Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings. (January 2022)

• Record Type: Journal Article
• Authors: Ghosh, Prakash; Chowdhury, Rajashree; Hossain, Mohammad Enayet; Hossain, Faria; Miah, Mojnu; Rashid, Md. Utba; Baker, James; Rahman, Mohammed Ziaur; Rahman, Mustafizur; Ma, Xuejun; Duthie, Malcolm S.; Wahed, Ahmed Abd El; Mondal, Dinesh
• Is Part Of: International journal of infectious diseases. Volume 114(2022)
• Page Start: 105
• Page End: 111
• Publication Date: 2022-01
• Subjects: SARS-CoV-2 -- RT-RPA -- RT-RAA -- Recombinase -- Diagnosis -- Point-of-need; Communicable diseases -- Periodicals; Communicable Diseases -- Periodicals; Communicable diseases; Periodicals; Electronic journals; 616.9
• DOI: 10.1016/j.ijid.2021.11.007
• Languages: English
• ISSNs: 1201-9712

Abstract

Highlights: Point-of-need diagnostics are required to contain the spread of SARS-CoV-2. Recombinase-based assays rapidly detect SARS-CoV-2 in clinical samples. The two isothermal amplification methods tested showed promising diagnostic efficiency. The incorporation of these techniques in a 'suitcase laboratory' may facilitate remote deployment. Abstract: 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.