Rabarison, Joelinotahina H.
Dussart, Phillipe
Kyei-Tuffuor, Louis
Agbanyo, Abigail
Adewumi, Olubusuyi Moses
Fowotade, Adeola
Raifu, Muideen Kolawole
Okitale-Talunda, Patient
Kashitu-Mujinga, Gracia
Mbelu-Kabongo, Christelle
Ahuka-Mundeke, Steve
Makaka-Mutondo, Anguy
Abdalla, Enas M.
Idris, Sanaa M.
Elmagzoub, Wisal A.
Ali, Rahma H.
Nour, Eman O.M.
Ebraheem, Rasha S.M.
Ahmed, Huda H.H.
Abdalla, Hamadelniel E.
Elnegoumi, Musab
Mukhtar, Izdihar
Adam, Muatsim A.M.
Mohamed, Nuha Y.I.
Bedri, Shahinaz A.
Hamdan, Hamdan Mustafa
Kisekka, Magid
Mpumwiire, Monica
Aloyo, Sharley Melissa
Wandera, Joanita Nabwire
Agaba, Andrew
Kamulegeya, Rogers
Kiprotich, Hosea
Kateete, David Patrick
Kadetz, Paul
Truyen, Uwe
Eltom, Kamal H.
Sakuntabhai, Anavaj
Okuni, Julius Boniface
Makiala-Mandanda, Sheila
Lacoste, Vincent
Ademowo, George Olusegun
Frimpong, Michael
Sall, Amadou Alpha
Weidmann, Manfred
Wahed, Ahmed Abd El
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Ceruti, A., Dia, N., Bakarey, A.S., Ssekitoleko, J., Andriamandimby, S.F., Malwengo-Kasongo, P., Ahmed, R.H.A., Kobialka, R.M., Heraud, J.M., Diagne, M.M., Dione, M.H.D., Dieng, I., Faye, M., Faye, O., Rafisandratantsoa, J.T., Ravalohery, J.-P., Raharinandrasana, C., Randriambolamanantsoa, T.H., Razanajatovo, N., Razanatovo, I., Rabarison, J.H., Dussart, P., Kyei-Tuffuor, L., Agbanyo, A., Adewumi, O.M., Fowotade, A., Raifu, M.K., Okitale-Talunda, P., Kashitu-Mujinga, G., Mbelu-Kabongo, C., Ahuka-Mundeke, S., Makaka-Mutondo, A., Abdalla, E.M., Idris, S.M., Elmagzoub, W.A., Ali, R.H., Nour, E.O.M., Ebraheem, R.S.M., Ahmed, H.H.H., Abdalla, H.E., Elnegoumi, M., Mukhtar, I., Adam, M.A.M., Mohamed, N.Y.I., Bedri, S.A., Hamdan, H.M., Kisekka, M., Mpumwiire, M., Aloyo, S.M., Wandera, J.N., Agaba, A., Kamulegeya, R., Kiprotich, H., Kateete, D.P., Kadetz, P., Truyen, U., Eltom, K.H., Sakuntabhai, A., Okuni, J.B., Makiala-Mandanda, S., Lacoste, V., Ademowo, G.O., Frimpong, M., Sall, A.A., Weidmann, M. and Wahed, A.A.E. (2023) ‘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’, Journal of Clinical Virology, p. 105422. Available at: https://doi.org/10.1016/j.jcv.2023.105422.
Abstract
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 minutes. 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.
Official URL
https://doi.org/10.1016/j.jcv.2023.105422Collections
Except where otherwise noted, this item's license is described as Attribution 4.0 International (CC BY 4.0)