Homegrown software helped SA detect Omicron variant

An online software platform developed by Hyrax Biosciences, a company that spun out of the University of the Western Cape (UWC), has played a critical role in South Africa’s early detection of the Omicron variant of the SARS-CoV-2 virus.

South Africa has been recognised both for the expertise of its scientists who were responsible for identifying the new variant and for swiftly sharing information with authorities around the world.

What is less well known is the role played by Hyrax Bioscience’s software platform (called Exatype) in enabling the scale-up of genomic surveillance that led to the detection of Omicron. Exatype automates the process of characterising variants through its capacity to analyse thousands of viral DNA sequences simultaneously. Automation of this process, which would otherwise need to be conducted manually by a highly-skilled bioinformatician in a complex series of steps, is key – finding variants cannot happen without scaling up sample analysis. Exatype makes this possible.  

“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,” says Simon Travers, a member of the UWC team that developed the system and now CEO of a spin-off company, Hyrax Biosciences. “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.”

Variants are detected through the ongoing sampling of positive COVID-19 test results and the genetic sequencing of these samples. Analysis of large batches of this data is the final step in the process and it is here that new “signals” are identified among the sequenced samples. If a sufficient number of samples with the same new “signal” (or mutations) is picked up then, depending on the characteristics of the mutations, the World Health Organization might declare such a variant one of “interest” or “concern”.

“Genetic sequencing produces a huge amount of data which is complex and noisy,” Travers explains. “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 Amazon Web Services cloud infrastructure, the amount of computing power available to Exatype is infinite.”

Exatype results were used in the discovery of the Omicron variant and 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 is quick to acknowledge that digital tools work best where organisational foundations are strong. “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.”

The South African National Institute for Communicable Diseases (NICD) uses Exatype for all its SARS-CoV-2 genome data analysis. Dr Jinal Bhiman, Principal Medical Scientist at the NICD, recognises the value of the platform: “The Exatype workflow has been a lifesaver as we’ve scaled genomic surveillance in South Africa.”

The application of Exatype is not confined to the SARS-CoV-2 virus: Exatype is already being used to scale up HIV drug resistance testing globally and it can easily be deployed to support a wide range of diagnostics for other infectious diseases.