Detecting SARS-CoV-2 in less than 5 minutes

1 July 2020

A group of researchers from the Department of Physics at Oxford University are working on ways to tackle the COVID-19 pandemic. The group, led by Professor Achillefs Kapanidis and Nicole Robb, are working on the development of ultrafast COVID-19 diagnostic tests, as well as using computational modelling to study virus reinfection dynamics.

A faster way to diagnose viruses

Rapid, sensitive and accurate diagnosis of viruses is fundamental to response efforts, however, methods for viral diagnostics tend to be either fast and cheap at the expense of specificity or sensitivity, or vice versa. Using influenza as a model virus, the Oxford group recently described a novel means for simple, efficient and instantaneous labelling of enveloped viruses; this method has now been adapted for use on SARS-CoV-2, the coronavirus that causes COVID-19.

The new method invented by the Oxford team uses positively charged molecules, like calcium ions, to bind short DNA strands to intact virus particles. When these DNA strands are labelled with bright fluorescent dyes, they result in rapid labelling of the exterior of the virus particle. Fluorescently-labelled viruses are easily observable by light microscopy, and machine learning algorithms are then used to detect and classify the virus particles.

The Oxford researchers have now taken their test from the lab to the clinic, and are currently working with clinical collaborators at the John Radcliffe Hospital to validate the assay on COVID-19 patient samples. Excitingly, the combination of rapid labelling and deep learning classification allows the detection of SARS-CoV-2 in less than 5 minutes, significantly faster than existing diagnostic tests.

Simple, fast and cost-effective

The new test works directly on throat swabs from COVID-19 patients, without the need for genome extraction or purification or amplification of the viruses; meaning the assay is simple, extremely rapid, and does not require expensive reagents.

A significant concern for the upcoming autumn and winter months is the unpredictable effects of co-circulation of SARS-CoV-2 with other seasonal respiratory viruses such as influenza and low pathogenic human coronaviruses. The Oxford team have shown that they can use their new method to reliably distinguish between these different viruses in clinical samples, a development that may be a crucial advantage in the next phase of the pandemic.

The group are also developing complementary diagnostic methods, such as a versatile, hybridization-based detection tool that uses fluorescent DNAs to specifically bind to and light up the SARS-CoV-2 virus genome in clinical samples. Together, the new technologies being developed should allow rapid and efficient detection of SARS-CoV-2, and will help significantly in efforts to control the virus.

COVID-19 reinfection modelling

As well as laboratory-based work, the group have also modelled empirical infection and fatality data generated during the outbreak to investigate the reinfection frequency of the disease. Their model predicts that cases of reinfection should have been seen by now if primary SARS-CoV-2 infection did not protect from subsequent exposure in the short term, however, no such cases have been documented, suggesting that infection provides short-term immunity. This work provides a useful insight for serological testing strategies, lockdown easing and vaccine design.