Rapid isothermal amplification diagnostic test to detect multiple COVID-19 genes

The COVID-19 pandemic has highlighted the importance of testing to limit the spread of the virus, and the need for rapid nucleic acid amplification tests (NAAT) to widen access to testing, particularly in low resource settings.

In response to this challenge, the UCL researchers led by Prof Rachel McKendry, developed a rapid NAAT using recombinase polymerase amplification (RPA) that simultaneously detects multiple genes to ensure that the test is still accurate, even when variants occur. This approach offers an alternative to standard lab-based polymer chain reaction (PCR) tests, which require a thermocycler for temperate control and has a relatively long time to result.

How the test works

As PCR reagents have become hard to access during the pandemic, isothermal molecular assays have emerged as a promising technology, given the faster turn-around time and minimal equipment compared to gold standard laboratory PCR methods. RPA is a method of isothermal amplification, meaning that it is performed at constant temperature, in this case at much lower temperature than PCR. Therefore, it requires minimal equipment to perform, making testing more widely accessible. In addition, the assay developed by the i-sense team has a shorter time to result.

Dounia Cherkaoui, first author and i-sense PhD student at UCL, said: “Using multi-gene detection is crucial as a mutation in the S gene of the B.1.1.7 variant, also known as the Kent variant, led to ‘S gene target failure’ in some molecular tests earlier in the pandemic. These cases may have been missed if PCR tests were not looking at multiple genes to confirm the presence of the virus. This is why multi-gene detection is vital and it can increase the accuracy of rapid tests.”

Dr Da Huang, joint first author and i-sense postdoctoral researcher at UCL, said: “To the best of our knowledge, this COVID-19 multi-gene detection RPA test is the first of its kind. It requires only one to two steps so that it can more easily be performed in settings with limited resources.”

The test was designed with two alternative readout methods; real-time fluorescence and a simple dipstick. The choice of two readout approaches aims to make the test is more accessible in different settings. The fluorescence method was designed to be read by a portable reader, whilst the dipstick method can be read by eye, making it easier to deploy in resource-limited settings.

The assay used model samples and tested specificity against a range of common seasonal respiratory viruses. It is envisaged that in a final clinical test format, users would provide a saliva sample for testing, which is approved by the World Health Organization for COVID-19 testing and is ideal as it is a non-invasive method for sample collection.

Next step clinical trials

Next steps for this research will include clinical validation with patient samples. By adapting the test in the future to include other gene targets, it could be used to identify different COVID-19 strains, including new variants, without the need for sequencing.

Acknowledgements

This research was funded by i-sense: EPSRC IRC in Agile Early Warning Sensing Systems for Infectious Diseases and Antimicrobial Resistance (EP/R00529X/1) and associated i-sense COVID-19 Plus Award. This research was also funded by EPSRC LCN studentship for Dounia Cherkaoui (EP/N509577/1).

The researchers involved in this paper include Dounia Cherkaoui, Dr Da Huang, Dr Benjamin S. Miller, Dr Valérian Turbé, and Prof Rachel A. McKendry.

Useful links

Biosensors and Bioelectronics paper: Harnessing recombinase polymerase amplification for rapid multi-gene detection of SARS-CoV-2 in resource-limited settings

i-sense EPSRC IRC 

McKendry group

Illustration credit: Dr Da Huang, i-sense EPSRC IRC, UCL

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