Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings

Objectives: The democratization of diagnostics is one of the key challenges towards containing the transmission of coronavirus disease 2019 (COVID-19) around the globe. The operational complexities of existing PCR-based methods, including sample transfer to advanced central laboratories with expensi...

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Autores principales:	Prakash Ghosh, Rajashree Chowdhury, Mohammad Enayet Hossain, Faria Hossain, Mojnu Miah, Md. Utba Rashid, James Baker, Mohammed Ziaur Rahman, Mustafizur Rahman, Xuejun Ma, Malcolm S. Duthie, Ahmed Abd El Wahed, Dinesh Mondal
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2022
Materias:	SARS-CoV-2 RT-RPA RT-RAA Recombinase Diagnosis Point-of-need Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/0bf6d75303944f858e799fd4ec6bcef9
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spelling	oai:doaj.org-article:0bf6d75303944f858e799fd4ec6bcef92021-11-28T04:29:17ZEvaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings1201-971210.1016/j.ijid.2021.11.007https://doaj.org/article/0bf6d75303944f858e799fd4ec6bcef92022-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1201971221008547https://doaj.org/toc/1201-9712Objectives: The democratization of diagnostics is one of the key challenges towards containing the transmission of coronavirus disease 2019 (COVID-19) around the globe. The operational complexities of existing PCR-based methods, including sample transfer to advanced central laboratories with expensive equipment, limit their use in resource-limited settings. However, with the advent of isothermal technologies, the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is possible at decentralized facilities. Methods: In this study, two recombinase-based isothermal techniques, reverse transcription recombinase polymerase amplification (RT-RPA) and reverse transcription recombinase-aided amplification (RT-RAA), were evaluated for the detection of SARS-CoV-2 in clinical samples. A total of 76 real-time reverse transcription PCR (real-time RT-PCR) confirmed COVID-19 cases and 100 negative controls were evaluated to determine the diagnostic performance of the isothermal methods. Results: This investigation revealed equally promising diagnostic accuracy of the two methods, with a sensitivity of 76.32% (95% confidence interval 65.18–85.32%) when the target genes were RdRP and ORF1ab for RT-RPA and RT-RAA, respectively; the combination of N and RdRP in RT-RPA augmented the accuracy of the assay at a sensitivity of 85.53% (95% confidence interval 75.58–92.55%). Furthermore, high specificity was observed for each of the methods, ranging from 94.00% to 98.00% (95% confidence interval 87.40–9.76%). Conclusions: Considering the diagnostic accuracies, both RT-RPA and RT-RAA appear to be suitable assays for point-of-need deployment for the detection of the pathogen, understanding its epidemiology, case management, and curbing transmission.Prakash GhoshRajashree ChowdhuryMohammad Enayet HossainFaria HossainMojnu MiahMd. Utba RashidJames BakerMohammed Ziaur RahmanMustafizur RahmanXuejun MaMalcolm S. DuthieAhmed Abd El WahedDinesh MondalElsevierarticleSARS-CoV-2RT-RPART-RAARecombinaseDiagnosisPoint-of-needInfectious and parasitic diseasesRC109-216ENInternational Journal of Infectious Diseases, Vol 114, Iss , Pp 105-111 (2022)
institution	DOAJ
collection	DOAJ
language	EN
topic	SARS-CoV-2 RT-RPA RT-RAA Recombinase Diagnosis Point-of-need Infectious and parasitic diseases RC109-216
spellingShingle	SARS-CoV-2 RT-RPA RT-RAA Recombinase Diagnosis Point-of-need Infectious and parasitic diseases RC109-216 Prakash Ghosh Rajashree Chowdhury Mohammad Enayet Hossain Faria Hossain Mojnu Miah Md. Utba Rashid James Baker Mohammed Ziaur Rahman Mustafizur Rahman Xuejun Ma Malcolm S. Duthie Ahmed Abd El Wahed Dinesh Mondal Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings
description	Objectives: The democratization of diagnostics is one of the key challenges towards containing the transmission of coronavirus disease 2019 (COVID-19) around the globe. The operational complexities of existing PCR-based methods, including sample transfer to advanced central laboratories with expensive equipment, limit their use in resource-limited settings. However, with the advent of isothermal technologies, the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is possible at decentralized facilities. Methods: In this study, two recombinase-based isothermal techniques, reverse transcription recombinase polymerase amplification (RT-RPA) and reverse transcription recombinase-aided amplification (RT-RAA), were evaluated for the detection of SARS-CoV-2 in clinical samples. A total of 76 real-time reverse transcription PCR (real-time RT-PCR) confirmed COVID-19 cases and 100 negative controls were evaluated to determine the diagnostic performance of the isothermal methods. Results: This investigation revealed equally promising diagnostic accuracy of the two methods, with a sensitivity of 76.32% (95% confidence interval 65.18–85.32%) when the target genes were RdRP and ORF1ab for RT-RPA and RT-RAA, respectively; the combination of N and RdRP in RT-RPA augmented the accuracy of the assay at a sensitivity of 85.53% (95% confidence interval 75.58–92.55%). Furthermore, high specificity was observed for each of the methods, ranging from 94.00% to 98.00% (95% confidence interval 87.40–9.76%). Conclusions: Considering the diagnostic accuracies, both RT-RPA and RT-RAA appear to be suitable assays for point-of-need deployment for the detection of the pathogen, understanding its epidemiology, case management, and curbing transmission.
format	article
author	Prakash Ghosh Rajashree Chowdhury Mohammad Enayet Hossain Faria Hossain Mojnu Miah Md. Utba Rashid James Baker Mohammed Ziaur Rahman Mustafizur Rahman Xuejun Ma Malcolm S. Duthie Ahmed Abd El Wahed Dinesh Mondal
author_facet	Prakash Ghosh Rajashree Chowdhury Mohammad Enayet Hossain Faria Hossain Mojnu Miah Md. Utba Rashid James Baker Mohammed Ziaur Rahman Mustafizur Rahman Xuejun Ma Malcolm S. Duthie Ahmed Abd El Wahed Dinesh Mondal
author_sort	Prakash Ghosh
title	Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings
title_short	Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings
title_full	Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings
title_fullStr	Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings
title_full_unstemmed	Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings
title_sort	evaluation of recombinase-based isothermal amplification assays for point-of-need detection of sars-cov-2 in resource-limited settings
publisher	Elsevier
publishDate	2022
url	https://doaj.org/article/0bf6d75303944f858e799fd4ec6bcef9
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Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings

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