Genotyping can detect Covid variants more rapidly: Study

The researchers studied data for more than 115,000 (1.15 lakh) cases where Covid variant information was available from both genotyping and whole genome sequencing.

New Delhi: Genotyping technique can detect new variants of SARS-CoV-2 almost a week more quickly than traditional methods, according to a study published in The Lancet Microbe journal.

Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence.

The researchers in the study said genotyping allowed Covid variant information to be more rapidly detected and communicated to frontline health protection professionals at the height of the pandemic.

The technique also helped to implement local control measures such as contact tracing more rapidly, they 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," said lead researcher Iain Lake, a professor at the University of East Anglia in the UK.

Whole genome sequencing is the gold standard diagnostic tool for identifying and genetically characterising variants. But in situations where large populations need to be assessed rapidly, cost, capacity and timeliness limit its utility.

"The technology— known as 'genotype assay testing' or genotyping—allows scientists to explore genetic variants," Lake said.

The team studied data for more than 115,000 (1.15 lakh) 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.

The researchers also found that 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, they said.

"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," Lake added.