New genetic test detects COVID variants faster than ever before

NORWICH, United Kingdom — Promising new research is revealing the incredible efficiency of a new genotyping method for detecting COVID-19 variants. The new technology, referred to as genotype assay testing, is capable of identifying specific COVID-19 variants close to a week faster than traditional whole genome sequencing methods — the current gold standard method of detecting SARS-CoV-2 variants. Moreover, this new approach is more cost effective as well.

Scientists from the University of East Anglia and the U.K. Health Security Agency explain that genotyping made it possible to identify important and sensitive COVID-19 variant information in a more rapid manner, providing frontline health protection professionals with crucial insights during the height of the pandemic. Perhaps even more importantly, study authors believe genotyping aided greatly in the implementation of local control measures. For example, rapid contact tracing.

“When the COVID pandemic began, the variant with which people were infected was initially determined using a highly accurate technique known as whole genome sequencing. This is the gold standard diagnostic tool for identifying and genetically characterizing variants. But where large populations need to be assessed rapidly – then cost, capacity and timeliness limit its utility,” says lead researcher Professor Iain Lake, from UEA’s School of Environmental Sciences, in a media release.

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

“We wanted to find out how this technology compares to traditional whole genome sequencing,” adds Neil Bray, from the UK Health Security Agency (UKHSA).

Immune system: Army Men Fight COVID
Genotype assay testing is capable of identifying specific COVID-19 variants close to a week faster than current genetic tests. (© Ezume Images –

While whole genome sequencing entails mapping out a virus’ entire, unique DNA pattern, genotype assay testing focuses on comparing DNA sequences in order to identify differences in genetic patterns.

To reach these conclusions, the research team assessed data encompassing over 115,000 cases in which COVID-19 variant data was available from both methods (genotyping and whole genome sequencing). Upon comparing the variant results from genotyping with results gathered from whole genome sequencing, researchers successfully demonstrated that genotyping results were especially accurate.

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

“Genotyping enabled a nine-fold increase in the quantity of samples tested for variants. This meant that variants were detected among many more people. Local control measures such as contact tracing could therefore happen more rapidly,” Lake adds. “Genotyping can be applied to finding variants in a wide range of organisms in humans and animals – so it has huge potential for guiding public health decision-making and disease control globally in future.”

“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,” comments Professor Susan Hopkins, UKHSA Chief Medical Advisor. “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.”

“Research such as this is really important to ensure that we build upon the huge advances in testing that occurred during COVID to bolster our defenses against future pandemic threats,” concludes Professor Dame Anna Dominiczak, Chief Scientist for Health in Scotland who previously led the U.K. government’s operation to expand and run the COVID lighthouse laboratories.

The study is published in The Lancet Microbe.

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John Anderer

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