Genotyping study shows how COVID variants can be detected faster

Genotyping technology detects COVID variants faster and more cheaply than ever before, according to a study from the University of East Anglia and the UK Health Security Agency. The new study published in The Lancet microbe reveals that the technique detects new variants almost a week faster than traditional whole genome sequencing methods.

The research team says genotyping allowed information about COVID variants to be detected and communicated more quickly to frontline health protection professionals during the height of the pandemic. Importantly, this allowed local control measures such as contact tracing to be implemented more quickly.

Lead researcher Professor Iain Lake, from UEA’s School of Environmental Sciences, said: “When the COVID pandemic began, the variant that people were infected with was initially determined using of a very precise technique known as whole genome sequencing. tool to identify and genetically characterize variants, but when large populations need to be assessed quickly, cost, capacity and speed limit its usefulness.

“At the start of 2021, the government was testing new technology to quickly detect new variants in NHS test and trace laboratories. The technology, known as “genotype testing” or genotyping, allows scientists to explore genetic variants.

Neil Bray, from the UK Health Safety Agency (UKHSA), said: “We wanted to know how this technology compares to traditional whole genome sequencing. »

The research team studied data from more than 115,000 cases for which information on COVID variants was available from genotyping and whole genome sequencing. By comparing the variable genotyping result with the whole genome sequencing result, they demonstrated that the genotyping results were very accurate.

Professor Lake said: “We found that genotyping was able to detect known COVID variants more quickly and cheaply than whole genome sequencing. They produced variant results six days faster than whole genome sequencing, with results in just three days, compared to nine days. for whole genome sequencing.

“Genotyping allowed a nine-fold increase in the amount of samples tested for variants. This meant that variants were detected among many more people. Local control measures such as contact tracing could therefore be implemented. works more quickly. Genotyping can be applied to the search for variants in a wide range of organisms in humans and animals – so it has enormous potential to guide public health decision-making and control diseases on a global scale in the future. “

Professor Susan Hopkins, UKHSA Chief Medical Advisor, said: “The cutting-edge genomic expertise that UKHSA and other UK institutions have been able to draw on throughout the pandemic has been essential to the UK’s response to COVID-19. Research like this will help us continue to build our capacity in this area and ensure that the UK is as well prepared as possible to respond quickly to emerging public health threats in the future.

Professor Dame Anna Dominiczak, Scotland’s chief scientist for health, who previously led the UK government’s operation to expand and manage flagship COVID laboratories, said: “Research like this is really important to ensure we build on the enormous progress made in testing. during COVID to strengthen our defenses against future pandemic threats.

This research was carried out by the UEA in collaboration with the UK Health Security Agency (UKHSA), BioClavis Ltd, Thermo Fisher Scientific (USA), NHS Test and Trace, the Department of Health and Social Care, the National Institute for Health and Care Research (NIHR), Alderley Lighthouse Labs Ltd and the University of Glasgow.