South Africa’s Hyrax Biosciences, known for its contributions to HIV drug-resistance testing, has released a software tool that significantly speeds up the detection of mutations in the genome of SARS-CoV-2, the coronavirus responsible for Covid-19.
The tool has been given a considerable boost as Hyrax Biosciences’ Exatype SARS-CoV-2 runs on the Amazon Web Services (AWS) cloud and is used worldwide in efforts to track the evolution of the virus as it spreads.
The sequencing of SARS-CoV-2 is critically important for two main reasons: first, global surveillance (that is, how the virus is spreading among individuals, countries and continents), and, second, monitoring the evolution of the virus (that is, how rapidly the virus is changing and whether these mutations are associated with changes in infectivity and/or virulence).
When a sample from an individual that has, or is suspected to have, COVID-19 arrives at Hyrax’s lab, the DNA of the virus is extracted from the sample and sequenced using a DNA sequencing machine. Exatype SARS-CoV-2 automates the analysis and interpretation of data, reducing the time spent analysing the data from days or weeks to a matter of hours.
Usually, sequencing machines produce large quantities of messy, complex data, which would usually require painstaking expert analysis. However, Hyrax Biosciences’ Exatype SARS-CoV-2 removes the need for this expert and speeds up the process to get results.
To get results at an efficient pace, Hyrax Biosciences runs its API servers on Amazon EC2. When a customer uploads data, that data is moved directly into an Amazon S3 bucket. Following that, a CloudFormation configured process on an Amazon EC2 instance downloads the data and analyses it and stores the results in an AWS RDS Aurora database instance.
Dr Simon Travers, CEO and co-founder of Hyrax Biosciences, says the Cape Town-based company was started in 2015 with four co-founders – Dr Travers, Dr Imogen Wright, Dr Natasha Wood and Baruch Lubinsky.
Hyrax Biosciences’ end-users are primarily pathology laboratories who purchase tests from the company’s partners and are based across the globe including the US, Central America, Africa and Asia.
Dr Travers explains that genetic diagnostics are a three-step process. “We do step three, which is analysing and interpreting the data to output a final result. Our typical business model involves partnering with companies who do steps one and/or two to enable them to offer a full sample to report solution to their customers, who are the end-users.
“Our product, Exatype, is a cloud-based solution. We use AWS for all of our infrastructure ranging from web-hosting through to auto-scaling,” says Dr Travers.
“Data security is critical for us, and AWS provides for all of our security needs. AWS enables us to effortlessly scale our product offerings and workloads; something that would not be possible without AWS. Without such infrastructure, we wouldn’t have been able to rapidly deploy our Covid-19 solution.”
He believes that Hyrax Biosciences’ COVID-19 solution will enable researchers and laboratories to easily analyse and interpret DNA information from SARS-CoV-2 infections and use this information towards characterising global diversity (important for vaccine development) and for studying viral transmission.
“While we historically supported genetic diagnostics for HIV, we are now a disease agnostic platform which means we can support a broad spectrum of genetic tests ranging from infectious disease to cancer.”
AWS though their AWS Diagnostic Development Initiative (DDI) have provided support for innovation in rapid and accurate patient testing for 2019 novel coronavirus (Covid-19), and other diagnostic solutions to mitigate future outbreaks. AWS offered technical support and providing promotional credits to support the use of AWS services to advance diagnostic research for Hyrax Biosciences.