DeepSARS: Innovative platform for sequencing and testing at the same time
The novel scientific platform DeepSARS, developed by the Systems Immunology group led by Sai Reddy, could support viral testing and tracking for future pandemics while performing both tasks simultaneously. This allows for earlier detection of emerging variants and profiling mutations at the population level, a recent study in BMC Genomics shows.
The ongoing COVID-19 pandemic remains a major global health concern with novel variants of SARS-CoV-2, such as alpha, beta, gamma, delta and omicron, that are continuously emerging and resulting in new waves of infection. Potentially exacerbating the situation, many of the masking and social distancing rules are relaxed around the world.
The latest variant of SARS-CoV-2, omicron, with over 50 mutations is able to infect at a greater capacity than previous strains and often possesses substantial immune evasion, leading to many breakthrough infections in vaccinated or previously infected individuals.
Genomic surveillance of SARS-CoV-2 has been a vital component in the monitoring of the pandemic, providing valuable information for guiding public health decisions. However, despite the fact that the SARS-CoV-2 genomes from infected patients have been sequenced at unprecedented levels, they still represent a small fraction of the total number of global infections. And countries vary widely in how they prioritise viral genome sequencing. What makes it even more problematic is that in the countries with low sequencing rates, they also tend to have high infection rates and are therefore at an especially high risk for new mutations to evolve. They are hotspots for new variants.
“"We have shown that DeepSARS can be rapidly adapted for identification of emerging variants and for profiling mutational changes at a small scale but for a pandemic, this requires population level implementation. Practically speaking, DeepSARS could be of immense benefit in future pandemics or possibly as SARS-CoV-2 transitions to an endemic stage."”Sai Reddy, Systems and Synthetic Immunology Lab at D-BSSE
That is where DeepSARS comes into play. "A number of researchers have previously embraced the idea that sequencing could be used not just for genomic surveillance, but also for diagnostic testing", says immunology professor Sai Reddy, principal investigator of the Laboratory for Systems and Synthetic Immunology at ETH Zurich and Vice Director of the external page Botnar Research Centre for Child Health (BRCCH), who has actually pursued this idea to a practical level. In a paper published recently in external page BMC Genomics, he, his team and collaborators have established a scientific concept which has proven that sequencing and testing can be done simultaneously. Their system is called DeepSARS.
Read the external page full article published by the Botnar Research Centre for Child Health.
Learn about the Systems and Synthetic Immunology lab led by Sai Reddy.