SARS-CoV-2 detection using reverse transcription strand invasion based amplification and a portable compact size instrument

Maiken Worsøe Rosenstierne ,Frederikke Holm Jensen,Julie Bjerring,Lærke Jørgensen,Claus Juel Jensen,Jan Gorm Lisby,Rikke Lind Jørgensen,Robert Elkjær,E Thomas Danielsen,Julie Hindkær,Mikkel Rohde Jacobsen,Anders Fomsgaard,Jakob Broberg Lind,Antti Tullila,Ebbe Finding,Mette Bjergaard Dragheim,Uffe Vest Schneider,Dac Mui Luong,Mirko Brummer,Julie Blauenfeldt,Steven Clauwaert,Shreya Joshi,Ask Bojesen,Thomas Warthoe,Flemming Holck,Charlotta Polacek,Helen Webb,Johnny Weber Lau,Lars Bangsgaard,Kristina Christensen,Tuomas Ojalehto,Peter Warthoe

doi:10.1038/s41598-021-01744-y

Abstract

Rapid nucleic-acid based tests that can be performed by non-professionals outside laboratory settings could help the containment of the pandemic SARS-CoV-2 virus and may potentially prevent further widespread lockdowns. Here, we present a novel compact portable detection instrument (the Egoo Health System) for extraction-free detection of SARS-CoV-2 using isothermal reverse transcription strand invasion based amplification (RT-SIBA). The SARS-CoV-2 RT-SIBA assay can be performed directly on crude oropharyngeal swabs without nucleic acid extraction with a reaction time of 30 min. The Egoo Health system uses a capsule system, which is automatically sealed tight in the Egoo instrument after applying the sample, resulting in a closed system optimal for molecular isothermal amplification. The performance of the Egoo Health System is comparable to the PCR instrument with an analytical sensitivity of 25 viral RNA copies per SARS-CoV-2 RT-SIBA reaction and a clinical sensitivity and specificity between 87.0–98.4% and 96.6–98.2% respectively.

Highlights

Rapid nucleic-acid based tests that can be performed by non-professionals outside laboratory settings could help the containment of the pandemic SARS-CoV-2 virus and may potentially prevent further widespread lockdowns
The Egoo Health System consists of a small Egoo instrument, a laptop or mobile phone, with the Egoo clinical app, and an Egoo capsule containing the assay of interest (Fig. 1a–d)
Because of the limited heating system in the Egoo instrument, we developed an isothermal SARS-CoV-2 RTSIBA assay for the Egoo capsule that target the RdRp gene in SARS-CoV-2 genome (Fig. 1e)

Summary

Introduction

Rapid nucleic-acid based tests that can be performed by non-professionals outside laboratory settings could help the containment of the pandemic SARS-CoV-2 virus and may potentially prevent further widespread lockdowns. The return to normality in daily life largely depends on identifying infected individuals, encouraging isolation and quarantine, and development of vaccines against the virus To this date 2,187,874,534 vaccine doses have been administered (https://covid19.who.int/) but there is still a huge demand for COVID-19 testing and many countries are screening their population for the presence of the virus using Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) and antigen tests[2,3,4]. The method is labour intensive, time-consuming (typically > 2 h), and requires transport to laboratories with specialized laboratory equipment and personnel, which can prolong the time to result up to 24 h or longer This extended turnaround time has pushed the development of simplified NAAT tests that can be performed locally. The SARS-CoV-2 RT-SIBA assay can be performed directly on crude oropharyngeal swabs without NA extraction with a reaction time of 30 min

Methods

Results

Conclusion