Rapid Coronavirus RNA detection using reverse transcription loop-mediated isothermal amplification (RT-LAMP)
a collaboration with Oxford Engineering (UK) and Oxford Suzhou Centre for Advanced Research (OSCAR, China)
Vice President of Research Donal Bradley identified the reverse transcription loop-mediated isothermal amplification or RT-LAMP research activity of Professors Zhanfeng Cui and Wei Huang from the Department of Engineering Science at Oxford University as being an interesting collaboration opportunity for the KAUST R3T program and contacted his former colleague Professor Cui on March 21 to initiate a discussion.
Professors Cui and Huang had started their RT-LAMP project in response to the COVID-19 situation in China where they both have research groups at the Oxford Suzhou Centre for Advanced Research (OSCAR) in Suzhou and had made good progress including specific detection of COVID-19 for patient samples in Shenzhen, China and Oxford, UK. The complementary bioscience skills of Professors Arnab Pain and Samir Hamdan at KAUST and our close collaborations with the local Ministry of Health (MoH) hospitals treating COVID-19 patients and the Saudi Center for Disease Control (Saudi-CDC) made the proposed collaboration attractive to both parties and a Memorandum of Understanding was signed on April 2, 2020.
RT-LAMP has the potential to be a much faster diagnostic test for COVID-19 (minutes rather than hours) and one that can be readily implemented in a hospital or other point-of-care environment. It uses a reverse transcription process as found in the standard RT-PCR test to convert the viral RNA into complementary DNA, but the subsequent DNA amplification step is performed at a single temperature unlike the polymerase chain reaction of RT-PCR, which requires thermal cycling. In addition, the results are easy to read through a simple solution color change rather than requiring measurement of a fluorescence marker using sophisticated analysis-lab-based instrumentation.
The R3T teams of Professors Pain and Hamdan are working hard to validate and optimize the RT-LAMP test for sensitivity and reliability and on production of reagents at scale for use in this test. The test will need to be re-optimized for the reagents that are produced here, but success would, in principle, allow RT-LAMP test kits to be assembled in KSA for deployment within the local healthcare system.
Other directions being studied at KAUST include implementation of the test using different detection methods, including alternative color change materials and fluorophores that could provide a back-up, second measurement option when the results may be ambiguous due to a low viral load or contamination concerns e.g. via swab-collected blood. Bradley has asked Professor Iain McCulloch and his team to look at this and they are synthesizing new chromophores and fluorophores to meet the challenge. Oxford are also working on making the test compatible with different swab solution media and on ways to remove the requirement for an RNA extraction step, to allow direct use of swab solutions, further simplifying the testing protocols.
KAUST received 30 RT-LAMP tests from Oxford on April 15 and these have very recently been used to test 30 individual patient samples at a Medina hospital facility. The patient samples had already been tested using RT-PCR in Medina and were subsequently re-tested at KAUST also using RT-PCR as a cross-check on RNA molecules extracted from nasal swab samples. Results are currently being analysed.