Genotyping technology quicker and cheaper for tracking COVID-19 variants

Genotyping technology is able to detect COVID-19 variants more quickly and cheaply than ever before – according to research from the University of East Anglia and the UK Health Security Agency.

A recently published study reveals that the technique detects new variants almost a week more quickly than traditional whole-genome sequencing methods. The research team say that genotyping allowed COVID-19 variant information to be more rapidly detected and communicated to frontline health protection professionals at the height of the pandemic. Importantly, it helped to implement local control measures such as contact tracing more rapidly.

Lead researcher Professor Iain Lake, from University of East Anglia’s (UEA) School of Environmental Sciences, said: “When the COVID-19 pandemic began, the variant with which people were infected was initially determined using a highly accurate technique known as whole-genome sequencing (WGS). This is the gold standard diagnostic tool for identifying and genetically characterising variants. But where large populations need to be assessed rapidly - then cost, capacity and timeliness limit its utility.

“By the start of 2021, new technology to rapidly detect new variants was being trialled by the government in NHS Test and Trace laboratories. The technology – known as ‘genotype assay testing’ or genotyping – allows scientists to explore genetic variants.”

Neil Bray, from the UK Health Security Agency (UKHSA), said: “We wanted to find out how this technology compares to traditional WGS.”

The research team studied data for more than 115,000 cases where COVID-19 variant information was available from both genotyping and WGS. By comparing the variant result from genotyping with the result from WGS, they demonstrated that the genotyping results were very accurate.

It was found that genotyping was able to detect known COVID-19 variants more quickly and cheaply that WGS. Genotyping produced variant results six days faster, with results back in just three days.

Professor Susan Hopkins, UKHSA Chief Medical Advisor, said: “The world-leading genomics expertise that UKHSA and other institutions across the UK were able to draw on throughout the pandemic was critical to the UK response to COVID-19. Research like this will help us continue to build on our capability in this area and ensure that the UK is as well-prepared as possible to respond quickly to emerging threats to public health in the future.”

The work was funded by the UKHSA and the National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Emergency Preparedness and Response.

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

  • Bray N, Sopwith W, Edmunds M, et al. RT-PCR genotyping assays to identify SARS-CoV-2 variants in England in 2021: a design and retrospective evaluation study. Lancet Microbe. Published online January 11, 2024. doi:10.1016/S2666-5247(23)00320-8


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