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A new study found that genotyping detected new variants of Covid almost a week more quickly than traditional whole genome sequencing methods. This could have potential benefits for guiding public health decision making and disease control globally.
The research from the University of East Anglia and the UK Health Security Agency found that genotyping allowed Covid variant information to be more rapidly detected and communicated to frontline health protection professionals at the height of the pandemic. It also helped to implement local control measures such as contact tracing more rapidly.
Lead researcher Professor Iain Lake, from UEA’s School of Environmental Sciences, said: “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 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.”
Genotyping results were very accurate
The research team studied data for more than 115,000 cases where Covid variant information was available from both genotyping and whole genome sequencing. By comparing the variant result from genotyping with the result from whole genome sequencing, they demonstrated that the genotyping results were very accurate.
It found that genotyping was able to detect known Covid variants more quickly and cheaply than whole genome sequencing. It enabled a nine-fold increase in the quantity of samples tested for variants. This meant that variants were detected among many more people.
Professor Lake said that these finding, published in The Lancet Microbe, could now be applied to finding variants in a wide range of organisms in humans and animals. This will have huge potential for guiding public health decision-making and disease control globally in 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.