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

Abstract Objectives Democratization of diagnostics is one of the key challenges towards harnessing the transmission of 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 the isothermal technologies, detection of SARS-CoV-2 is possible at decentralized facilities. Methods In this current study, two recombinase-based isothermal techniques, reverse transcription recombinase polymerase amplification assay (RT-RPA) and reverse transcription recombinase aided amplification assay (RT-RAA), were evaluated for detection of SARS-CoV-2 in clinical samples. In total,76 real-time reverse transcription polymerase chain reaction (real-time RT-PCR) confirmed COVID-19 cases and 100 negative controls were evaluated to determine the diagnostic performance of the isothermal methods. Results Our investigation revealed equally promising diagnostic accuracy of the methods with a sensitivity of 76.32% (95% CI: 65.18%-85.32%) when the target genes were RdRP and ORF1ab for RT-RPA and RT-RAA, respectively, while the combination of N and RdRP in RT-RPA augmenting the accuracy of the assay at a sensitivity of 85.53% (95% CI: 75.58% -92.55%). Furthermore, high specificity was observed for each of the methods ranged 94.00%-98.00%(95% CI: 87.40-9.76%). Conclusion Considering the diagnostic accuracies, both RT-RPA and RT-RAA assays appear suitable for point-of-need deployment towards detection of the pathogen, understanding its epidemiology, case management, and curbing the transmission.