SA’s Hyrax hailed for helping to detect Omicron variant

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Diagnostics company Hyrax Biosciences has been applauded for its online software platform, Exatype, which was instrumental in SA’s early detection of the Omicron variant of the SARS-CoV-2 virus (COVID-19).

Exatype enabled the scale-up of genomic surveillance that led to the detection of Omicron. The Omicron variant was first reported to the World Health Organisation from 24 November.

The Exatype platform automates the process of characterising variants through its capacity to analyse thousands of viral DNA sequences simultaneously.

In a statement, Hyrax Biosciences says automation of this process, which would otherwise need to be conducted manually by a highly-skilled bio informatician in a complex series of steps, is key, as finding variants cannot happen without scaling up sample analysis.

The South African National Institute for Communicable Diseases (NICD), which uses Exatype for all its SARS-CoV-2 genome data analysis, has lauded the platform for making genomic surveillance in the country bearable.

“The Exatype workflow has been a lifesaver as we’ve scaled genomic surveillance in South Africa,” says Dr Jinal Bhiman, principal medical scientist at the NICD.

Explaining how the platform works, Simon Travers, CEO of Hyrax Biosciences, says: “Exatype removes all the complexities in genetic sequence analysis. It enables laboratories that lack the expertise necessary to undertake manual analysis to perform high-throughput genomic surveillance.

“To date, Exatype has been used by laboratories across Africa to analyse the equivalent of 42% of all the data generated on the African continent – that is more than 25 000 SARS-CoV-2 genomes.

“Genetic sequencing produces a huge amount of data which is complex and noisy. Analysis enables us to separate the important signals from the noise. And automated analysis through Exatype is endlessly scalable and able to overcome limitations of human capacity. By working through the Amazon Web Services cloud infrastructure, the amount of computing power available to Exatype is infinite.”

In the statement, Hyrax Biosciences says Exatype will continue to play an important role in tracking this new variant to establish what impact it is having on the course of the COVID-19 pandemic in South Africa.

“This ongoing surveillance is important both in terms of informing public health measures to contain the spread of COVID-19 and identifying other new variants as they arise.”

Travers adds: “In South Africa, we have an enormous advantage in the Network for Genomics Surveillance, a collaboration among various universities, research institutes and clinical laboratories to sequence and characterise COVID-19-positive samples. This level of national cooperation cannot be taken for granted and is invaluable.”

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