HELSINKI, Finland, August 2021. Finnish bioinformatics software company Euformatics has been awarded funding through the Amazon Web Services (AWS) Diagnostic Development Initiative to deliver a revolutionary COVID-19 variant surveillance software tool. SYNLAB has agreed to be the first customer of the solution developed under the program. The funding also covers broader deployment of cloud-based tools around human variant analysis for Next Generation Sequencing (NGS) pipelines as well as an international research program studying autism spectrum disorders.
The Diagnostics Development Initiative from AWS aims to help accelerate research and innovation to advance the collective understanding and detection of COVID-19 and other infectious diseases in order to mitigate current and future outbreaks.
Euformatics’ expertise in the NGS software arena combined with the scalable cloud services offered by AWS will make it possible to develop a software tool that will enable SYNLAB to quickly identify and classify new variants of the Sars-CoV-2 disease, as well as potentially help to mitigate further outbreaks of highly contagious variants through rapid screening patient samples.
Even within the first few months of SARS-CoV-2 being detected in 2019, it was clear that new variants of the disease would inevitably appear and make tackling the global pandemic even more challenging. Being able to quickly and correctly identify different strains of the disease is essential in determining suitable treatment and efficacy of available vaccines. While open-source tools have been developed, such as Pangolin, which are now used by many laboratories to classify strains of SARS-CoV-2 against a reference genome provided by Ensembl, there are still significant challenges in being able to reliably both classify and understand more broadly the effects that a new strain could have on patients.
Guidance from the World Health Organisation in recent months has instructed member states to actively test for new variant strains, in particular focusing on the use of NGS techniques. This has led to an increase in genomic profiling of the virus but left a hole for a comprehensive analysis which does not require extensive logistics operations to send samples and data between laboratories and potentially over borders. Indeed, in an unrestricted scenario of virus transmission, reducing the time before starting countermeasures by even one day reduces the cumulative number of cases by 40 % according to evidence from Hubei/China at the start of the pandemic.
As the first customer, SYNLAB will take advantage of the software functionality as part of their work testing SARS-CoV-2 samples in Switzerland. Being an NGS powerhouse in Europe, with sequencing capacity in several countries, SYNLAB is in an ideal position to pioneer usage of the new tool with the aim of expanding its usage to the greater SYNLAB European network.
“As part of our role in providing COVID-19 testing capabilities to the European healthcare sector, we were in need of a comprehensive software tool to enable quick classification and annotations of positive patient samples. Most importantly, we were looking for a tool that would save us time in identifying known and new variants of the virus. We knew that Euformatics had the expertise and skill to design and deliver this for us. There is great value in having a tool that can structure and automate reporting, including to national and international pandemic surveillance bodies”, notes Dr Michael Morris, Director of Genetics at SYNLAB Switzerland.
For Euformatics, this project marks a major milestone in the scale of their collaborations that are essential to making a larger impact in the wider healthcare sector. The company has seen rapid expansion of its client and partner base since the start of 2021 through an expanded distributor network. Both funding and market access are key to the continued success of its products, highlighting the importance of this collaboration with AWS and SYNLAB.
“Cloud-powered diagnostic tools are critical in the fight against COVID-19 and other infectious diseases,” said Maggie Carter, Global Lead, Social Impact at AWS. “Over the last year, AWS has seen inspirational results from the Diagnostic Development Initiative. We look forward to helping Euformatics and other organizations worldwide use the cloud to mitigate current and future infectious disease outbreaks.”
The SARS-CoV-2 pandemic has increased the focus on NGS solutions to prevent the spread of the virus as well as to understand it and its variants. In doing so, it has also inadvertently set the stage for greater use of NGS techniques moving forwards. The partnership highlights Euformatics commitment to accelerating the transition to precision medicine, particularly in a time when global pandemics are predicted to become a more common occurrence.
“For us this is a chance to work together with two organisations who share our mission of accelerating the transition to precision medicine through scalable cloud-based solutions. The support from AWS for this project means that we are able to dedicate more resources to building a tool that makes a difference not just for the current pandemic but also in the future. As the delta variant continues to make headlines, we can see now more than ever just how quickly and unpredictably the COVID-19 virus changes and spreads. Built on the backbone of our successful clinical variant interpretation product omnomicsNGS, this new tool will mean that we can continue to help ensure the successful use of NGS techniques both within the public sector through our work with partners such as MassGeneral Hospital for Children, as well as with one of the largest players in the private sector. We are excited to introduce a tool that aims to revolutionise the way we currently view and understand the SARS-CoV-2 virus, while ensuring that NGS technologies continue to provide the best possible insight into how such pandemics could be predicted or even prevented in the future”, explains Tommi Kaasalainen, Euformatics CEO.
To find out more about Euformatics, please go to our website www.euformatics.com. More information about the AWS DDI can be found at the program website, and SYNLAB Group can be found at https://www.synlab.com