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Covid variants can be detected more rapidly than ever before

Genotyping technology can detect Covid variants more rapidly and cheaply than ever before, according to a new study led by the University of East Anglia. This advancement marks a pivotal moment in the ongoing fight against the Covid-19 pandemic.

Rapid detection of new variants

At the core of this innovation is the ability of genotyping to identify Covid variants more effectively than the previously used whole genome sequencing methods. The new study highlights that genotyping can detect new variants almost a week faster than traditional methods.

The significance of this development cannot be overstated. During the height of the pandemic, the rapid detection and communication of variant information to frontline health protection professionals were critical. 

The new genotyping technology not only facilitated this but also expedited the implementation of local control measures, such as contact tracing.

Whole genome sequencing 

“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,” said lead researcher Professor Iain Lake from UEA’s School of Environmental Sciences.

“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.”

“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.”

Transition to genotyping

The transition to genotyping began early in 2021, with the UK government trialing new technology in NHS Test and Trace laboratories. 

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

The study, involving data from over 115,000 Covid cases, revealed that genotyping not only provides highly accurate results but also delivers these results six days faster than whole genome sequencing. 

Critical new insights 

“We found that genotyping was able to detect known Covid variants more quickly and cheaply that whole genome sequencing,” said Professor Lake.

“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.”

“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 future.”

Study implications 

“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,” said 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.”

Professor Dame Anna Dominiczak is the chief scientist for Health in Scotland who previously led the UK government’s operation to expand and run the Covid lighthouse laboratories. 

“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,” said Professor Anna Dominiczak. 

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