Genotyping tech may help detect Covid variants more rapidly

London: Genotyping technology can detect Covid variants more quickly and cheaply than ever before, according to research.

The new study, published in The Lancet Microbe, reveals that the technique detects new variants almost a week more quickly than traditional whole genome sequencing methods.

The team from the University of East Anglia and the UK Health Security Agency (UHSA) said that genotyping allowed Covid 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.

"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,” said lead researcher Prof. Iain Lake, from UEA's School of Environmental Sciences.

However, the new technology “known as 'genotype assay testing' or genotyping -- allows scientists to explore genetic variants", he said, noting that it has been trialled by the UK government in NHS Test and Trace laboratories since 2021.

The 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.

"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 back in just three days, compared to nine days for whole genome sequencing,” Lake said.

"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. 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 the future."